A list of jupyter notebooks in bioinformatics

jupyter_notebooks.md

Introduction to linux command line/ipython/git/R for bioinformatics:

• https://github.com/biom262/biom262-2016
• https://github.com/ricket-sjtu/bi028
• https://github.com/YeoLab/single-cell-bioinformatics/
• https://github.com/YeoLab/single-cell-bioinformatics/tree/master/notebooks
• https://github.com/ltminty/Bioinformatics-and-R/blob/master/Rbioinformatics.ipynb

RNA-seq:

• https://github.com/Caroldm/RNA-Seq-Tutorial---Jupyter-notebook/blob/master/RNAseq%20tutorial.ipynb

Proteomics/PPI:

• https://github.com/hussius/TCGA_proteomics_tutorial/blob/master/TCGA_protein_tutorial.ipynb
• https://github.com/dhimmel/ppi/blob/master/compile-PPIs.ipynb

Single-cell RNA:

• https://github.com/YeoLab/single-cell-bioinformatics-scrm-2016
• https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts/blob/master/Trapnell_pipeline/Trapnell_Analysis.ipynb
• https://github.com/govinda-kamath/clustering_on_transcript_compatibility_counts/blob/master/Zeisel_pipeline/Zeisel_Analysis.ipynb

Fully ipynb reproduced papers:

• https://github.com/olgabot/olgabot.github.io-source/blob/master/content/shalek2013.ipynb
• http://nbviewer.jupyter.org/github/maayanlab/Zika-RNAseq-Pipeline/blob/master/Zika.ipynb
• https://github.com/cdeboever3/deboever-sf3b1-2015/blob/master/notebooks/figure01.ipynb
• http://ged.msu.edu/papers/2012-diginorm/notebook/
• http://reproduced-papers.github.io/ (physics)

Other resources of interest:

RNA-seq

• https://github.com/crazyhottommy/RNA-seq-analysis
• A benchmark for RNA-seq quantification pipelines
• RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Courses

• resource files for PH525x series on Biomedical Data Science; there is also a link to the book https://github.com/genomicsclass/labs