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V0.2.2 development#51

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dimalvovs wants to merge 89 commits intomasterFertigLab/dominoSignal:masterfrom v0.2.2_developmentFertigLab/dominoSignal:v0.2.2_developmentCopy head branch name to clipboard

+3,909,174-1,710

Commits

Commits on Aug 29, 2023

• linkage summary class definition

  Show description for d662331
  jmitchell81

  committed
  d662331

• define summarize_linkages

  jmitchell81

  committed
  28bd4ef

Commits on Aug 30, 2023

• class name correction

  jmitchell81

  committed
  3825bc6

• accounting for incomplete subject names

  jmitchell81

  committed
  edbbbc0

• warning for extra subject_names

  jmitchell81

  committed
  20dfab2

• defined linkage summary result

  jmitchell81

  committed
  e906e9f

• subject_meta is subset to provided names

  jmitchell81

  committed
  16247a7

• define count_linkage

  jmitchell81

  committed
  4efc8a0

Commits on Aug 31, 2023

• update documentation

  kjkrishnan

  committed
  8aa3b1e

• domino1 references

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  kjkrishnan

  committed
  86a60c3

• refining class checks

  kjkrishnan

  committed
  09592c0

• testing input checks

  kjkrishnan

  committed
  fd73956

• define test differential linkages

  jmitchell81

  committed
  d77d173

• documentation for testing linkages

  jmitchell81

  committed
  18efd0c

• export differential_fxns

  jmitchell81

  committed
  00576ca

• fix export linkage_summary

  jmitchell81

  committed
  686c78e

• include total subjects in test results

  jmitchell81

  committed
  d663143

• add _n result definitions

  jmitchell81

  committed
  2a07033

Commits on Sep 1, 2023

• define differential linkage plot

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  jmitchell81

  committed
  8e6bda9

• formatting <- to =

  jmitchell81

  committed
  2c8767c

• roxygen differential plotting function

  jmitchell81

  committed
  a095840

Commits on Sep 6, 2023

• Merge pull request #27 from FertigLab/krishnan_documentation

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  jmitchell81

  authored
  be55012

• Merge pull request #28 from FertigLab/krishnan_class_check

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  jmitchell81

  authored
  46d3079

• Merge branch 'alt_gene_conversion&class_checks' into krishnan_input_check

  jmitchell81

  authored
  bd35c89

• Merge pull request #29 from FertigLab/krishnan_input_check

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  jmitchell81

  authored
  8e8f10a

• Update NAMESPACE

  Show description for 099537f
  jmitchell81

  committed
  099537f

• building pkgdown site

  kjkrishnan

  committed
  81b1944

Commits on Sep 7, 2023

• build site, alter vignette, logo

  kjkrishnan

  committed
  e2afaa1

• add rds to gitignore

  kjkrishnan

  committed
  5941d75

Commits on Sep 14, 2023

• Refining vignette, organizing references, adding site pages

  kjkrishnan

  committed
  9bd7ed4

Commits on Sep 18, 2023

• theming and organization

  kjkrishnan

  committed
  2b1a82f

Commits on Sep 21, 2023

• print and show functions

  kjkrishnan

  committed
  1dc07f5

Commits on Sep 26, 2023

• precompile vignettes, standardize documentation, rebuild

  kjkrishnan

  committed
  734d8ec

Commits on Oct 4, 2023

• Merge pull request #30 from FertigLab/krishnan_pkgdown

  Show description for 3e78082
  jmitchell81

  authored
  3e78082

• adjust function export names

  jmitchell81

  committed
  62e0338

• Merge branch 'v0.2.2_development' into alt_gene_conversion_and_class_checks

  jmitchell81

  authored
  66ecb56

• Merge pull request #31 from FertigLab/alt_gene_conversion_and_class_checks

  Show description for 564e589
  jmitchell81

  authored
  564e589

• Merge branch 'v0.2.2_development' into compare_domino_linkages

  jmitchell81

  authored
  7a5cf6c

• Merge pull request #33 from FertigLab/compare_domino_linkages

  Show description for 912b1e3
  jmitchell81

  authored
  912b1e3

• roxygen compilation

  jmitchell81

  committed
  73ac74d

Commits on Oct 5, 2023

• troubleshooting build

  kjkrishnan

  committed
  1a61015

Commits on Oct 6, 2023

• assign maintainer

  jmitchell81

  committed
  80d1bf1

• format all names as given, family

  jmitchell81

  committed
  6fc2072

• FormatR grammar correction

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  jmitchell81

  committed
  44b637a

• revision to 2 space indents

  Show description for 3c6293c
