In [1]:
import qancode as q
In [2]:
qa = q.QANCODE(rc_url="https://v71rc1-master.demo.encodedcc.org/")
In [3]:
qa.compare_facets(users=['Public'], browsers=['Chrome'], browser_comparison=False)
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Experiment
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=File
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Library
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=AntibodyLot
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Biosample
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Donor
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: search/?type=GeneticModification
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=FileSet
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Annotation
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Series
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=OrganismDevelopmentSeries
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=UcscBrowserComposite
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=ReferenceEpigenome
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Project
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=ReplicationTimingSeries
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=PublicationData
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=MatchedSet
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Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=TreatmentConcentrationSeries
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=TreatmentTimeSeries
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Target
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Pipeline
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Publication
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /search/?type=Software
Search page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /matrix/?type=Experiment
Matrix page detected
Opening https://www.encodeproject.org in Chrome
Getting type: /matrix/?type=Annotation
Matrix page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Experiment
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=File
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Library
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Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=AntibodyLot
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Biosample
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Donor
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: search/?type=GeneticModification
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=FileSet
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Annotation
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Series
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=OrganismDevelopmentSeries
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=UcscBrowserComposite
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=ReferenceEpigenome
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Project
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=ReplicationTimingSeries
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=PublicationData
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Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=MatchedSet
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Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=TreatmentConcentrationSeries
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Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=TreatmentTimeSeries
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Target
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Pipeline
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Publication
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /search/?type=Software
Search page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /matrix/?type=Experiment
Matrix page detected
Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome
Getting type: /matrix/?type=Annotation
Matrix page detected
---------------------------------- Experiment ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Experiment
ASSAY
prod: [("5' RLM RACE", '2'), ('5C', '13'), ('ATAC-seq', '180'), ('CAGE', '121'), ('CRISPR RNA-seq', '50'), ('CRISPRi RNA-seq', '77'), ('ChIA-PET', '62'), ('ChIP-seq', '8911'), ('Circulome-seq', '1'), ('DNA-PET', '6'), ('DNAme array', '259'), ('DNase-seq', '873'), ('FAIRE-seq', '37'), ('Hi-C', '36'), ('MNase-seq', '2'), ('MRE-seq', '68'), ('MS-MS', '14'), ('MeDIP-seq', '55'), ('PAS-seq', '47'), ('RAMPAGE', '168'), ('RIP-chip', '32'), ('RIP-seq', '73'), ('RNA Bind-n-Seq', '161'), ('RNA microarray', '291'), ('RNA-PET', '31'), ('RRBS', '218'), ('Repli-chip', '63'), ('Repli-seq', '119'), ('Switchgear', '2'), ('TAB-seq', '8'), ('WGBS', '258'), ('eCLIP', '359'), ('genetic modification DNase-seq', '40'), ('genotyping HTS', '16'), ('genotyping array', '142'), ('iCLIP', '7'), ('microRNA counts', '115'), ('microRNA-seq', '185'), ('polyA RNA-seq', '817'), ('polyA depleted RNA-seq', '32'), ('shRNA RNA-seq', '533'), ('siRNA RNA-seq', '113'), ('single cell RNA-seq', '120'), ('small RNA-seq', '216'), ('total RNA-seq', '413'), ('whole genome sequencing assay', '21')]
ASSAY CATEGORY
prod: [('3D chromatin structure', '111'), ('DNA accessibility', '1132'), ('DNA binding', '8911'), ('DNA methylation', '866'), ('DNA sequencing', '22'), ('Genotyping', '164'), ('Proteomics', '14'), ('RNA binding', '634'), ('Replication timing', '182'), ('Transcription', '3331')]
AUDIT CATEGORY
prod: [('control extremely low read depth', '24'), ('extremely low coverage', '7'), ('extremely low read depth', '221'), ('extremely low read length', '10'), ('extremely low spot score', '49'), ('inconsistent control', '3'), ('inconsistent library biosample', '1'), ('inconsistent read count', '2'), ('missing antibody', '75'), ('missing control alignments', '418'), ('missing donor', '1'), ('missing nih_institutional_certification', '33'), ('missing possible_controls', '2')]
AUDIT CATEGORY2
prod: [('antibody not characterized to standard', '25'), ('control insufficient read depth', '952'), ('insufficient coverage', '4'), ('insufficient read depth', '1757'), ('insufficient read length', '511'), ('insufficient replicate concordance', '48'), ('missing RNA fragment size', '2'), ('missing controlled_by', '596'), ('missing documents', '30'), ('missing input control', '2'), ('missing possible_controls', '27'), ('missing spikeins', '173'), ('partially characterized antibody', '139'), ('poor library complexity', '283'), ('severe bottlenecking', '271'), ('uncharacterized antibody', '11'), ('unreplicated experiment', '341')]
