Merge branch 'main' into devel
getIMGT function robust against IMGT website downtime
 

 IMGT fix pass checks
 

 I've made the `getIMGT` function more robust against website downtime in your examples and vignette. Here's a summary of my changes:

- The `getIMGT` example is now wrapped in `\dontrun{}` to prevent it from running during R CMD check.
- The vignette now includes a check for IMGT website availability before attempting to run the `getIMGT` function, preventing errors when the site is down.
 

 Tests changed...
 

 Modify function project pseudotime to cell (#75)

* modify the projection function and add vignette for slingshot

The modifications aim at two goals:
   1. Remove the check that enforces the input to contain probability values, and instead allow the user to choose which values to project.
   2. Exclude pseudobulks with NA values when projecting back to the cell level.

* modify documents

* Update the other two vignettes to reflect the changes in the modified function.

* Update DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION

* Update dandelionR_with_slingshot.Rmd

* Update dandelionR_with_slingshot.Rmd

* Update DESCRIPTION

* modify test-that

* ok this should fix the tests

* this fixes local builds

* Update projectPseudotimeToCell.R

---------

Co-authored-by: Zewen Kelvin Tuong <z.tuong@uq.edu.au> 

 successfully created and previewed html files for cytoscape viz (#53)

 

 `ungroup` should now properly remove the named group AND not drop other
groups in other contexts
 

 version bump
 

 merged bioc/devel
 

 Merge branch 'RELEASE_3_21' into devel
 

 Update NEWS
 

 should be using vars_pull()
 

 Should have lazy data - ignore BiocCheck note
 

 Some other edits
 

 Typo `nrows()` does not exsist
 

 version bump
 

 Version bump
 

 version bump
 

 Version bump
 

 relying on the existance of unset variables. should fix
 

 version bump
 

 version bump
 

 update actions
 

 I forget what I was doing here
 

 more changes
 

 on new mac
 

 tweak and fix to vignette
 

 reformat and faster 'n_groups' call
 

 vignette tweak
 

 CMakeLists.txt
 

 new check_requirements.sh script
 

 Addressed reviewer comments
 

 address warnings 2
 

 CmakeLists.txt
 

 Merge branch 'main' of https://github.com/yberda/ChIPDBData
updated vignette and bump version
 

 fixed errors
 

 fixed errors
 

 added knitr
 

 Fix warnings
 

 check_requirements.sh
 

 check_requirements.sh
 

 update
 

 update new
 

 update 0.99.2
 

 update
 

 Clean ignored files and update .gitignore
 

 NEWS file
 

 fixed bug in BacDive DB
 

 CMakeLists.txt changes
 

 complete check_requirements.sh
 

 update 15
 

 version and date
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 -reduce running time examples
 

 Propagate nvBowtie/nvBWT errors to R
 

 -Exclude evaluation of long running example
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Merge pull request #164 from Huber-group-EMBL/H5D_additions

Added H5Dget_num_chunks 

 Merge remote-tracking branch 'upstream/devel'
 

 Merge pull request #171 from gdrplatform/GDR-3067

Gdr 3067 

 refactor: resolve conflict
 

 chore: Update NEWS.md

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 

 ci: trigger build
 

 Merge branch 'main' into GDR-3067
 

 chore: update news.md
 

 chore: bump version and update NEWS.md
 

 fix unit test to match new ggplot2 S7 infrastructure (#17)

* fix unit test to match new ggplot2 S7 infrastructure

* update github action (using iSEE as template)

* empty commit to trigger github action 

 fix Rbuildignore to keep .png files
 

 Update DESCRIPTION and vignette tutorial
 

 version bump 0.99.2
 

 update man
 

 adding some helper functions, to avoid redundancy throughout the pkg and make the code readable
 

 updating constructor function, to accomodate the creation of an empty DDE object from an empty SCE object
 

 changing the generics & methods naming to adopt a camelCase style
 

 Fix GenomeSeqInfo dependancy
 

 Merge remote-tracking branch 'origin/dev' into devel
 

 Ensure as.list method is imported correctly.
 

