Code

update master to 0.99.2#116

Code

Merged

jmitchell81 merged 213 commits intomasterFertigLab/dominoSignal:masterfrom devFertigLab/dominoSignal:devCopy head branch name to clipboardMay 8, 2024

+12,060-3,702

Commits

Commits on Dec 7, 2023

• add description

  dimalvovs

  committed
  5e18571

• update docs

  dimalvovs

  committed
  5e38f97

• adjust tests (to tiny)

  dimalvovs

  committed
  112cc70

Commits on Jan 3, 2024

• Init orphan branch

  kjkrishnan

  committed
  c387982

• Remove temp file

  kjkrishnan

  committed
  34f521e

• initial gha for site updates

  kjkrishnan

  committed
  de0f784

• add readme

  kjkrishnan

  committed
  81228b9

Commits on Jan 4, 2024

• add caching for vignettes

  dimalvovs

  committed
  cb45793

• adjust tests

  dimalvovs

  committed
  59a0c6d

• debug

  dimalvovs

  committed
  5d81626

• roxygenize, add cache fun

  dimalvovs

  committed
  75ff664

• add value to man

  dimalvovs

  committed
  57c891c

• add \value

  dimalvovs

  committed
  ecf0e68

Commits on Jan 5, 2024

• Merge pull request #71 from FertigLab/70-persistent-cache

  Show description for 07b9c11
  jmitchell81

  authored
  07b9c11

• Update document.yaml

  Show description for 319d227
  kjkrishnan

  authored
  319d227

• make logo available for README

  kjkrishnan

  committed
  837e8f6

• Merge branch 'gh-pages' of https://github.com/FertigLab/domino2 into gh-pages

  kjkrishnan

  committed
  417ff5f

• update domino class name

  kjkrishnan

  committed
  ba2cbea

• Deploying to gh-pages from @ 1c68aa2 🚀

  kjkrishnan

  committed
  b006946

Commits on Jan 8, 2024

• remove old readme

  jmitchell81

  committed
  adc8367

• remove old scenic bash script examples

  jmitchell81

  committed
  0adffcf

• Merge pull request #72 from FertigLab/jtm_remove_vestigial_documentation

  Show description for fbff73b
  jmitchell81

  authored
  fbff73b

Commits on Jan 10, 2024

• simplify & use default Bioc location

  dimalvovs

  committed
  d592633

• add object saving test

  dimalvovs

  committed
  223dd41

• Merge pull request #73 from FertigLab/70-persistent-cache

  Show description for bf65c41
  jmitchell81

  authored
  bf65c41

Commits on Jan 11, 2024

• empty workflow

  kjkrishnan

  committed
  44b78b5

• Merge pull request #74 from FertigLab/krishnan_empty

  Show description for b7ff808
  jmitchell81

  authored
  b7ff808

Commits on Jan 29, 2024

• adding workflow files

  kjkrishnan

  committed
  8473f69

Commits on Jan 31, 2024

• bash script to update files

  kjkrishnan

  committed
  1c37abb

Commits on Feb 2, 2024

• Merge pull request #80 from FertigLab/krishnan_workflows

  Show description for 2a610f6
  jmitchell81

  authored
  2a610f6

• Merge branch 'master' into dev

  jmitchell81

  authored
  5427b65

• Update documentation

  jmitchell81

  committed
  1d4ea03

• Deploying to gh-pages from @ 1d4ea03 🚀

  jmitchell81

  committed
  3f05be2

Commits on Feb 5, 2024

• bioc action branch target change

  jmitchell81

  committed
  fcfe349

• new target branch for copy

  jmitchell81

  committed
  4da4366

• copy action refers to the target of action

  jmitchell81

  committed
  4552b4e

• new submission branch

  jmitchell81

  committed
  c34d66f

• Revert "new submission branch"