AUDIT CATEGORY3
prod: [('antibody characterized with exemption', '676'), ('borderline replicate concordance', '455'), ('control low read depth', '659'), ('file validation error', '40'), ('high lambda C methylation ratio', '3'), ('inconsistent assembly', '18'), ('inconsistent control read length', '907'), ('inconsistent control run_type', '158'), ('inconsistent platforms', '1032'), ('inconsistent target of control experiment', '217'), ('low coverage', '4'), ('low read depth', '2545'), ('low read length', '3292'), ('low replicate concordance', '89'), ('low spot score', '321'), ('mild to moderate bottlenecking', '2873'), ('missing external identifiers', '330'), ('missing genetic modification characterization', '2307'), ('missing genotype', '116'), ('missing spikeins', '28'), ('mixed read lengths', '482'), ('mixed run types', '101'), ('moderate library complexity', '1280')]
AVAILABLE DATA
prod: [('CEL', '4'), ('bam', '12757'), ('bed bed12', '43'), ('bed bed3', '7'), ('bed bed3+', '869'), ('bed bed6+', '115'), ('bed bed9', '18'), ('bed bedExonScore', '27'), ('bed bedGraph', '30'), ('bed bedLogR', '64'), ('bed bedMethyl', '278'), ('bed bedRnaElements', '288'), ('bed broadPeak', '2451'), ('bed idr_peak', '134'), ('bed modPepMap', '6'), ('bed narrowPeak', '7324'), ('bed pepMap', '6'), ('bed peptideMapping', '8'), ('bed tss_peak', '235'), ('bedpe', '5'), ('bigBed bed12', '43'), ('bigBed bed3', '7'), ('bigBed bed3+', '13'), ('bigBed bed6+', '115'), ('bigBed bed9', '18'), ('bigBed bedExonScore', '27'), ('bigBed bedLogR', '63'), ('bigBed bedMethyl', '278'), ('bigBed bedRnaElements', '288'), ('bigBed broadPeak', '1992'), ('bigBed idr_peak', '134'), ('bigBed modPepMap', '6'), ('bigBed narrowPeak', '7313'), ('bigBed pepMap', '6'), ('bigBed peptideMapping', '8'), ('bigBed tss_peak', '235'), ('bigWig', '11714'), ('csfasta', '25'), ('csqual', '13'), ('fasta', '3'), ('fastq', '13745'), ('gff gff3', '235'), ('gtf', '269'), ('hdf5', '20'), ('hic', '5'), ('idat', '277'), ('rcc', '115'), ('sam', '59'), ('sra', '672'), ('tagAlign', '1368'), ('tar', '110'), ('tsv', '2470'), ('vcf', '13'), ('wig', '59')]
BIOSAMPLE TREATMENT
prod: [('17β-estradiol', '38'), ('17β-hydroxy-17-methylestra-4,9,11-trien-3-one', '4'), ('17β-hydroxy-5α-androstan-3-one', '3'), ('20-hydroxyecdysone', '16'), ('Lipopolysaccharide', '66'), ('Sendai virus', '1'), ('Sindbis virus', '4'), ('Transforming growth factor beta-1', '1'), ('UT189', '3'), ('afimoxifene', '16'), ('all-trans-retinoic acid', '21'), ('bisphenol A', '4'), ('cadmium dichloride', '4'), ('caffeine', '3'), ('calcium', '52'), ('cisplatin', '1'), ('cold shock treatment', '2'), ('copper(II) sulfate', '32'), ('dexamethasone', '293'), ('differentiation', '1'), ('dimethyl sulfoxide', '39'), ('doxycycline', '1'), ('doxycycline hyclate', '33'), ('erythropoietin', '9'), ('estradiol', '8'), ('ethanol', '57'), ('forskolin and pyruvate', '8'), ('genistein', '4'), ('heat shock treatment', '1'), ('hydrocortisone succinate', '9'), ('hydroxyurea', '1'), ('insulin and 22-hydroxycholesterol', '2'), ('interferon alpha', '19'), ('interferon gamma', '18'), ('interleukin-3', '9'), ('ionomycin', '14'), ('kit ligand', '9'), ('lactate', '3'), ('methyltrienolone', '1'), ('paraquat', '2'), ('phorbol 13-acetate 12-myristate', '14'), ('pravastatin', '4'), ('resveratrol', '1'), ('retinoic acid', '2'), ('rotenone', '3'), ('serum free', '2'), ('sodium butyrate', '3'), ('tamoxifen', '2'), ('tumor necrosis factor', '20'), ('vorinostat', '1'), ('zinc dichloride', '3')]
BIOSAMPLE TYPE
prod: [('cell line', '5779'), ('cell-free sample', '161'), ('in vitro differentiated cells', '679'), ('induced pluripotent stem cell line', '137'), ('primary cell', '1678'), ('stem cell', '506'), ('tissue', '4375'), ('whole organisms', '2052')]
DATE SUBMITTED
prod: [('2010-11-16', '12'), ('2011-01-11', '18'), ('2011-06-25', '14'), ('2011-07-13', '12'), ('2011-10-27', '10'), ('2011-12-23', '14'), ('2012-01-23', '29'), ('2013-05-09', '16'), ('2013-07-16', '15'), ('2013-07-18', '10'), ('2014-01-30', '23'), ('2014-02-25', '53'), ('2014-03-13', '24'), ('2014-03-15', '161'), ('2014-03-19', '69'), ('2014-03-20', '23'), ('2014-04-04', '15'), ('2014-04-29', '11'), ('2014-05-13', '39'), ('2014-05-14', '16'), ('2014-05-29', '36'), ('2014-06-10', '18'), ('2014-06-17', '20'), ('2014-06-30', '22'), ('2014-07-01', '22'), ('2014-07-03', '12'), ('2014-07-04', '71'), ('2014-07-06', '25'), ('2014-07-26', '35'), ('2014-07-30', '30'), ('2014-09-15', '26'), ('2014-09-17', '24'), ('2014-09-27', '32'), ('2014-09-29', '41'), ('2014-10-07', '21'), ('2014-10-24', '41'), ('2014-10-26', '25'), ('2014-10-29', '33'), ('2014-11-04', '31'), ('2014-11-21', '12'), ('2014-12-05', '13'), ('2014-12-08', '23'), ('2014-12-11', '53'), ('2014-12-13', '48'), ('2014-12-16', '21'), ('2014-12-17', '51'), ('2015-02-19', '24'), ('2015-02-21', '10'), ('2015-03-11', '13'), ('2015-03-13', '10'), ('2015-03-27', '29'), ('2015-03-31', '55'), ('2015-04-02', '19'), ('2015-05-22', '10'), ('2015-05-29', '16'), ('2015-06-18', '57'), ('2015-06-25', '19'), ('2015-06-28', '17'), ('2015-06-30', '30'), ('2015-07-16', '36'), ('2015-07-19', '96'), ('2015-07-23', '166'), ('2015-07-24', '123'), ('2015-07-29', '184'), ('2015-07-30', '54'), ('2015-08-05', '14'), ('2015-08-12', '18'), ('2015-08-13', '36'), ('2015-08-14', '43'), ('2015-08-24', '14'), ('2015-09-23', '12'), ('2015-09-24', '22'), ('2015-09-29', '27'), ('2015-09-30', '59'), ('2015-10-03', '27'), ('2015-10-21', '16'), ('2015-10-22', '12'), ('2015-10-30', '32'), ('2015-10-31', '27'), ('2015-12-07', '11'), ('2015-12-08', '13'), ('2015-12-10', '36'), ('2015-12-11', '38'), ('2015-12-14', '20'), ('2015-12-15', '20'), ('2015-12-16', '25'), ('2015-12-17', '16'), ('2015-12-22', '12'), ('2016-01-13', '20'), ('2016-01-22', '23'), ('2016-01-27', '22'), ('2016-02-01', '10'), ('2016-02-06', '20'), ('2016-02-10', '31'), ('2016-02-11', '25'), ('2016-02-16', '10'), ('2016-02-17', '10'), ('2016-02-26', '39'), ('2016-03-02', '17'), ('2016-03-03', '16'), ('2016-03-04', '45'), ('2016-03-07', '17'), ('2016-03-08', '11'), ('2016-03-09', '16'), ('2016-03-11', '62'), ('2016-03-13', '23'), ('2016-03-14', '35'), ('2016-03-15', '20'), ('2016-03-16', '56'), ('2016-03-17', '70'), ('2016-03-21', '155'), ('2016-03-22', '109'), ('2016-03-23', '29'), ('2016-03-25', '16'), ('2016-03-26', '21'), ('2016-03-30', '10'), ('2016-03-31', '98'), ('2016-04-09', '40'), ('2016-04-10', '16'), ('2016-04-11', '111'), ('2016-04-12', '14'), ('2016-04-13', '12'), ('2016-04-18', '11'), ('2016-04-19', '16'), ('2016-04-23', '43'), ('2016-04-24', '29'), ('2016-04-26', '20'), ('2016-04-27', '89'), ('2016-04-28', '51'), ('2016-04-29', '15'), ('2016-05-03', '17'), ('2016-05-09', '20'), ('2016-05-12', '19'), ('2016-05-13', '27'), ('2016-05-20', '20'), ('2016-05-26', '31'), ('2016-05-30', '83'), ('2016-06-22', '24'), ('2016-06-28', '45'), ('2016-06-29', '29'), ('2016-07-07', '19'), ('2016-07-20', '32'), ('2016-07-27', '12'), ('2016-07-29', '131'), ('2016-07-30', '156'), ('2016-07-31', '13'), ('2016-08-01', '57'), ('2016-08-02', '15'), ('2016-08-03', '66'), ('2016-08-04', '26'), ('2016-08-05', '18'), ('2016-08-23', '12'), ('2016-08-24', '40'), ('2016-09-16', '16'), ('2016-09-24', '14'), ('2016-09-25', '18'), ('2016-10-04', '26'), ('2016-10-11', '20'), ('2016-10-12', '21'), ('2016-10-14', '13'), ('2016-10-18', '13'), ('2016-10-19', '94'), ('2016-10-20', '68'), ('2016-10-21', '18'), ('2016-10-22', '27'), ('2016-10-24', '12'), ('2016-10-28', '23'), ('2016-10-31', '56'), ('2016-11-18', '39'), ('2016-12-05', '13'), ('2016-12-08', '14'), ('2016-12-09', '44'), ('2016-12-12', '25'), ('2016-12-15', '49'), ('2016-12-16', '12'), ('2016-12-20', '45'), ('2016-12-21', '48'), ('2016-12-31', '13'), ('2017-01-01', '11'), ('2017-01-12', '15'), ('2017-01-18', '25'), ('2017-01-23', '12'), ('2017-01-24', '29'), ('2017-01-25', '50'), ('2017-01-26', '26'), ('2017-01-27', '55'), ('2017-01-29', '25'), ('2017-01-30', '16'), ('2017-01-31', '118'), ('2017-02-10', '14'), ('2017-02-22', '11'), ('2017-03-08', '15'), ('2017-03-14', '65'), ('2017-03-17', '22'), ('2017-05-02', '14'), ('2017-06-30', '18'), ('2017-07-28', '27'), ('2017-09-11', '84'), ('2017-10-05', '41'), ('2018-02-21', '12')]
DATE RELEASED
prod: [('April, 2011', '149'), ('April, 2012', '77'), ('April, 2013', '6'), ('April, 2014', '2'), ('April, 2015', '28'), ('April, 2016', '170'), ('April, 2017', '52'), ('April, 2018', '48'), ('August, 2011', '88'), ('August, 2012', '257'), ('August, 2015', '180'), ('August, 2016', '265'), ('August, 2017', '71'), ('December, 2010', '68'), ('December, 2011', '87'), ('December, 2014', '247'), ('December, 2015', '40'), ('December, 2016', '174'), ('December, 2017', '139'), ('February, 2011', '255'), ('February, 2012', '264'), ('February, 2013', '1'), ('February, 2014', '7'), ('February, 2015', '3'), ('February, 2016', '183'), ('February, 2017', '138'), ('February, 2018', '177'), ('January, 2011', '6'), ('January, 2012', '59'), ('January, 2015', '8'), ('January, 2016', '110'), ('January, 2017', '399'), ('January, 2018', '156'), ('July, 2009', '22'), ('July, 2011', '263'), ('July, 2012', '128'), ('July, 2013', '2761'), ('July, 2014', '300'), ('July, 2015', '103'), ('July, 2016', '614'), ('July, 2017', '39'), ('June, 2011', '83'), ('June, 2012', '75'), ('June, 2014', '432'), ('June, 2015', '106'), ('June, 2016', '221'), ('June, 2017', '272'), ('March, 2011', '160'), ('March, 2012', '170'), ('March, 2013', '1'), ('March, 2014', '887'), ('March, 2015', '2'), ('March, 2016', '291'), ('March, 2017', '96'), ('March, 2018', '134'), ('May, 2011', '35'), ('May, 2012', '138'), ('May, 2013', '2'), ('May, 2014', '8'), ('May, 2015', '12'), ('May, 2016', '569'), ('May, 2017', '66'), ('May, 2018', '15'), ('November, 2010', '9'), ('November, 2011', '76'), ('November, 2012', '7'), ('November, 2014', '98'), ('November, 2015', '225'), ('November, 2016', '400'), ('November, 2017', '428'), ('October, 2009', '4'), ('October, 2010', '1'), ('October, 2011', '456'), ('October, 2014', '86'), ('October, 2015', '106'), ('October, 2016', '485'), ('October, 2017', '200'), ('September, 2011', '134'), ('September, 2012', '190'), ('September, 2014', '41'), ('September, 2015', '17'), ('September, 2016', '209'), ('September, 2017', '115')]
EXPERIMENT STATUS
prod: [('archived', '1012'), ('released', '14124'), ('revoked', '231')]
GENOME ASSEMBLY (VISUALIZATION)
prod: [('GRCh38', '7315'), ('ce10', '838'), ('ce11', '897'), ('dm3', '835'), ('dm6', '811'), ('hg19', '7492'), ('mm10', '1508'), ('mm9', '338')]
LAB
prod: [('Alexander Urban, Stanford', '3'), ('Ali Mortazavi, UCI', '231'), ('Andrew Z. Fire, Stanford', '4'), ('Barbara Wold, Caltech', '287'), ('Bing Ren, UCSD', '1379'), ('Bradley Bernstein, Broad', '1957'), ('Brenton Graveley, UConn', '789'), ('Brian Oliver, NIH', '27'), ('Chris Burge, MIT', '161'), ('Christina Leslie, MSKCC', '32'), ('David Gilbert, FSU', '77'), ('David MacAlpine, Duke', '39'), ('Eric Lécuyer, IRCM', '30'), ('Gene Yeo, UCSD', '366'), ('Gregory Crawford, Duke', '162'), ('Jason Lieb, UNC', '37'), ('Job Dekker, UMass', '26'), ('Joe Ecker, Salk', '193'), ('John Rinn, Broad', '35'), ('John Stamatoyannopoulos, UW', '1594'), ('Joseph Costello, UCSF', '595'), ('Kevin Struhl, HMS', '43'), ('Kevin White, UChicago', '1064'), ('Manuel Garber, UMass', '68'), ('Michael Snyder, Stanford', '2401'), ('Morgan Giddings, UNC', '14'), ('Paul Khavari, Stanford', '13'), ('Peggy Farnham, USC', '125'), ('Piero Carninci, RIKEN', '78'), ('Richard Myers, HAIB', '1423'), ('Ross Hardison, PennState', '128'), ('Scott Tenenbaum, SUNY-Albany', '42'), ('Sherman Weissman, Yale', '65'), ('Susan Celniker, LBNL', '239'), ('Terry Orr-Weaver, MIT', '2'), ('Thomas Gingeras, CSHL', '736'), ('Tim Reddy, Duke', '298'), ('Valerie Reinke, Yale', '361'), ('Vishwanath Iyer, UTA', '85'), ('Will Greenleaf, Stanford', '13'), ('Xiang-Dong Fu, UCSD', '97'), ('Yijun Ruan, JAX', '48')]
LIBRARY DEPLETED IN
prod: [('polyadenylated mRNA', '57'), ('rRNA', '870')]
LIBRARY INSERT SIZE (NT)
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LIBRARY MADE FROM
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LIBRARY TREATMENT
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LIFE STAGE
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MAPPED READ LENGTH (NT)
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ORGAN
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ORGANISM
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PLATFORM
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PROJECT
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RFA
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READ LENGTH (NT)
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REPLICATION TYPE
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RUN TYPE
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TARGET OF ASSAY
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------------------------------------- File -------------------------------------
Comparing data between URLs.
