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greenelab / pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
MIT License
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Adding Variant Passage Flow Visualizations and Data #41

Closed gwaybio closed 6 years ago

gwaybio commented 6 years ago

Closes #33

Two major notebooks are added in this PR

  1. mutations_across_passages.ipynb - takes 8 groups of samples and outputs venn diagrams showing how variants are called across PDX passages. Also outputs tables describing the specific overlapping genes and cosmic IDs
  2. metastatic_passages.ipynb - takes 2 groups of samples (both have unique relationships and several metastatic samples) and visualizes gene variant calls across several passages using UpSetR

The pull request also adds all the figures and tables that were generated by these two notebooks

gwaybio commented 6 years ago

Thanks @danich1 and @huqiwen0313 - ready again for rereview!