  Show description for 38e3522
  jmitchell81

  committed
  38e3522

Commits on Feb 13, 2024

• fix bslib preset

  Show description for dafac98
  kjkrishnan

  authored
  dafac98

Commits on Mar 1, 2024

• Merge master branch so pkgdown will be up to date

  kjkrishnan

  committed
  d8c0f77

• Update documentation

  kjkrishnan

  committed
  4677c74

• Rebuild pkgdown files after merge from master branch

  kjkrishnan

  committed
  55e7d0d

• Merge branch 'krishnan_bslib_pkgdown' of https://github.com/FertigLab/domino2 into krishnan_bslib_pkgdown

  kjkrishnan

  committed
  caddea7

• Separate cellphonedb and scenic vignettes

  kjkrishnan

  committed
  2877682

• cleanup and domino2 -> dominoSignal

  kjkrishnan

  committed
  db1a9a8

• Update documentation

  kjkrishnan

  committed
  808fed4

Commits on Mar 4, 2024

• initial create_domino.R

  jmitchell81

  committed
  71e43ac

• Merge pull request #88 from FertigLab/master

  Show description for b432d7a
  jmitchell81

  authored
  b432d7a

• initial parse function commit

  Show description for 1ba512b
  jmitchell81

  committed
  1ba512b

Commits on Mar 6, 2024

• rename variables

  jmitchell81

  committed
  e2cd820

• apply variable name fix

  jmitchell81

  committed
  d0ec34e

• read_rl_map_genes test

  Show description for 598c2de
  jmitchell81

  committed
  598c2de

• document test purpose

  jmitchell81

  committed
  63324c0

• initial read_rl_map_complexes

  Show description for 176538d
  jmitchell81

  committed
  176538d

• initial unit test read_rl_map_complexes

  Show description for 2a99ec7
  jmitchell81

  committed
  2a99ec7

Commits on Mar 8, 2024

• merge previous refactoring

  dimalvovs

  committed
  c2b9310

• add required var checker

  dimalvovs

  committed
  16a41e7

• fix merge

  dimalvovs

  committed
  a5afcfd

• Update documentation

  dimalvovs

  committed
  0302f67

• add missing doc entry

  dimalvovs

  committed
  8972e0b

• Merge branch '94-input-checks-utils-+-customize-for-arguments' of github.com:FertigLab/domino2 into 94-input-checks-utils-+-customize-for-arguments

