Adeschen patch 1#614

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adeschen wants to merge 738 commits intoKrasnitzLab:adeschen-patch-1from

adeschen:adeschen-patch-1

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Commits on Sep 29, 2023

Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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belleau
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Update the man for pathGeno

belleau
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belleau
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Move genotypes CSV files to sub-directory in inst/extdata and adapt documentation accordingly
adeschen
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Merge pull request #530 from belleau/main
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Merge branch 'KrasnitzLab:main' into main
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Merge pull request #531 from adeschen/main
adeschen
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Cange extension of README file and update content
adeschen
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Update the vignette with VCF

belleau
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belleau
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Update the vignette with VCF

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belleau
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Merge pull request #532 from adeschen/main
adeschen
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Update README
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Merge pull request #533 from belleau/main
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Merge pull request #534 from adeschen/main
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Update README
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Merge pull request #535 from adeschen/main
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Update README example

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Merge pull request #536 from belleau/main
adeschen
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Correct indents in Reference GDS vignette
adeschen
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Update text in main vignette
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Merge pull request #537 from adeschen/main
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Merge pull request #538 from adeschen/main
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Update package version to 0.99.12
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Merge pull request #539 from adeschen/main
adeschen
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Add values to biocViews in DESCRIPTION
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Merge pull request #540 from adeschen/main
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Update doc for addGeneBlockGDSRefAnnot() function
adeschen
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Update doc for generateGeneBloc() function
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Commits on Sep 30, 2023

Commits on Oct 5, 2023

Commits on Oct 13, 2023

Commits on Oct 24, 2023

Commits on Apr 30, 2024

Commits on Aug 5, 2024

We stop to use pedProfile rownames. We changed function addStudyGDSSample.

belleau
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belleau
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Update check-bioc.yaml
adeschen
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Merge pull request #1 from adeschen/patch-1
belleau
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Commits on Aug 17, 2024

Merge pull request #550 from adeschen/main
adeschen
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Commits on Aug 19, 2024

Merge branch 'KrasnitzLab:main' into main
belleau
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Commits on Aug 31, 2024

Updata addStudyGDSSample in gdsWrapper_internal.R

belleau
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belleau
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In generateMapSnvSel change read.csv2 to read.csv

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belleau
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Commits on Sep 4, 2024

Merge pull request #551 from belleau/main
adeschen
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Commits on Sep 9, 2024

add function select1KGPopForSynthetic in synthetic.R

belleau
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belleau
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Commits on Sep 10, 2024

Add functions runDNAAncestryProfile and runRNAAncestryProfile

belleau
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belleau
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Rename functions runDNAAncestryProfile to inferAncestry.Rd and runRNAAncestryProfile to inferAncestryGeneAware

belleau
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belleau
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Commits on Sep 11, 2024

Add computeAncestryFromSynthetic

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Add function profileAncestry

belleau
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belleau
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Changed the man of profileAncestry

belleau
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belleau
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Add function wrapperAncestry

belleau
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belleau
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Update function inferAncestry and inferAncestryGeneAware

belleau
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Add function createAUROCGraph

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belleau
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Merge pull request #553 from belleau/main
adeschen
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Commits on Oct 10, 2024

Solve a variable problem in profileAncestry and add some comments

belleau
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belleau
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Commits on Oct 11, 2024

Don't allow createStudy2GDS1KG when the gds exists.

belleau
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belleau
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Add a test for createStudy2GDS1KG.

belleau
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belleau
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Add the function getRefSuperPop

belleau
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belleau
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Commits on Oct 15, 2024

Add the function identifyRelativeRef wrapper of identifyRelative

belleau
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belleau
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Merge pull request #554 from belleau/main
adeschen
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Update check-bioc.yaml
adeschen
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Update check-bioc.yaml
adeschen
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Merge pull request #555 from adeschen/main
adeschen
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Update check-bioc.yaml
adeschen
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Update generatePhase1KG2GDS and add wrapper generatePhaseRef

belleau
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Merge pull request #556 from belleau/main
adeschen
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Merge branch 'KrasnitzLab:main' into main
adeschen
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Merge pull request #557 from adeschen/main
adeschen
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Update main steps figure
adeschen
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Add function processBlockChr and correct some importFrom

belleau
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belleau
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Add function addGeneBlockRefAnnot wrapper of addGeneBlockGDSRefAnnot

belleau
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belleau
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Adding wrapper vignette
adeschen
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Merge pull request #558 from belleau/main
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Merge branch 'KrasnitzLab:main' into main
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Commits on Oct 16, 2024

