Instructions for installation and configuration of Jupyterlab

These instructions form a quick and simple setup to get Jupyterlab running via Anaconda.

Install software

Visit (anaconda.org)[anaconda.org]
Download and install Anaconda
Visit (nodejs.org )[nodejs.org]
Download and install nodejs

Setup environment

Open Anaconda
Click on "Environments" tab on left panel
Click on "Create" at bottom of middle panel to create new environment
Give new environment a name and select python3 (and any additional choices)
Select "Chanels" in the top of the right-hand panel
Select "Add..." in the top right corner
Enter conda-forge and hit enter.
Click "Update channels" and then close the window.
Select "All" from the dropdown menu in the top of the right-hand panel.
Click "Update index"
Enter jupyterlab in the textbox to the right.
Select "jupyterlab" from the options.
Click "Apply" in the bottom right corner.
A window will pop up showing the updates that will be made. Select "Accept" to install jupyterlab.
Repeat from step 11 to add any additional libraries (eg pandas, scipy, scikit-learn)

Install google-drive extension

in terminal, ensure that anaconda/bin is included in your path:

eg. export PATH="/User/Guest/anaconda/bin:$PATH

activate the environment created above:

source activate <envt_name>

install (google-drive)[https://github.com/jupyterlab/jupyterlab-google-drive] extension :

jupyter labextension install @jupyterlab/google-drive

Launch JupyterLab server

In terminal, enter:

jupyter lab

ipywidgets

jupyter labextension install @jupyter-widgets/jupyterlab-manager

oops. Looks like this is broken in 0.27.0

Jupyterlab renderers

plotly
json
geojson

https://github.com/jupyterlab/jupyter-renderers

A few Jupyter examples



In [1]:

    
%matplotlib inline
import matplotlib.pyplot as plt
from ipywidgets import interact, interactive
import ipywidgets



In [2]:

    
import pandas as pd



In [3]:

    
df = pd.read_csv("DESeq2_pvalues.out", sep=' ')
df["pathway"] = df.baseMean.apply(lambda x: int(x)%7)



In [4]:

    
df.head()









    Out[4]:







  
    
      
      baseMean
      log2FoldChange
      lfcSE
      stat
      pvalue
      padj
      pathway
    
  
  
    
      ENSG00000000003.10
      1.958923
      1.507327
      2.280241
      5.898438
      4.346629e-01
      5.167232e-01
      1
    
    
      ENSG00000000005.5
      0.000000
      NaN
      NaN
      NaN
      NaN
      NaN
      0
    
    
      ENSG00000000419.8
      1245.038399
      -0.240458
      0.114002
      319.074644
      6.667458e-66
      3.164103e-65
      6
    
    
      ENSG00000000457.8
      573.445192
      0.114238
      0.125212
      88.851140
      5.248090e-17
      1.258779e-16
      6
    
    
      ENSG00000000460.12
      790.056229
      0.411113
      0.119781
      1170.842594
      9.775789e-250
      1.707693e-248
      6

	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	pathway
ENSG00000000003.10	1.958923	1.507327	2.280241	5.898438	4.346629e-01	5.167232e-01	1
ENSG00000000005.5	0.000000	NaN	NaN	NaN	NaN	NaN	0
ENSG00000000419.8	1245.038399	-0.240458	0.114002	319.074644	6.667458e-66	3.164103e-65	6
ENSG00000000457.8	573.445192	0.114238	0.125212	88.851140	5.248090e-17	1.258779e-16	6
ENSG00000000460.12	790.056229	0.411113	0.119781	1170.842594	9.775789e-250	1.707693e-248	6