  dimalvovs

  committed
  489eab7

• write_rec_lig_linkages initial

  Show description for ebf6059
  jmitchell81

  committed
  ebf6059

• initial unit test

  Show description for 7d6c962
  jmitchell81

  committed
  7d6c962

• add test for bad rl_map

  dimalvovs

  committed
  a2f9be6

• add test for bad features

  dimalvovs

  committed
  87b77f9

• add test for seurat/counts params

  dimalvovs

  committed
  d26bd01

• add min_thresh tests

  dimalvovs

  committed
  d32a5c0

• add test for tf_selection_method

  dimalvovs

  committed
  b52fd24

• initial select_cluster_tf

  Show description for 1a8dd29
  jmitchell81

  committed
  1a8dd29

• select_cluster_tf unit test

  Show description for 5d04a0f
  jmitchell81

  committed
  5d04a0f

• add test for arg range

  dimalvovs

  committed
  879071a

• initial test_tfs_rec_linkage

  Show description for 07a06e2
  jmitchell81

  committed
  07a06e2

• allow not checking class

  dimalvovs

  committed
  cf876e4

• add names and value checkers

  dimalvovs

  committed
  4f2b267

• update tests

  dimalvovs

  committed
  726f0ea

• rewrite input checks

  dimalvovs

  committed
  ea34261

• update documentation

  dimalvovs

  committed
  5fd7f60

Commits on Mar 10, 2024

• suppress cor.test warnings

  Show description for e791271
  jmitchell81

  committed
  e791271

• test_tfs_rec_linkage unit test initial

  Show description for d6704d1
  jmitchell81

  committed
  d6704d1

• filter_tf_regulon_receptors initial

  jmitchell81

  committed
  18dcc7b

• filter_tf_regulon_receptors unit test initial

  jmitchell81

  committed
  22be917

Commits on Mar 11, 2024

• Merge pull request #92 from FertigLab/91-parse_rl_map

  Show description for b218c78
  jmitchell81

  authored
  b218c78

• Merge branch 'dev' into 93-parse-rl_map-complexes

  jmitchell81

  authored
  d7dfd33

• Merge pull request #95 from FertigLab/93-parse-rl_map-complexes

  Show description for 6bb6299
  jmitchell81

  authored
  6bb6299

• Merge branch 'dev' into 96-build_rl_linkages

  jmitchell81

  authored
  5a727bc

• Merge pull request #97 from FertigLab/96-build_rl_linkages

  Show description for 0fb2687
  jmitchell81

  authored
  0fb2687

• Merge branch 'dev' into 98-run_feature_de

  jmitchell81

  authored
  0acf9ee

• Merge pull request #99 from FertigLab/98-run_feature_de

  Show description for 898c773
  jmitchell81

  authored
  898c773

• Merge branch 'dev' into 89-calculate_correlations

  jmitchell81

  authored
  f469031

• Merge pull request #101 from FertigLab/89-calculate_correlations

  Show description for 9fc9cbe
  jmitchell81

  authored
  9fc9cbe

• Merge pull request #100 from FertigLab/94-input-checks-utils-+-customize-for-arguments

  Show description for e0cbda5
  jmitchell81

  authored
  e0cbda5

• assess_complex_receptor_cor initial

  Show description for c1ccdba
  jmitchell81

  committed
  c1ccdba

• test assess_complex_receptor_cor initial

  Show description for cde9f9f
  jmitchell81

  committed
  cde9f9f

• adjust unit test spacing

  jmitchell81

  authored
  e735a3e

• Merge pull request #104 from FertigLab/correlation_of_receptor_complexes

  Show description for fe9e399
  jmitchell81

  authored
  fe9e399

• calc_rec_percentage initial

  Show description for 326fb85
  jmitchell81

  committed
  326fb85

• test calc_rec_percentage initial

  Show description for 55ef11e
  jmitchell81

  committed
  55ef11e

• Merge branch 'dev' into receptor_percent_expression

  jmitchell81

  authored
  6ef0f58

• Merge pull request #106 from FertigLab/receptor_percent_expression

  Show description for 1c892bd
  jmitchell81

  authored
  1c892bd

Commits on Mar 13, 2024

• merge earlier changes

  dimalvovs

  committed
  457e7e6

• merge earlier changes

  dimalvovs

  committed
  084860c

• rewrite input checks

  dimalvovs

  committed
  db401c0

• fix copypaste error

  dimalvovs

  committed
  9c3083a

• rewrite readins

  dimalvovs

  committed
  4efa5f1

• rewrite python/R bool conversion

  dimalvovs

  committed
  5fd637f

• address case of character vector passed as param

  dimalvovs

  committed
  bd01e01

Commits on Mar 18, 2024

• Merge pull request #109 from FertigLab/108-create_rl_map_cellphonedb-input-checks-and-readins

  Show description for f53f030
  dimalvovs

  authored
  f53f030

Commits on Mar 20, 2024

• add script to generate SCE example data

  kjkrishnan

  committed
  d287cbc

• change Seurat objects to SCE objects

  kjkrishnan

  committed
  bb82dca

• remove duplicate dependencies folder

  kjkrishnan

  committed
  74b744a

• Remove seurat arguments from functions

  kjkrishnan

  committed
  e905d78

• Change code, URL, example references for domino2 to dominoSignal

  kjkrishnan

  committed
  72be0dc

• Update documentation to dominoSignal

  kjkrishnan

  committed
  e9792a6

• Update library call for domino2 to dominoSignal

  kjkrishnan

  committed
  02a5f60

Commits on Mar 21, 2024

• rename in DESCRIPTION

  dimalvovs

  committed
  229016a

• rebuilt testdata

  dimalvovs

  committed
  330673f

• udate zenodo link

  dimalvovs

  committed
  486d847

• resolve conflicts

  dimalvovs

  committed
  d8502f6

• first working version w harcoded path

  dimalvovs

  committed
  30ee98f

• rm hard path, update zenodo, update tiny objects

  dimalvovs

  committed
  533a257

Commits on Mar 26, 2024

• import singleCellExperiment, fix incorrect correlation access function, remove input checks including seurat objects

  kjkrishnan

  committed
  79ea3e4

• Organize structure of articles

  kjkrishnan

  committed
  e9e6744

• Update version and installation directions

  kjkrishnan

  committed
  ee13e00

• update object use in vignettes

  kjkrishnan

  committed
  5d3ca96

• update documentation to remove references to seurat objects

  kjkrishnan

  committed
  1a1fcf4

• fix & to && in utility function

  kjkrishnan

  committed
  405a295

• Clear site to rebuild without unneeded dependencies

  kjkrishnan

  committed
  4218fba

• rebuild site

  kjkrishnan

  committed
  d226b51

• update class of stored object to "domino"

  dimalvovs

  committed
  cbc3676

Commits on Mar 27, 2024

• Merge branch 'dev' into krishnan_bslib_pkgdown

  dimalvovs

  committed
  45d6242

• update zenodo paths

  dimalvovs

  committed
  5a883f6

• rm renamed vignette

  dimalvovs

  committed
  51bc6e7

• rename package name

  dimalvovs

  committed
  7676469

• Revert "rm renamed vignette"

