Code

Decoupler Pathway Inference#308

Code

Merged

anilthanki merged 60 commits intodevelopebi-gene-expression-group/container-galaxy-sc-tertiary:developfrom feature/decoupler_pathway_inferenceebi-gene-expression-group/container-galaxy-sc-tertiary:feature/decoupler_pathway_inferenceCopy head branch name to clipboardMar 15, 2024

+419

Commits

Commits on Nov 10, 2023

• first commit for decoupler_pathway_inference

  anilthanki

  committed
  6ce05c3

• code refactoring

  anilthanki

  committed
  1db7706

• uses progeny network

  anilthanki

  committed
  1b88053

• adds function to download anndata for decoupler_pathway_inference

  anilthanki

  committed
  9022bc9

• adds network file and option to use network file

  anilthanki

  committed
  9adf85e

• replaces python with wget and zenodo link

  anilthanki

  committed
  8f68f11

• adds use_raw and min_n options

  anilthanki

  committed
  118b327

Commits on Nov 17, 2023

• removes unnecessary args

  anilthanki

  committed
  5afc617

• adds Galaxy wrapper

  anilthanki

  committed
  b99d9de

Commits on Nov 24, 2023

• updates anndata key

  anilthanki

  committed
  7f25d64

• fixes arg type for min_n and enables use_raw arg

  anilthanki

  committed
  7944106

• first commit for decoupler_pathway_inference

  anilthanki

  committed
  f699633

• code refactoring

  anilthanki

  committed
  02659ce

• uses progeny network

  anilthanki

  committed
  965753d

• adds function to download anndata for decoupler_pathway_inference

  anilthanki

  committed
  4efaff7

• adds network file and option to use network file

  anilthanki

  committed
  47073ce

• replaces python with wget and zenodo link

  anilthanki

  committed
  012cff5

• adds use_raw and min_n options

  anilthanki

  committed
  a0a0116

• removes unnecessary args

  anilthanki

  committed
  3fa15df

• adds Galaxy wrapper

  anilthanki

  committed
  a37d403

• updates anndata key

  anilthanki

  committed
  827cbe8

• fixes arg type for min_n and enables use_raw arg

  anilthanki

  committed
  fd8f001

• Merge branch 'feature/decoupler_pathway_inference' of https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary into feature/decoupler_pathway_inference

  anilthanki

  committed
  388b89b

• fixes params and output name

  anilthanki

  committed
  8efaba9

• updates key in anndata

  anilthanki

  committed
  e34e93d

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for ec2de3f
  

  anilthanki

  and

  nsoranzo

  authored
  ec2de3f

• removes hdf5plugin

  anilthanki

  committed
  0751eb5

• renames arg

  anilthanki

  committed
  df5616a

• shortens args

  anilthanki

  committed
  e24a71e

Commits on Nov 29, 2023

• adds --output and removes quotes around

  anilthanki

  committed
  40fe7c7

• updates test parameter

  anilthanki

  committed
  8c38a2b

• updates test parameter

  anilthanki

  committed
  d8fca4a

Commits on Dec 12, 2023

• testing raw input

  anilthanki

  committed
  3258a1a

• testing raw input

  anilthanki

  committed
  182d056

• makes output anndata with activities path optional

  anilthanki

  committed
  a1ea2ab

• makes output anndata with activities path optional adds filter in output tag

  anilthanki

  committed
  37d5afa

• removes param

  anilthanki

  committed
  23c67d6

• removes progeny.tsv

  anilthanki

  committed
  4891666

• fixes activities output file

  anilthanki

  committed
  ecb4867

• merges mlm files into one

  anilthanki

  committed
  6428552

Commits on Dec 13, 2023

• merges mlm files into one

  anilthanki

  committed
  38a657f

• updates number of output in test

  anilthanki

  committed
  ba18fbd

• concat pd before writing to a file

  anilthanki

  committed
  f72770c

• updates test verification in wrapper

  anilthanki

  committed
  e14317f

Commits on Dec 18, 2023

• removed test.h5ad and downloads it from zenodo

  anilthanki

  committed
  0f0a4e2

Commits on Feb 13, 2024

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for 7b34514
  

  anilthanki

  and

  pcm32

  authored
  7b34514

Commits on Mar 7, 2024

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for b869140
  

  anilthanki

  and

  pcm32

  authored
  b869140

• Update decoupler_pathway_inference.xml

  anilthanki

  authored
  d833bdf

• adds ULM method

  anilthanki

  committed
  86a9763

Commits on Mar 8, 2024

• adds alternative sample network file

  anilthanki

  committed
  3f4efd6

• adds unindexed network file and test

  anilthanki

  committed
  2d76c11

Commits on Mar 12, 2024

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for b662f08
  

  anilthanki

  and

  pcm32

  authored
  b662f08

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for 45c6b86
  

  anilthanki

  and

  pcm32

  authored
  45c6b86

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for 3b9ef4a
  

  anilthanki

  and

  pcm32

  authored
  3b9ef4a

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for 420dd03
  

  anilthanki

  and

  pcm32

  authored
  420dd03

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for b0a7cc3
  

  anilthanki

  and

  pcm32

  authored
  b0a7cc3

• Update tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml

  Show description for 9eac4a1
  

  anilthanki

  and

  pcm32

  authored
  9eac4a1

Commits on Mar 14, 2024

• adds network file parameters

  anilthanki

  authored
  9d91561

• Removes unused argument and comments

  anilthanki

  authored
  aa07b02

Commits on Mar 15, 2024

• to re-run test

  anilthanki

  authored
  9326fae