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Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=File
AUDIT CATEGORY
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AUDIT CATEGORY2
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AUDIT CATEGORY3
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CONTENT CATEGORY
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CONTENT TYPE
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FILE FORMAT
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FILE STATUS
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LAB
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MAPPING ASSEMBLY
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PLATFORM
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PROJECT
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SPECIFIC FILE FORMAT TYPE
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----------------------------------- Library ------------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Library
AUDIT CATEGORY
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AUDIT CATEGORY2
prod: [('missing external identifiers', '484'), ('missing genotype', '173')]
LIBRARY STATUS
prod: [('released', '27070'), ('revoked', '182')]
--------------------------------- AntibodyLot ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=AntibodyLot
AUDIT CATEGORY
prod: [('inconsistent ontology term', '5')]
AUDIT CATEGORY2
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CHARACTERIZATION METHOD
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CLONALITY
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ELIGIBILITY STATUS
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HOST ORGANISM
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LAB
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SOURCE
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TARGET ORGANISM
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TARGET OF ANTIBODY
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---------------------------------- Biosample -----------------------------------
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AUDIT CATEGORY2
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BIOSAMPLE STATUS
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BIOSAMPLE TREATMENT
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BIOSAMPLE TYPE
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HAS NIH INSTITUTIONAL CERTIFICATION
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LAB
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ORGAN
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ORGANISM
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PROJECT
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RFA
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SEX
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SOURCE
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SUBCELLULAR FRACTION
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------------------------------------ Donor -------------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Donor
AUDIT CATEGORY
prod: [('missing external identifiers', '120'), ('missing genetic modification characterization', '657'), ('missing genotype', '83')]
DATA TYPE
prod: [('Donor', '1586'), ('FlyDonor', '451'), ('HumanDonor', '780'), ('MouseDonor', '40'), ('WormDonor', '315')]
----------------------------- GeneticModification ------------------------------
Comparing data between URLs.
As user: Public
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First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: search/?type=GeneticModification
AUDIT CATEGORY
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CATEGORY
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GENETIC MODIFICATION STATUS
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LAB
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METHOD
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PURPOSE
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----------------------------------- FileSet ------------------------------------
Comparing data between URLs.
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Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=FileSet
AUDIT CATEGORY
prod: [('inconsistent assembly', '32'), ('inconsistent control read length', '1')]
DATA TYPE
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---------------------------------- Annotation ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Annotation
ANNOTATION TYPE
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ASSAY
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AUDIT CATEGORY
prod: [('inconsistent assembly', '28')]
AVAILABLE DATA
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BIOSAMPLE TYPE
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DATE RELEASED
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ENCYCLOPEDIA VERSION
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FILE SET STATUS
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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LIFE STAGE
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ORGAN
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ORGANISM
prod: [('Homo sapiens', '4951'), ('Mus musculus', '784')]
PROJECT
prod: [('ENCODE', '5510'), ('Roadmap', '225')]
RFA
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READ LENGTH (NT)
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RUN TYPE
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SOFTWARE USED
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TARGET(S) OF ASSAY
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TARGET(S) OF ASSAY2
prod: [('CTCF', '235'), ('H3K27ac', '684'), ('H3K4me1', '1'), ('H3K4me3', '860'), ('H3K9ac', '1')]
------------------------------------ Series ------------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Series
AUDIT CATEGORY
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DATA TYPE
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-------------------------- OrganismDevelopmentSeries ---------------------------
Comparing data between URLs.
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Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=OrganismDevelopmentSeries
ASSAY
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AVAILABLE DATA
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BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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LIBRARY DEPLETED IN
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LIBRARY INSERT SIZE (NT)
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LIBRARY MADE FROM
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LIBRARY TREATMENT
prod: [('Tobacco Acid Pyrophosphatase', '1')]
LIFE STAGE
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MAPPED READ LENGTH
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ORGAN
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PROJECT
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READ LENGTH
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SERIES STATUS
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TARGET OF ASSAY
prod: [('broad histone mark', '33'), ('control', '7'), ('histone', '49'), ('narrow histone mark', '16')]
----------------------------- UcscBrowserComposite -----------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=UcscBrowserComposite
AVAILABLE DATA
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COMPOSITE STATUS
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
prod: [('hg19', '2')]
LAB
prod: [('Barbara Wold, Caltech', '4'), ('Bing Ren, UCSD', '3'), ('Bradley Bernstein, Broad', '2'), ('David Gilbert, FSU', '2'), ('ENCODE Consortium Analysis Working Group', '1'), ('Gregory Crawford, Duke', '5'), ('Job Dekker, UMass', '1'), ('John Stamatoyannopoulos, UW', '10'), ('Kevin White, UChicago', '1'), ('Michael Snyder, Stanford', '6'), ('Morgan Giddings, UNC', '2'), ('Peggy Farnham, USC', '1'), ('Piero Carninci, RIKEN', '1'), ('Richard Myers, HAIB', '9'), ('Roderic Guigo, CRG', '2'), ('Ross Hardison, PennState', '4'), ('Scott Tenenbaum, SUNY-Albany', '4'), ('Thomas Gingeras, CSHL', '4'), ('Thomas Tullius, BU', '1'), ('Timothy Hubbard, Sanger', '1'), ('Yijun Ruan, JAX', '4')]