  Show description for f4c201c
  dimalvovs

  committed
  f4c201c

• remove resurrected domino2 vignette

  dimalvovs

  committed
  5192668

• resurrect domino2.rmd again

  dimalvovs

  committed
  a198338

• hide .nojekyll from build

  dimalvovs

  committed
  e53371c

• Update documentation

  dimalvovs

  committed
  bc7e111

• Undo & operator error, add caching to getting started vignette, change test data cluster vector names to cell barcodes

  kjkrishnan

  committed
  03a644d

• Add SingleCellExperiment to suggested package, remove ser from argument list of create_domino, and update BiocFileCache based on requirements in newest version

  kjkrishnan

  committed
  984d590

• remove argument checks for seurat object in create domino

  kjkrishnan

  committed
  0b3131b

• Rebuild pkgdown files

  kjkrishnan

  committed
  0e79f61

Commits on Mar 28, 2024

• Merge pull request #85 from FertigLab/krishnan_bslib_pkgdown

  Show description for c27c4ad
  dimalvovs

  authored
  c27c4ad

• Update r-build-check.yml

  Show description for 92615e8
  dimalvovs

  authored
  92615e8

• Update pull_request_template.md

  dimalvovs

  authored
  b305964

• debug example_data.R

  dimalvovs

  committed
  6300a5c

• change pbmc dom save path

  dimalvovs

  committed
  3690d72

• change zenodo link

  dimalvovs

  committed
  a3c088a

• add names to clusters in example data

  dimalvovs

  committed
  44c7441

• replace NAs with zeroes to prove that vignette builds

  dimalvovs

  committed
  3317163

Commits on Apr 3, 2024

• Merge pull request #111 from FertigLab/110-recreate-pbmc_domino_builtrds-for-examples-in-the-vignette

  Show description for 644e0a1
  jmitchell81

  authored
  644e0a1

• SCE removed from imports

  Show description for 28e73ca
  jmitchell81

  committed
  28e73ca

• remove non-expressed genes from sce

  jmitchell81

  committed
  90075ec

Commits on Apr 4, 2024

• example_data full pipeline

  Show description for 18234c5
  jmitchell81

  committed
  18234c5

• update to minimal feature set

  jmitchell81

  committed
  8aca99e

• update sysdata

  jmitchell81

  committed
  e36f862

• circos plot example to CXCR3

  jmitchell81

  committed
  7072263

• Update documentation

  jmitchell81

  committed
  506e5f8

• documentation update

  jmitchell81

  committed
  1c3c169

• Merge branch 'sce_tinydata_featureset' of https://github.com/FertigLab/dominoSignal into sce_tinydata_featureset

  jmitchell81

  committed
  c140417

• update second circos example

  jmitchell81

  committed
  afd5dc8

• update cor_scatter example

  jmitchell81

  committed
  ae8d170

Commits on Apr 9, 2024

• simpliify example data / gather in one current dir

  dimalvovs

  committed
  aecb221

• update testdata

  dimalvovs

  committed
  64b82dd

Commits on Apr 10, 2024

• update vignettes

  dimalvovs

  committed
  3de51a7

• fix data name

  dimalvovs

  committed
  ebee79f

• add happy test case

  dimalvovs

  committed
  db2d8a7

• add a test that fails

  dimalvovs

  committed
  2f950ca

• Allow domino cluster rename function to implement changes even when not all clusters are present

  kjkrishnan

  committed
  a53ed0d

• Only retain changes to dev in rename_clusters function

  kjkrishnan

  committed
  b094770

• update rename_clusters documentation

  kjkrishnan

  committed
  0e096c3

Commits on Apr 11, 2024

• Merge branch 'sce_tinydata_featureset' into krishnan_rename_clusters

  dimalvovs

  committed
  8c32486

• Merge sce_tinydata_featureset to add newest updates and rename_clusters test to krishnan_rename_clusters

