Code

First draft of Toolbox use cases#4

Code

Merged

jkgoodrich merged 34 commits intodevelopmentbroadinstitute/gnomad-toolbox:developmentfrom qh/draft_toolboxbroadinstitute/gnomad-toolbox:qh/draft_toolboxCopy head branch name to clipboardDec 18, 2024

+14,274-32

Commits

Commits on Sep 27, 2024

• Add a draft notebook

  KoalaQin

  committed
  e835bf6

Commits on Sep 30, 2024

• Add more use cases in notebook

  KoalaQin

  committed
  c9f0e22

• Add example to get AF for one ancestry for one variant

  KoalaQin

  committed
  a44e72d

Commits on Oct 1, 2024

• Add table of contents and screenshot

  KoalaQin

  committed
  4bc936c

• Format gnomad_methods in requirements.txt

  KoalaQin

  committed
  2f1156e

• Remove setup.py

  KoalaQin

  committed
  ff64d86

• Remove setup.py

  KoalaQin

  committed
  bc85e6f

• Reorganize the notebook

  KoalaQin

  committed
  e083fbf

Commits on Oct 29, 2024

• Function to import data by version

  KoalaQin

  committed
  b5101ba

• Modify import_data function to match gnomad_methods repo version by datatype

  KoalaQin

  committed
  2bd494e

• Formatting

  KoalaQin

  committed
  3cfb1bd

• Formatting

  KoalaQin

  committed
  8d904cf

• Formatting

  KoalaQin

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  49b2cb0

• Formatting

  KoalaQin

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  a7c8e53

• Formatting

  KoalaQin

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  6d3471f

• Formatting

  KoalaQin

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  1b847b4

• Formatting docstring block

  KoalaQin

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  22c40f7

• Function to extract callstats for one variant in one genetic ancestry group

  KoalaQin

  committed
  66770ea

• Function to extract callstats for genetic ancestry groups

  KoalaQin

  committed
  71a33bd

• indent correctly

  KoalaQin

  committed
  80b1f91

Commits on Nov 1, 2024

• Add functions to filter variants by gene symbol, interval and csqs

  KoalaQin

  committed
  8dcce6c

Commits on Nov 2, 2024

• Correct small errors

  KoalaQin

  committed
  34fab76

• Update notebook

  KoalaQin

  committed
  0ccdb5b

Commits on Dec 9, 2024

• - Restructure files

  Show description for c183470
  jkgoodrich

  committed
  c183470

• - Restructure files

  Show description for 095a234
  jkgoodrich

  committed
  095a234

• - Modifications to support setting a default data_type and version

  Show description for 5fe3010
  jkgoodrich

  committed
  5fe3010

Commits on Dec 11, 2024

• More clean-up of notebooks and functions

  jkgoodrich

  committed
  5330ea6

• Add notebooks to git

  jkgoodrich

  committed
  b853fc2

Commits on Dec 13, 2024

• Fix unterminated string error

  KoalaQin

  authored
  710bdcf

Commits on Dec 18, 2024

• Apply suggestions from code review

  Show description for 4bfc305
  

  jkgoodrich

  and

  KoalaQin

  authored
  4bfc305

• format

  jkgoodrich

  committed
  ecb664b

• Put back setup.py

  KoalaQin

  committed
  06de980

• Merge pull request #5 from broadinstitute/jg/draft_toolbox

  Show description for d09953c
  jkgoodrich

  authored
  d09953c

• move setup to the correct location

  jkgoodrich

  committed
  c37ad6c