PROJECT
prod: [('ENCODE', '68')]
RFA
prod: [('ENCODE', '5'), ('ENCODE2', '45'), ('ENCODE2-Mouse', '16'), ('ENCODE3', '2')]
------------------------------ ReferenceEpigenome ------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=ReferenceEpigenome
ASSAY
prod: [('ATAC-seq', '66'), ('ChIP-seq', '248'), ('DNase-seq', '117'), ('MRE-seq', '16'), ('MeDIP-seq', '16'), ('RNA-seq', '164'), ('RRBS', '61'), ('microRNA counts', '10'), ('microRNA-seq', '98'), ('transcription profiling by array assay', '24'), ('whole-genome shotgun bisulfite sequencing', '118')]
AUDIT CATEGORY
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AVAILABLE DATA
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BIOSAMPLE TREATMENT
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BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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LIBRARY DEPLETED IN
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LIBRARY INSERT SIZE (NT)
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LIBRARY MADE FROM
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LIBRARY TREATMENT
prod: [('Tobacco Acid Pyrophosphatase', '21')]
LIFE STAGE
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MAPPED READ LENGTH
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ORGAN
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ORGANISM
prod: [('Homo sapiens', '163'), ('Mus musculus', '85')]
PROJECT
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RFA
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READ LENGTH
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SERIES STATUS
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TARGET OF ASSAY
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----------------------------------- Project ------------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=Project
ASSAY
prod: [('ChIP-seq', '8'), ('DNase-seq', '2'), ('RAMPAGE', '1'), ('RNA-seq', '5'), ('single cell isolation followed by RNA-seq', '2')]
AUDIT CATEGORY
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AVAILABLE DATA
prod: [('bam', '5'), ('bed bed3', '1'), ('bed idr_peak', '1'), ('bed narrowPeak', '1'), ('bed tss_peak', '1'), ('bigBed idr_peak', '1'), ('bigBed narrowPeak', '1'), ('bigBed tss_peak', '1'), ('bigWig', '5'), ('fasta', '1'), ('fastq', '16'), ('gff gff3', '1'), ('tsv', '4')]
BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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ORGAN
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ORGANISM
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PROJECT
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PROJECT STATUS
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PROJECT TYPE
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RFA
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READ LENGTH
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RUN TYPE
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TARGET OF ASSAY
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--------------------------- ReplicationTimingSeries ----------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=ReplicationTimingSeries
ASSAY
prod: [('Repli-seq', '22')]
AVAILABLE DATA
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BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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LIBRARY INSERT SIZE (NT)
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LIBRARY MADE FROM
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LIFE STAGE
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ORGAN
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ORGANISM
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PROJECT
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RFA
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READ LENGTH
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SERIES STATUS
prod: [('released', '22')]
TARGET OF ASSAY
prod: [('nucleotide modification', '2')]
------------------------------- PublicationData --------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=PublicationData
ASSAY
prod: [('CAGE', '1'), ('ChIA-PET', '2'), ('RNA-seq', '2'), ('Repli-chip', '1'), ('shRNA knockdown followed by RNA-seq', '1')]
BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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ORGAN
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ORGANISM
prod: [('Drosophila melanogaster', '2'), ('Drosophila pseudoobscura', '1'), ('Homo sapiens', '5')]
PROJECT
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PUBLICATION DATA STATUS
prod: [('released', '7')]
RFA
prod: [('ENCODE', '1'), ('ENCODE3', '4'), ('modENCODE', '2')]
---------------------------------- MatchedSet ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=MatchedSet
ASSAY
prod: [('ChIP-seq', '2'), ('DNase-seq', '3')]
AVAILABLE DATA
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BIOSAMPLE TERM NAME
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BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
prod: [('GRCh38', '3'), ('hg19', '3')]
LAB
prod: [('Gregory Crawford, Duke', '1'), ('J. Michael Cherry, Stanford', '2'), ('John Stamatoyannopoulos, UW', '2')]
LIBRARY INSERT SIZE (NT)
prod: [('450-650', '2')]
LIBRARY MADE FROM
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LIFE STAGE
prod: [('adult', '1'), ('embryonic', '4')]
MAPPED READ LENGTH
prod: [('101', '2')]
ORGAN
prod: [('eye', '1'), ('kidney', '2'), ('mouth', '1'), ('tongue', '1')]
ORGAN3
prod: [('eye', '1'), ('kidney', '2'), ('mouth', '1'), ('tongue', '1')]
ORGANISM
prod: [('Homo sapiens', '5')]
PROJECT
prod: [('ENCODE', '5')]
RFA
prod: [('ENCODE2', '1'), ('ENCODE3', '4')]
READ LENGTH
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SERIES STATUS
prod: [('released', '5')]
TARGET OF ASSAY
prod: [('control', '2')]
------------------------- TreatmentConcentrationSeries -------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=TreatmentConcentrationSeries
ASSAY
prod: [('ChIP-seq', '1'), ('RNA-seq', '1')]
AVAILABLE DATA
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BIOSAMPLE TREATMENT
prod: [('dexamethasone', '2')]
DATE RELEASED
prod: [('December, 2015', '2')]
GENOME ASSEMBLY (VISUALIZATION)
prod: [('GRCh38', '2'), ('hg19', '2')]
LAB
prod: [('Richard Myers, HAIB', '2')]
LIBRARY INSERT SIZE (NT)
prod: [('>200', '1')]
LIBRARY MADE FROM
prod: [('DNA', '1'), ('polyadenylated mRNA', '1')]
LIFE STAGE
prod: [('adult', '2')]
MAPPED READ LENGTH
prod: [('36', '1')]
ORGAN
prod: [('lung', '2')]
ORGANISM
prod: [('Homo sapiens', '2')]
PROJECT
prod: [('ENCODE', '2')]
RFA
prod: [('ENCODE2', '2')]
READ LENGTH
prod: [('36', '2'), ('76', '1')]
SERIES STATUS
prod: [('released', '2')]
TARGET
prod: [('NR3C1', '1')]
TARGET OF ASSAY
prod: [('transcription factor', '1')]
----------------------------- TreatmentTimeSeries ------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /search/?type=TreatmentTimeSeries
ASSAY
prod: [('ATAC-seq', '2'), ('CRISPR genome editing followed by RNA-seq', '1'), ('ChIP-seq', '26'), ('DNase-seq', '1'), ('HiC', '2'), ('PAS-seq', '1'), ('RAMPAGE', '1'), ('RNA-seq', '3')]
AVAILABLE DATA
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BIOSAMPLE TREATMENT
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BIOSAMPLE TYPE
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DATE RELEASED
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GENOME ASSEMBLY (VISUALIZATION)
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LAB
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LIBRARY DEPLETED IN
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LIBRARY INSERT SIZE (NT)
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LIBRARY MADE FROM
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LIFE STAGE
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MAPPED READ LENGTH
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ORGAN
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ORGANISM
prod: [('Homo sapiens', '37')]
PROJECT
prod: [('ENCODE', '2'), ('GGR', '35')]
RFA
prod: [('ENCODE2', '1'), ('ENCODE3', '1'), ('GGR', '35')]
READ LENGTH