Merge pull request #559 from adeschen/main
adeschen
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Warning in red about new functions available
adeschen
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Merge branch 'main' of https://github.com/adeschen/RAIDS
adeschen
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Merge branch 'KrasnitzLab:main' into main
adeschen
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Remove old image for main steps section
adeschen
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Merge branch 'main' of https://github.com/adeschen/RAIDS
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Merge pull request #560 from adeschen/main
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authored
Merge branch 'KrasnitzLab:main' into main
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Merge pull request #561 from adeschen/main
adeschen
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Update main vignette
adeschen
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Merge branch 'main' of https://github.com/adeschen/RAIDS
adeschen
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Merge pull request #562 from adeschen/main
adeschen
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Update main vignette
adeschen
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Merge pull request #563 from adeschen/main
adeschen
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Update to parse the plink output for LD blocks.

belleau
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belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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belleau
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Correct example for addGDS1KGLDBlock

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belleau
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Merge pull request #564 from belleau/main
adeschen
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Update Description

belleau
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belleau
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Correct example for addGDS1KGLDBlock

belleau
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belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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Merge pull request #565 from belleau/main
adeschen
authored

Commits on Oct 18, 2024

Add a validation to addBlockFromDetFile.

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Merge branch 'main' of https://github.com/belleau/RAIDS

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Commits on Oct 21, 2024

Commits on Oct 22, 2024

Update function documentation and correct indents
adeschen
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Update vignette
adeschen
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Merge pull request #567 from adeschen/main
adeschen
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Merge branch 'KrasnitzLab:main' into main
belleau
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Merge pull request #568 from belleau/main
adeschen
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Increase version

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belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

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Merge pull request #569 from belleau/main
adeschen
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Merge remote-tracking branch 'origin/main'

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Commits on Oct 29, 2024

Commits on Apr 10, 2025

Commits on Apr 11, 2025

Merge pull request #576 from adeschen/main
adeschen
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Add function readSNVBAM

belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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Merge pull request #577 from belleau/main
adeschen
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Update doc and format processPileupChrBin() function
adeschen
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Update RAIDS.Rmd
krasnitz
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Merge pull request #578 from adeschen/main
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Merge pull request #5 from KrasnitzLab/main
adeschen
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Add unit test for processPileupChrBin() function
adeschen
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Merge branch 'main' of https://github.com/adeschen/RAIDS
adeschen
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Merge pull request #579 from adeschen/main
adeschen
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Add function generateProfileGDS

belleau
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belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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belleau
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Merge pull request #580 from belleau/main
adeschen
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Update example in doc for processPileupChrBin() function
adeschen
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Merge branch 'main' of https://github.com/KrasnitzLab/RAIDS

belleau
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Merge remote-tracking branch 'upstream/devel'

belleau
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belleau
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Update to version 1.5.1

belleau
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belleau
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Update RAIDS.Rmd
krasnitz
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Merge pull request #582 from belleau/main
adeschen
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Merge pull request #581 from adeschen/main
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Commits on Apr 13, 2025

Add function createProfile and adapted the rest

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belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

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Commits on Apr 14, 2025

Update vignette step 1
adeschen
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Merge pull request #583 from adeschen/main
adeschen
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Update vignette
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Merge pull request #584 from adeschen/main
adeschen
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Update vignette
adeschen
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Merge branch 'main' of https://github.com/adeschen/RAIDS
adeschen
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Merge pull request #586 from belleau/main
adeschen
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Merge pull request #585 from adeschen/main
adeschen
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Tuning the functions for Rsamtools part 2

belleau
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Merge branch 'main' of https://github.com/belleau/RAIDS

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Commits on Apr 16, 2025

Update RAIDS.Rmd
belleau
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Tuning the functions for Rsamtools part 3

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Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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Merge pull request #589 from belleau/main
adeschen
authored
Merge branch 'main' of https://github.com/belleau/RAIDS

belleau
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Update version

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belleau
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Merge remote-tracking branch 'origin/main'

belleau
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belleau
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Merge pull request #590 from belleau/main
adeschen
authored

Commits on May 1, 2025

Commits on May 2, 2025

Commits on May 6, 2025

Commits on May 8, 2025

Commits on May 9, 2025

Commits on May 10, 2025

Merge pull request #610 from adeschen/main
adeschen
authored

Commits on May 12, 2025

Add unit test for pruning1KGbyChr() function
adeschen
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Commits on May 13, 2025

Commits on Sep 10, 2025

Commits on Sep 11, 2025

Update check-bioc actions
adeschen
committed

Commits on Sep 16, 2025