Code

Ipage2 merge#38

Code

Merged

noamteyssier merged 48 commits intomaingoodarzilab/pypage:mainfrom ipage2-mergegoodarzilab/pypage:ipage2-mergeCopy head branch name to clipboardJun 30, 2022

+1,072-125

Commits

Commits on Jun 9, 2022

• added_module_to_switch_accessions

  artemy-bakulin

  committed
  27ea9d8

  Copy full SHA for 27ea9d8

• modified get_gene_subset, fixed error

  artemy-bakulin

  committed
  6a1a40a

  Copy full SHA for 6a1a40a

• added a function to convert accessions, connected with accession_types module

  artemy-bakulin

  committed
  4e57810

  Copy full SHA for 4e57810

• add functions to calculate a membership profile

  artemy-bakulin

  committed
  cc47d8a

  Copy full SHA for cc47d8a

• add a function to process annotation files

  artemy-bakulin

  committed
  b1440dc

  Copy full SHA for b1440dc

• add a new unit test for read_annotation and convert_from_to functions

  artemy-bakulin

  committed
  8f2ac4c

  Copy full SHA for 8f2ac4c

• add description of functions

  artemy-bakulin

  committed
  c191683

  Copy full SHA for c191683

• added a test for convert_from_to function

  artemy-bakulin

  committed
  333f2a1

  Copy full SHA for 333f2a1

• create membership programs

  artemy-bakulin

  committed
  ac98d8e

  Copy full SHA for ac98d8e

• calculate CMI

  artemy-bakulin

  committed
  c911caf

  Copy full SHA for c911caf

• added 'function' parameter to control whether to calculate mi or cmi

  artemy-bakulin

  committed
  80321f8

  Copy full SHA for 80321f8

• added 'function' parameter to control whether to calculate mi or cmi

  artemy-bakulin

  committed
  81a849a

  Copy full SHA for 81a849a

• added cmi calculation to calculate_informative

  artemy-bakulin

  committed
  9ea06ec

  Copy full SHA for 9ea06ec

• change a strategy for '_consolidate_pathways', sort according to cmi, choose pathways if redundancy is less than redundancy ratio

  artemy-bakulin

  committed
  cf25cde

  Copy full SHA for cf25cde

• made a fuller description of results by modifying _gather_results function

  artemy-bakulin

  committed
  9ec18c8

  Copy full SHA for 9ec18c8

• made calculation of the survival overrepresentation probability more correct by substraction one from the number k

  artemy-bakulin

  committed
  bf09795

  Copy full SHA for bf09795

• fixed problems which occur if zero pathways are found

  artemy-bakulin

  committed
  202f4ac

  Copy full SHA for 202f4ac

• fixed problems which occur if zero pathways are found, returns empty DataFrame

  artemy-bakulin

  committed
  cbc2bdd

  Copy full SHA for cbc2bdd

• add heatmap module

  artemy-bakulin

  committed
  06268ea

  Copy full SHA for 06268ea

• add tests for heatmap module

  artemy-bakulin

  committed
  c713a16

  Copy full SHA for c713a16

• add function to calculate cmi permutations, otherwise _calculate_informative does not work

  artemy-bakulin

  committed
  e180839

  Copy full SHA for e180839

• connect page with heatmap module

  artemy-bakulin

  committed
  2ae579c

  Copy full SHA for 2ae579c

• add test for latest pypage version

  artemy-bakulin

  committed
  fd65cda

  Copy full SHA for fd65cda

Commits on Jun 12, 2022

• add pybiomart

  artemy-bakulin

  authored
  d6b783e

  Copy full SHA for d6b783e

• "bin only after subsetting"

  Show description for fe68880
  artemy-bakulin

  authored
  fe68880

  Copy full SHA for fe68880

• "bin membership profile only after subsetting"

  Show description for 11aae93
  artemy-bakulin

  authored
  11aae93

  Copy full SHA for 11aae93

• new_defaults

  artemy-bakulin

  authored
  1db8188

  Copy full SHA for 1db8188

• change default k

  artemy-bakulin

  authored
  0ee3210

  Copy full SHA for 0ee3210

Commits on Jun 13, 2022

• update default n_jobs

  artemy-bakulin

  authored
  114c861

  Copy full SHA for 114c861

Commits on Jun 27, 2022

• Merge pull request #32 from artemy-bakulin/main

  Show description for 06e17b1
  noamteyssier

  authored
  06e17b1

  Copy full SHA for 06e17b1

• fix missing matplotlib dependency

  noamteyssier

  committed
  91bdc86

  Copy full SHA for 91bdc86

• exposed Heatmap to top level imports

  noamteyssier

  committed
  6c33c77

  Copy full SHA for 6c33c77

• reverting changes from commit fe68880

  noamteyssier

  committed
  c7ac144

  Copy full SHA for c7ac144

• added pandas to fix import error

  noamteyssier

  committed
  21ea973

  Copy full SHA for 21ea973

• fixed typo; isreg -> show_reg

  noamteyssier

  committed
  50e0bd9

  Copy full SHA for 50e0bd9

• added explicit gene subset test

  noamteyssier

  committed
  7149ffa

  Copy full SHA for 7149ffa

Commits on Jun 28, 2022

• gzip cistrome index + truncated to save space + fixed bug on IO for gzip files in accession

  noamteyssier

  committed
  8141962

  Copy full SHA for 8141962

• added explicit test for .txt and .txt.gz in ontology

  noamteyssier

  committed
  62e2c2e

  Copy full SHA for 62e2c2e

• split heatmap into separate function from run

  noamteyssier

  committed
  cc92d04

  Copy full SHA for cc92d04

• small formatting change

  noamteyssier

  committed
  5fcd414

  Copy full SHA for 5fcd414

• rewrote _gather_results to return bin/pathway level results and adj_pvalue

  noamteyssier

  committed
  79ddd6b

  Copy full SHA for 79ddd6b

• fixed sign on graphical_ar

  noamteyssier

  committed
  c70774f

  Copy full SHA for c70774f

Commits on Jun 29, 2022

• give heatmap the correct size ontology pathways regardless of results dataframe shape + correct sign on graphical array

  noamteyssier

  committed
  dd19928

  Copy full SHA for dd19928

• fixed index bug + corrected sign of comparison in redundancy ratio

  noamteyssier

  committed
  c7a274f

  Copy full SHA for c7a274f

• added summary function to return bin aggregated data

  noamteyssier

  committed
  24f4f81

  Copy full SHA for 24f4f81

• consolidated test_run and test_run_2 to the same file

  noamteyssier

  committed
  b01dede

  Copy full SHA for b01dede

• bump version

  noamteyssier

  committed
  6c0511f

  Copy full SHA for 6c0511f

• updated usage in README

  noamteyssier

  committed
  7e013ef

  Copy full SHA for 7e013ef