prod: [('100', '1'), ('101', '10'), ('151', '2'), ('36', '1'), ('50', '1'), ('51', '22'), ('76', '1')]
SERIES STATUS
prod: [('released', '37')]
TARGET OF ASSAY
prod: [('RNA binding protein', '3'), ('broad histone mark', '4'), ('control', '7'), ('histone', '8'), ('narrow histone mark', '4'), ('transcription factor', '13')]
------------------------------------ Target ------------------------------------
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ORGANISM
prod: [('Aequorea victoria', '2'), ('Caenorhabditis elegans', '1968'), ('Discosoma striata', '1'), ('Drosophila melanogaster', '1595'), ('Homo sapiens', '5935'), ('Mus musculus', '75'), ('enterobacteria phage t7', '1'), ('influenzavirus', '1'), ('synthetic', '2')]
TARGET OF ASSAY
prod: [('RNA binding protein', '1126'), ('broad histone mark', '28'), ('chromatin remodeller', '80'), ('control', '183'), ('histone', '101'), ('narrow histone mark', '17'), ('nucleotide modification', '4'), ('other context', '8'), ('other post-translational modification', '6'), ('recombinant protein', '4303'), ('tag', '10'), ('transcription factor', '8236')]
----------------------------------- Pipeline -----------------------------------
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ASSAY
prod: [('ATAC-seq', '5'), ('CAGE', '1'), ('CRISPR genome editing followed by RNA-seq', '2'), ('CRISPRi followed by RNA-seq', '1'), ('ChIP-seq', '12'), ('DNase-seq', '7'), ('HiC', '1'), ('PAS-seq', '1'), ('RAMPAGE', '1'), ('RIP-seq', '1'), ('RNA-seq', '5'), ('Repli-seq', '1'), ('eCLIP', '1'), ('genetic modification followed by DNase-seq', '4'), ('genotyping by high throughput sequencing assay', '3'), ('microRNA counts', '1'), ('microRNA-seq', '2'), ('shRNA knockdown followed by RNA-seq', '2'), ('siRNA knockdown followed by RNA-seq', '1'), ('single cell isolation followed by RNA-seq', '1'), ('whole-genome shotgun bisulfite sequencing', '3')]
DEVELOPED BY
prod: [('Ali Mortazavi, UCI', '2'), ('Brenton Graveley, UConn', '1'), ('Christina Leslie, MSKCC', '2'), ('David Gilbert, FSU', '1'), ('ENCODE Consortium Analysis Working Group', '2'), ('ENCODE Processing Pipeline', '18'), ('Erez Lieberman-Aiden, Baylor', '1'), ('Gene Yeo, UCSD', '1'), ('John Rinn, Broad', '1'), ('John Stamatoyannopoulos, UW', '1'), ('Kevin White, UChicago', '1'), ('Manuel Garber, UMass', '1'), ('Ross Hardison, PennState', '1'), ('Thomas Gingeras, CSHL', '3'), ('Tim Reddy, Duke', '4'), ('Zhiping Weng, UMass', '3')]
PIPELINE GROUPS
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PIPELINE STATUS
prod: [('archived', '4'), ('released', '39')]
SOFTWARE
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--------------------------------- Publication ----------------------------------
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AVAILABLE SUPPLEMENTAL DATA
prod: [('HMM regions', '4'), ('HOT regions', '2'), ('RNA annotations', '1'), ('connectivity', '8'), ('enhancer annotations', '3'), ('genomic annotations', '2'), ('motifs', '2'), ('peak calls', '3'), ('promoter regions', '2'), ('website', '1')]
CATEGORY
prod: [('basic biology', '833'), ('data standard', '6'), ('database', '4'), ('genomic annotations', '3'), ('human disease', '722'), ('model organism biology', '172'), ('pilot phase publication', '141'), ('production', '560'), ('software tool', '303'), ('technology development', '167')]
HAS DATASET
prod: [('no', '3198'), ('yes', '6')]
JOURNAL
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Cardiovascular genetics', '2'), ('Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology', '3'), ('Cold Spring Harbor protocols', '3'), ('Cold Spring Harbor symposia on quantitative biology', '2'), ('Current biology : CB', '4'), ('Current opinion in genetics & development', '7'), ('Current opinion in structural biology', '2'), ('Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]', '7'), ('Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]', '2'), ('Current protocols in molecular biology / edited by Frederick M. Ausubel ... 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International Conference on Genome Informatics', '3'), ('Genome medicine', '10'), ('Genome research', '244'), ('Genomics', '7'), ('Genomics & informatics', '2'), ('Genomics data', '2'), ('Haematologica', '2'), ('Human Molecular Genetics', '3'), ('Human genetics', '7'), ('Human molecular genetics', '52'), ('Human mutation', '9'), ('Immunity', '5'), ('In Vitro', '2'), ('Insect biochemistry and molecular biology', '2'), ('Insect molecular biology', '2'), ('International Journal of Cancer', '4'), ('International journal of cancer', '5'), ('Journal of Biological Chemistry', '3'), ('Journal of Neuropathology and Experimental Neurology', '2'), ('Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research', '2'), ('Journal of cellular biochemistry', '2'), ('Journal of computational biology : a journal of computational molecular cell biology', '6'), ('Journal of human genetics', '3'), ('Journal of immunology (Baltimore, Md. : 1950)', '2'), ('Journal of medical genetics', '3'), ('Journal of molecular and cellular cardiology', '2'), ('Journal of proteome research', '9'), ('Journal of the National Cancer Institute', '6'), ('Journal of virology', '7'), ('Leukemia', '5'), ('Mammalian genome : official journal of the International Mammalian Genome Society', '2'), ('Methods (San Diego, Calif.)', '12'), ('Methods in enzymology', '2'), ('Methods in molecular biology (Clifton, N.J.)', '14'), ('Molecular Cancer', '2'), ('Molecular Cell', '5'), ('Molecular Psychiatry', '2'), ('Molecular and Cellular Biology', '2'), ('Molecular and cellular biology', '27'), ('Molecular autism', '6'), ('Molecular biology and evolution', '11'), ('Molecular cancer', '5'), ('Molecular cell', '38'), ('Molecular cytogenetics', '3'), ('Molecular oncology', '2'), ('Molecular psychiatry', '7'), ('Molecular systems biology', '5'), ('Mutation research', '2'), ('Nat Methods.', '2'), ('Nature', '97'), ('Nature Biotechnology', '5'), ('Nature Communications', '21'), ('Nature Genetics', '28'), ('Nature Medicine', '2'), ('Nature Methods', '3'), ('Nature biotechnology', '26'), ('Nature cell biology', '5'), ('Nature communications', '55'), ('Nature genetics', '101'), ('Nature medicine', '4'), ('Nature methods', '56'), ('Nature neuroscience', '5'), ('Nature protocols', '11'), ('Nature reviews. Genetics', '9'), ('Nature reviews. Molecular cell biology', '2'), ('Nature structural & molecular biology', '16'), ('Neurobiology of Disease', '2'), ('Neurology', '2'), ('Neuron', '9'), ('Nucleic Acids Research', '19'), ('Nucleic acids research', '191'), ('Oncogene', '5'), ('Oncotarget', '13'), ('PLoS biology', '8'), ('PLoS computational biology', '53'), ('PLoS genetics', '128'), ('PLoS pathogens', '7'), ('Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing', '3'), ('PloS one', '196'), ('Proceedings of the National Academy of Sciences of the United States of America', '91'), ('Proteomics', '3'), ('RNA (New York, N.Y.)', '16'), ('RNA biology', '3'), ('Retrovirology', '5'), ('Schizophrenia bulletin', '3'), ('Science', '5'), ('Science (New York, N.Y.)', '51'), ('Scientific Reports', '12'), ('Scientific reports', '35'), ('Stem cell reports', '3'), ('Stem cells and development', '3'), ('The EMBO journal', '14'), ('The Journal of allergy and clinical immunology', '4'), ('The Journal of biological chemistry', '14'), ('The Journal of clinical investigation', '8'), ('The Journal of experimental medicine', '4'), ('The Journal of neuroscience : the official journal of the Society for Neuroscience', '3'), ('Trends in genetics : TIG', '3'), ('eLIFE', '6'), ('eLife', '15')]
PUBLICATION STATUS
prod: [('released', '3204')]
PUBLICATION YEAR
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PUBLISHED BY
prod: [('ENCODE', '971'), ('community', '1949'), ('historical reference', '101'), ('modENCODE', '176'), ('mouseENCODE', '42')]
----------------------------------- Software -----------------------------------
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CREATED BY
prod: [('ENCODE', '39'), ('community', '21'), ('historical reference', '4'), ('modENCODE', '3'), ('mouseENCODE', '1')]
PURPOSE IN PROJECT
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SOFTWARE TYPE
