A collection of Jupyter Notebooks

• ChiCMaxima algorithm review
• Load library
• Read count table
• Specify design matrix, control + treatment
• Get count matrix
• RUN DEseq2
• Save result (this is the result without LFC shrinkage)
• apply LFC shrinkage
• save new result
• GSEA dot plot
• How to run GSEA analysis using user defined gene sets
• define gene sets
• define your ranked list
• run GSEA
• save GSEA stat
• plot GSEA figure
• run everything for another ranked gene list
• GWAS plot example
• ggplot correlation with values shown
• ggplot Manhattan plot
• ggplot Scatter plot gRNA counts version 2
• ggpubr violin plot for comparing number of fragments
• adding custom p-value bar to your ggplot
• ggseqlogo for variant motifs
• Scatter plot for pairwise comparison (gRNA counts)
• Step 1, read data
• generate density plot for each column
• merge each density
• Tutorial: how to make single-cell ATAC-seq coverage plot
• load Seurat Obj
• Coverage plot, just replace your coordinates in line 1

Use R and Python in Jupyter Notebook

First, create a conda environment:

conda create -n Rplot

Then, activate this envrionment:

(Windows OS) conda activate Rplot

(Linux / Mac) source activate Rplot

Then, do the following:

conda install -c bioconda r-pheatmap

conda install -c r r-irkernel

conda install -c anaconda jupyter

conda install -c anaconda pandas

conda install -c anaconda seaborn

Last, type jupyter notebook and you should be able to run R and Python in the same jupyter notebook.

FAQ

1. no ‘R’ in jupyter notebook

These could due to many reason.

One note: on the same computer, just within 2 week, conda install -c r r-irkernel worked for me. But now, after I reinstalled conda, it didn’t.

First, check if you can see ir in jupyter kernelspec list? For me, I can’t see it. Then I did: R -> install.packages(‘IRkernel’) -> IRkernel::installspec(user = FALSE)

ref: https://github.com/IRkernel/IRkernel/issues/163 https://irkernel.github.io/installation/

2. add python2 to a jupyter notebook (python3)

Can’t use conda install. Tried but permission denied. Should do the following:

python2 -m pip install ipykernel

python2 -m ipykernel install –user

Then reinstall pandas, seaborn for python2.

python2 -m pip install pandas

python2 -m pip install seaborn

3. add your conda env python to jupyter notebook

sometime python will be installed on your local conda env when you specifying python version. and jupyter notebook won’t add this python automatically.

python -m pip install ipykernel

python -m ipykernel install –user –name myenv –display-name “Python (myenv)”

Comments

code @ github.