  jmitchell81

  committed
  3c6293c

Commits on Oct 9, 2023

• apostrophe notation in manuals

  jmitchell81

  committed
  ae44261

• spacing in linkage_summary definition

  jmitchell81

  committed
  2f89448

Commits on Oct 10, 2023

• reorganize vignette and test data

  kjkrishnan

  committed
  c349c00

• labeling imported functions and classes

  Show description for b6314f2
  jmitchell81

  committed
  b6314f2

• update ignored files for git and R BUILD

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  jmitchell81

  committed
  02d80f0

• Merge pull request #34 from FertigLab/jtm/v0.2.2/R_CHECK_errors

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  jmitchell81

  authored
  77eb3d0

Commits on Oct 11, 2023

• rm obsolete package, bump version, add biocViews stub

  dimalvovs

  committed
  46f2bef

• add toy test that runs on check()

  dimalvovs

  committed
  9638968

• add testthat to suggests (warnings)

  dimalvovs

  committed
  932de81

• add quotes for consistency

  dimalvovs

  committed
  15cae35

Commits on Oct 18, 2023

• unit tests initial commit

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  jmitchell81

  committed
  4a3e2d3

• utilities script initial commit

  jmitchell81

  committed
  0d16a1c

• track rda files for unit tests

  jmitchell81

  committed
  b38a3fc

• Use importFrom for all external functions

  jmitchell81

  committed
  7a92963

Commits on Oct 19, 2023

• switch to package-level import

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  jmitchell81

  committed
  05c368b

Commits on Oct 20, 2023

• documentation of domino class

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  jmitchell81

  committed
  bf815fd

• Merge pull request #36 from FertigLab/35-error

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  jmitchell81

  authored
  6d96b82

Commits on Oct 24, 2023

• Added BiocViews

  Show description for e7e358d
  jmitchell81

  committed
  e7e358d

• full length TRUE/FALSE logicals

  jmitchell81

  committed
  81f085d

• LazyData: false

  jmitchell81

  committed
  b9ee5f3

• removed tabs from vignette

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  jmitchell81

  committed
  00be26d

Commits on Oct 25, 2023

• value added for docs on plotting functions

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  jmitchell81

  committed
  565a3d4

• Merge pull request #43 from FertigLab/42-return_descriptions_for_plotting_functions

  Show description for c9d8ecb
  jmitchell81

  authored
  c9d8ecb

Commits on Oct 30, 2023

• add basic workflow

  dimalvovs

  committed
  06b3b8b

• try copypaste from working repo

  dimalvovs

  committed
  060afd5

• add manual run option

  dimalvovs

  committed
  cfa94d0

• try adding secrets

  dimalvovs

  committed
  a85f08e

• Update r-build-check.yml

  dimalvovs

  authored
  3b82d8a

• Update r-build-check.yml

  dimalvovs

  authored
  b10724e

Commits on Oct 31, 2023

• pull domino2 v0.2.2_devel to pkgdown branch

  kjkrishnan

  committed
  1cb193d

• change workflow logic

  dimalvovs

  committed
  1fb4501

Commits on Nov 2, 2023

• Merge branch 'v0.2.2_development' of https://github.com/FertigLab/domino2 into krishnan_pkgdown

  kjkrishnan

  committed
  6553e57

• example data and test data organization

  kjkrishnan

  committed
  2aaed4f

• rebuild site

  kjkrishnan

  committed
  c7b7f66

• adjust for R CMD check

  kjkrishnan

  committed
  0d75e75

• (minimally) adjust for BiocCheck

  kjkrishnan

  committed
  b62dd35

Commits on Nov 10, 2023

• ComplexHeatmap for Plotting functions

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  jmitchell81

  committed
  6dec513

• vingette comments moved from argument lines

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  jmitchell81

  committed
  d3b1f05

• pkgdown update

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  jmitchell81

  committed
  c4f45d0

• removed redundant mean_ligand_expression

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  jmitchell81

  committed
  0182947

• Merge pull request #48 from FertigLab/krishnan_pkgdown

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  jmitchell81

  authored
  da8bc45

• NMF removed from DESCRIPTION

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  jmitchell81

  committed
  7a92f9f

Commits on Nov 13, 2023

• suggest packages used in vignette

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  jmitchell81

  committed
  bf91791

• cleanup tests

  dimalvovs

  committed
  523a895