  kjkrishnan

  committed
  5adbb75

• rename_clusters test updated to use test object with correct object structure; incomplete cases included in test

  kjkrishnan

  committed
  f0ccd35

• Remove L_ or R_ prefix only based on reviewer comment

  kjkrishnan

  committed
  e5889a9

Commits on Apr 12, 2024

• Merge branch 'krishnan_rename_clusters' of github.com:FertigLab/dominoSignal into krishnan_rename_clusters

  dimalvovs

  committed
  0de794e

• simplify prefix removal

  dimalvovs

  committed
  5e36309

• Merge pull request #113 from FertigLab/krishnan_rename_clusters

  Show description for bef0292
  dimalvovs

  authored
  bef0292

• Merge pull request #112 from FertigLab/sce_tinydata_featureset

  Show description for 6263046
  dimalvovs

  authored
  6263046

Commits on Apr 17, 2024

• add tiny linkage summary to sysdata

  Show description for d73086c
  jmitchell81

  committed
  d73086c

• differential signaling tables for link sum tiny

  Show description for 0e19f83
  jmitchell81

  committed
  0e19f83

• replace dontrun examples for differential functions

  jmitchell81

  committed
  3566bdf

• tiny list of domino objects in sysdata

  Show description for d8b0e11
  jmitchell81

  committed
  d8b0e11

• remove dontrun from summarize linkage example

  jmitchell81

  committed
  4ef6bd7

• functional example for plot_differential_linkages

  jmitchell81

  committed
  3f61bfd

• update documentation

  jmitchell81

  committed
  8913dd5

• remove create_domino modules

  Show description for 30cba9b
  jmitchell81

  committed
  30cba9b

• remove create_domino.R tests

  jmitchell81

  committed
  d5b3e1a

Commits on Apr 18, 2024

• Merge pull request #114 from FertigLab/differential_domino_testdata

  Show description for 618f0fb
  jmitchell81

  authored
  618f0fb

• use <- for assignment

  jmitchell81

  committed
  d55a61c

• Update import_fxns.R

  Show description for 17d2a4b
  jmitchell81

  committed
  17d2a4b

• remove receptor not passing parameter message

  Show description for bf57c99
  jmitchell81

  committed
  bf57c99

• plot_fxn paste in condition signals

  jmitchell81

  committed
  a6cace2

• replace 1: with seq() or seq_along()

  jmitchell81

  committed
  fb72994

• replace sapply with vapply

  jmitchell81

  committed
  68467ce

• select first gene in multiple uniprot mapping

  Show description for ccc29ac
  jmitchell81

  committed
  ccc29ac

• simple unit test for build domino

  jmitchell81

  committed
  8e21c5e

• specify return value for check_arg

  jmitchell81

  committed
  6568c06

• accessor function in circos example

  jmitchell81

  committed
  d9be866

• update documentation

  jmitchell81

  committed
  eb0aa93

• replace sapply in utils

  jmitchell81

  committed
  1acefbf

• replace sapply in differential functions

  jmitchell81

  committed
  dbcbbfe

Commits on Apr 19, 2024

• eliminate \value warning

  dimalvovs

  committed
  c0a54a9

• message for multiple genes mapping to one uniprot

  jmitchell81

  committed
  4f3c1ee

• check for length 0 rl_reading

  Show description for 3b7171a
  jmitchell81

  committed
  3b7171a

• removal of verbose condition on create_rl_map

  jmitchell81

  committed
  1e6beaa

Commits on Apr 23, 2024

• fix bioc branch script to only reference master branch

  kjkrishnan

  committed
  a8ceabb

• replace seq with seq_len

  Show description for 7f03e90
  jmitchell81

  committed
  7f03e90

Commits on Apr 24, 2024

• Merge pull request #115 from FertigLab/bioc_coding_practice_notes

  Show description for 289eb0a
  dimalvovs

  authored
  289eb0a

Commits on May 1, 2024

• fix bioc workflow hopefully

  kjkrishnan

  committed
  23960d4

• Merge branch 'dev' of https://github.com/FertigLab/domino2 into dev

  kjkrishnan

  committed
  22fb883

Commits on May 8, 2024

• increment version to 0.99.2

  jmitchell81

  committed
  05fb96f

• v0.99.2 NEWS update

  jmitchell81

  committed
  8bb1db7