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---------------------------------- Experiment ----------------------------------
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ASSAY
prod: [("5' RLM RACE", '2'), ('5C', '13'), ('ATAC-seq', '180'), ('CAGE', '121'), ('CRISPR RNA-seq', '50'), ('CRISPRi RNA-seq', '77'), ('ChIA-PET', '62'), ('ChIP-seq', '8911'), ('Circulome-seq', '1'), ('DNA-PET', '6'), ('DNAme array', '259'), ('DNase-seq', '873'), ('FAIRE-seq', '37'), ('Hi-C', '36'), ('MNase-seq', '2'), ('MRE-seq', '68'), ('MS-MS', '14'), ('MeDIP-seq', '55'), ('PAS-seq', '47'), ('RAMPAGE', '168'), ('RIP-chip', '32'), ('RIP-seq', '73'), ('RNA Bind-n-Seq', '161'), ('RNA microarray', '291'), ('RNA-PET', '31'), ('RRBS', '218'), ('Repli-chip', '63'), ('Repli-seq', '119'), ('Switchgear', '2'), ('TAB-seq', '8'), ('WGBS', '258'), ('eCLIP', '359'), ('genetic modification DNase-seq', '40'), ('genotyping HTS', '16'), ('genotyping array', '142'), ('iCLIP', '7'), ('microRNA counts', '115'), ('microRNA-seq', '185'), ('polyA RNA-seq', '817'), ('polyA depleted RNA-seq', '32'), ('shRNA RNA-seq', '533'), ('siRNA RNA-seq', '113'), ('single cell RNA-seq', '120'), ('small RNA-seq', '216'), ('total RNA-seq', '413'), ('whole genome sequencing assay', '21')]
ASSAY CATEGORY
prod: [('3D chromatin structure', '111'), ('DNA accessibility', '1132'), ('DNA binding', '8911'), ('DNA methylation', '866'), ('DNA sequencing', '22'), ('Genotyping', '164'), ('Proteomics', '14'), ('RNA binding', '634'), ('Replication timing', '182'), ('Transcription', '3331')]
AUDIT CATEGORY
prod: [('control extremely low read depth', '24'), ('extremely low coverage', '7'), ('extremely low read depth', '221'), ('extremely low read length', '10'), ('extremely low spot score', '49'), ('inconsistent control', '3'), ('inconsistent library biosample', '1'), ('inconsistent read count', '2'), ('missing antibody', '75'), ('missing control alignments', '418'), ('missing donor', '1'), ('missing nih_institutional_certification', '33'), ('missing possible_controls', '2')]
AUDIT CATEGORY2
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AUDIT CATEGORY3
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AVAILABLE DATA
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BIOSAMPLE TYPE
prod: [('cell line', '5779'), ('cell-free sample', '161'), ('in vitro differentiated cells', '679'), ('induced pluripotent stem cell line', '137'), ('primary cell', '1678'), ('stem cell', '506'), ('tissue', '4375'), ('whole organisms', '2052')]
DATE RELEASED
prod: [('April, 2011', '149'), ('April, 2012', '77'), ('April, 2013', '6'), ('April, 2014', '2'), ('April, 2015', '28'), ('April, 2016', '170'), ('April, 2017', '52'), ('April, 2018', '48'), ('August, 2011', '88'), ('August, 2012', '257'), ('August, 2015', '180'), ('August, 2016', '265'), ('August, 2017', '71'), ('December, 2010', '68'), ('December, 2011', '87'), ('December, 2014', '247'), ('December, 2015', '40'), ('December, 2016', '174'), ('December, 2017', '139'), ('February, 2011', '255'), ('February, 2012', '264'), ('February, 2013', '1'), ('February, 2014', '7'), ('February, 2015', '3'), ('February, 2016', '183'), ('February, 2017', '138'), ('February, 2018', '177'), ('January, 2011', '6'), ('January, 2012', '59'), ('January, 2015', '8'), ('January, 2016', '110'), ('January, 2017', '399'), ('January, 2018', '156'), ('July, 2009', '22'), ('July, 2011', '263'), ('July, 2012', '128'), ('July, 2013', '2761'), ('July, 2014', '300'), ('July, 2015', '103'), ('July, 2016', '614'), ('July, 2017', '39'), ('June, 2011', '83'), ('June, 2012', '75'), ('June, 2014', '432'), ('June, 2015', '106'), ('June, 2016', '221'), ('June, 2017', '272'), ('March, 2011', '160'), ('March, 2012', '170'), ('March, 2013', '1'), ('March, 2014', '887'), ('March, 2015', '2'), ('March, 2016', '291'), ('March, 2017', '96'), ('March, 2018', '134'), ('May, 2011', '35'), ('May, 2012', '138'), ('May, 2013', '2'), ('May, 2014', '8'), ('May, 2015', '12'), ('May, 2016', '569'), ('May, 2017', '66'), ('May, 2018', '15'), ('November, 2010', '9'), ('November, 2011', '76'), ('November, 2012', '7'), ('November, 2014', '98'), ('November, 2015', '225'), ('November, 2016', '400'), ('November, 2017', '428'), ('October, 2009', '4'), ('October, 2010', '1'), ('October, 2011', '456'), ('October, 2014', '86'), ('October, 2015', '106'), ('October, 2016', '485'), ('October, 2017', '200'), ('September, 2011', '134'), ('September, 2012', '190'), ('September, 2014', '41'), ('September, 2015', '17'), ('September, 2016', '209'), ('September, 2017', '115')]
GENOME ASSEMBLY (VISUALIZATION)
prod: [('GRCh38', '7315'), ('ce10', '838'), ('ce11', '897'), ('dm3', '835'), ('dm6', '811'), ('hg19', '7492'), ('mm10', '1508'), ('mm9', '338')]
LAB
prod: [('Alexander Urban, Stanford', '3'), ('Ali Mortazavi, UCI', '231'), ('Andrew Z. Fire, Stanford', '4'), ('Barbara Wold, Caltech', '287'), ('Bing Ren, UCSD', '1379'), ('Bradley Bernstein, Broad', '1957'), ('Brenton Graveley, UConn', '789'), ('Brian Oliver, NIH', '27'), ('Chris Burge, MIT', '161'), ('Christina Leslie, MSKCC', '32'), ('David Gilbert, FSU', '77'), ('David MacAlpine, Duke', '39'), ('Eric Lécuyer, IRCM', '30'), ('Gene Yeo, UCSD', '366'), ('Gregory Crawford, Duke', '162'), ('Jason Lieb, UNC', '37'), ('Job Dekker, UMass', '26'), ('Joe Ecker, Salk', '193'), ('John Rinn, Broad', '35'), ('John Stamatoyannopoulos, UW', '1594'), ('Joseph Costello, UCSF', '595'), ('Kevin Struhl, HMS', '43'), ('Kevin White, UChicago', '1064'), ('Manuel Garber, UMass', '68'), ('Michael Snyder, Stanford', '2401'), ('Morgan Giddings, UNC', '14'), ('Paul Khavari, Stanford', '13'), ('Peggy Farnham, USC', '125'), ('Piero Carninci, RIKEN', '78'), ('Richard Myers, HAIB', '1423'), ('Ross Hardison, PennState', '128'), ('Scott Tenenbaum, SUNY-Albany', '42'), ('Sherman Weissman, Yale', '65'), ('Susan Celniker, LBNL', '239'), ('Terry Orr-Weaver, MIT', '2'), ('Thomas Gingeras, CSHL', '736'), ('Tim Reddy, Duke', '298'), ('Valerie Reinke, Yale', '361'), ('Vishwanath Iyer, UTA', '85'), ('Will Greenleaf, Stanford', '13'), ('Xiang-Dong Fu, UCSD', '97'), ('Yijun Ruan, JAX', '48')]
ORGAN
prod: [('adipose tissue', '137'), ('adrenal gland', '105'), ('artery', '42'), ('blood', '2614'), ('blood vessel', '208'), ('bodily fluid', '2614'), ('bone element', '117'), ('bone marrow', '38'), ('brain', '937'), ('breast', '49'), ('bronchus', '20'), ('connective tissue', '571'), ('embryo', '984'), ('epithelium', '723'), ('esophagus', '117'), ('extraembryonic component', '203'), ('eye', '36'), ('gonad', '130'), ('heart', '340'), ('intestine', '559'), ('kidney', '571'), ('large intestine', '359'), ('limb', '356'), ('liver', '1184'), ('lung', '927'), ('lymph node', '169'), ('lymphatic vessel', '6'), ('lymphoid tissue', '41'), ('mammary gland', '427'), ('mouth', '25'), ('musculature of body', '553'), ('nerve', '39'), ('nose', '2'), ('ovary', '55'), ('pancreas', '146'), ('penis', '212'), ('pericardium', '4'), ('placenta', '65'), ('prostate gland', '118'), ('skeleton', '5'), ('skin of body', '565'), ('small intestine', '107'), ('spinal cord', '28'), ('spleen', '195'), ('stomach', '250'), ('testis', '69'), ('thymus', '53'), ('thyroid gland', '60'), ('tongue', '5'), ('trachea', '3'), ('ureter', '31'), ('urinary bladder', '21'), ('uterus', '230'), ('vagina', '29'), ('vasculature', '231'), ('vein', '69')]
ORGANISM
prod: [('Caenorhabditis elegans', '975'), ('Drosophila ananassae', '1'), ('Drosophila melanogaster', '1435'), ('Drosophila mojavensis', '4'), ('Drosophila pseudoobscura', '12'), ('Drosophila simulans', '8'), ('Drosophila virilis', '1'), ('Drosophila yakuba', '1'), ('Homo sapiens', '10891'), ('Mus musculus', '1864')]
PROJECT
prod: [('ENCODE', '9701'), ('GGR', '461'), ('Roadmap', '2761'), ('community', '7'), ('modENCODE', '1330'), ('modERN', '1107')]
TARGET OF ASSAY
prod: [('RNA binding protein', '1466'), ('broad histone mark', '1727'), ('chromatin remodeller', '254'), ('control', '2568'), ('histone', '3102'), ('narrow histone mark', '1265'), ('nucleotide modification', '70'), ('other context', '58'), ('other post-translational modification', '76'), ('recombinant protein', '1271'), ('tag', '1'), ('transcription factor', '3971')]
---------------------------------- Annotation ----------------------------------
Comparing data between URLs.
As user: Public
Browser: Chrome
First URL: https://www.encodeproject.org
Second URL: https://v71rc1-master.demo.encodedcc.org/
Item type: /matrix/?type=Annotation
ANNOTATION TYPE
prod: [('binding sites', '2'), ('blacklist', '3'), ('candidate regulatory elements', '2178'), ('chromatin state', '330'), ('enhancer predictions', '111'), ('gene expression', '14'), ('other', '3048'), ('overlap', '17'), ('representative DNase hypersensitivity sites', '6'), ('transcript expression', '14'), ('validated enhancers', '6')]
AUDIT CATEGORY
prod: [('inconsistent assembly', '28')]
AVAILABLE DATA
prod: [('bam', '3'), ('bed bed3', '4'), ('bed bed3+', '2164'), ('bed bed6', '2'), ('bed bed9', '91'), ('bed candidate enhancer predictions', '46'), ('bed enhancer predictions', '50'), ('bed enhancerAssay', '2'), ('bed narrowPeak', '2'), ('bed openChromCombinedPeaks', '17'), ('bigBed bed3+', '2154'), ('bigBed bed6', '2'), ('bigBed bed9', '218'), ('bigBed broadPeak', '1'), ('bigBed enhancerAssay', '2'), ('bigBed openChromCombinedPeaks', '17'), ('bigBed unknown', '9'), ('bigWig', '3049'), ('fasta', '1'), ('fastq', '20'), ('tsv', '39')]
BIOSAMPLE TYPE
prod: [('cell line', '393'), ('in vitro differentiated cells', '124'), ('induced pluripotent stem cell line', '44'), ('primary cell', '603'), ('stem cell', '101'), ('tissue', '1362'), ('whole organisms', '6')]
DATE RELEASED
prod: [('April, 2014', '3'), ('April, 2017', '3'), ('April, 2018', '3048'), ('August, 2015', '92'), ('August, 2016', '452'), ('August, 2017', '779'), ('December, 2011', '1'), ('February, 2012', '10'), ('February, 2015', '2'), ('July, 2013', '225'), ('July, 2016', '3'), ('June, 2011', '16'), ('June, 2015', '2'), ('June, 2016', '276'), ('March, 2014', '9'), ('March, 2016', '1'), ('November, 2016', '17'), ('October, 2011', '2'), ('October, 2015', '10'), ('September, 2012', '2'), ('September, 2014', '22'), ('September, 2015', '2'), ('September, 2017', '758')]
ENCYCLOPEDIA VERSION
prod: [('1', '3'), ('2', '141'), ('3', '847'), ('4', '4587'), ('Blacklists', '2'), ('ENCODE2', '27'), ('ROADMAP', '127')]
GENOME ASSEMBLY (VISUALIZATION)
prod: [('hg19', '4166'), ('mm10', '455'), ('mm9', '17')]
ORGAN
prod: [('adipose tissue', '9'), ('adrenal gland', '21'), ('artery', '10'), ('blood', '228'), ('blood vessel', '52'), ('bodily fluid', '228'), ('bone element', '33'), ('bone marrow', '15'), ('brain', '331'), ('breast', '1'), ('bronchus', '8'), ('connective tissue', '200'), ('embryo', '217'), ('epithelium', '174'), ('esophagus', '17'), ('extraembryonic component', '52'), ('eye', '30'), ('gonad', '26'), ('heart', '109'), ('intestine', '156'), ('kidney', '123'), ('large intestine', '90'), ('limb', '108'), ('liver', '89'), ('lung', '162'), ('lymph node', '50'), ('lymphatic vessel', '2'), ('lymphoid tissue', '2'), ('mammary gland', '44'), ('mouth', '17'), ('musculature of body', '155'), ('ovary', '12'), ('pancreas', '33'), ('penis', '54'), ('placenta', '27'), ('prostate gland', '15'), ('skin of body', '129'), ('small intestine', '41'), ('spinal cord', '15'), ('spleen', '29'), ('stomach', '70'), ('testis', '13'), ('thymus', '34'), ('thyroid gland', '8'), ('tongue', '4'), ('ureter', '14'), ('urinary bladder', '2'), ('uterus', '22'), ('vagina', '3'), ('vasculature', '64'), ('vein', '15')]
ORGANISM
prod: [('Homo sapiens', '4951'), ('Mus musculus', '784')]
PROJECT
prod: [('ENCODE', '5510'), ('Roadmap', '225')]
TARGET(S) OF ASSAY
prod: [('CTCF', '235'), ('H3K27ac', '684'), ('H3K4me1', '1'), ('H3K4me3', '860'), ('H3K9ac', '1')]
In [4]:
#qa.compare_facets(users=['encoded.test4@gmail.com'], browsers=['Chrome'], item_types=['/search/?type=Experiment'], browser_comparison=False)
In [5]:
#.find_differences(users=['encoded.test4@gmail.com'], browsers=['Safari'])
In [6]:
#qa.find_differences(users=['encoded.test4@gmail.com'], browsers=['Chrome'], item_types=['/experiments/ENCSR524OCB/'])
In [7]:
#qa.show_differences()
In [8]:
#qa.check_downloads(browsers=['Safari'], users=['Public'])
In [9]:
#qa.check_trackhubs(browsers=['Safari'], users=['Public'])
In [10]:
#qa.check_permissions(browsers=['Chrome'], users=['Public'])
In [11]:
#qa.check_permissions(browsers=['Chrome'], users=['encoded.test@gmail.com'])
In [12]:
#qa.check_permissions(browsers=['Chrome'], users=['encoded.test2@gmail.com'])
In [13]:
#qa.check_permissions(browsers=['Chrome'], users=['encoded.test4@gmail.com'])
In [14]:
#qa.check_requests()
In [15]:
#qa.check_tools()
Content source: ENCODE-DCC/pyencoded-tools
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