 Fix problems with method definitions
 

 git ignore docker compose
 

 Update CITATION
 

 Correcting aggregate figure language 

 Merge pull request #30 from EricSDavis/dev

Merge latest developments 

 Merge pull request #29 from EricSDavis/featureChanges

Renaming several functions 

 Change functionality of subsetBySource

subsetBySource now returns all combinations of sets from a MergedGInteractions object by default.

Also refactor the internal logic for include/exclude dispatch methods. 

 Add verbose parameter usage in docs.

 

 Add additional aggInteractions changes

 

 Change name of calcApa to aggInteractions

Also add spanInteractions function. 

 Fix blank page on pdf creation.

When using pdf to save a single plot, plotMatrix will create a blank page before the real plot. This fixes the issue.


Co-authored-by: Sarah <57263711+sarmapar@users.noreply.github.com> 

 Correct typo in example

 

 fix minPairDist param name

 

 calcApa wrapper function

 

 Version bump
 

 Merge branch 'dev' into main 

 Bugfix pullHic

After running .prepareInputs() which involves snapping ranges to bins, the adjusted ranges were not being used to calculate the expected matrix dimensions. This can sometimes cause a missmatch between the data used for enumerating bins, and the data that is extracted from the Hi-C file. Fixed by using the adjusted interactions to set the matrix dimensions. 

 Merge pull request #26 from EricSDavis/pullHicVignette

Add pullHic vignette 

 Add more sections to pull Hi-C vignette
 

 Bug fix - regularize

Fix a bug where it is unable to properly regularize matrices with a single row, column or both.
 

 Start pullHic vignette

Add Sarah to citation; rename the introduction vignette, start pullHic vignette.
 

 Merge pull request #24 from EricSDavis/main

Merge pull request #23 from EricSDavis/dev 

 Pass R cmd checks

Co-Authored-By: Sarah Parker <57263711+sarmapar@users.noreply.github.com>
 

 Update MergedGInteractions.md
 

 Merge branch 'refactorLoopEnrich' into dev 

 Add Contributing section to README

Also add code of conduct.
 

 Update docker-image.yml

Set push command to use newly created tag.
 

 Add docker build action to repository
 

 Update test snapshots to reflect changes in DelayedArray and its dependent packages.
 

 Adding author & updating namespace
 

 Creating helper functions for parsing custom functions
 

 Fix bug in removeShortPairs.
 

 Adding tests for calcLoopEnrichment and defaultBuffer functions
 

 Adding Sarah Parker as author
 

 Fix subsetting of JaggedArrays so that the subscript positions are more intuitive (and match previous functions).
 

 Add function for making random GRanges and GInteractions; Improve docs for InteractionJaggedArray and JaggedArray.
 

 Allow delayed subsetting.
 

 Update codecov badge.
 

 Create codecov.yml 

 Merge pull request #169 from gdrplatform/GDR-3066

Gdr 3066 

 build: trigger buidl
 

 Merge branch 'main' into GDR-3066
 

 build: trigger build
 

 chore: typos
 

 feat: improve logic in `split_SE_components`

Details:
 - assure that order of optional columns for treatment_md and condition_md is the same across the assays
 

 remove directories cleanup
 

 version bump 0.99.1 - minor adjustments functions
 

 version bump to 1.9.2 in devel
 

 Update Lee2019-data.R
 

 updated citation
 

 Update check-bioc R version
 

 Merge remote-tracking branch 'upstream/devel' into devel
 

 Update check-bioc.yml 

 version
 

 partly reverted from basilisk to reticulate for samtools installation. basilisk does not support conda package installation at least for now.
 

 tests(converters): fix spectronaut and metamorpheus tests (#117)

 

 fix dim error
 

 made changes to fix build issue
 

 update 14
 

 fix bug with expected TRUE in .hasAllChunkLabels
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 add initial content to NEWS file
 

 Update NEWS.md 

 Update DESCRIPTION 

 Update check.R 

 add initial content to news file
 

 Tests: fix check for RI markers detection

There was bug in the function that simulates RI markers, where the
expected maximum is assigned in the wrong position in some cases.

This fixes this by basically duplicating the logic of the internal
function.
 

 bioc review (#113)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 find empty directories depth-first
 

 version
 

 move cleanup to separate target step in Makefile
 

 update vignettes Makefile to clean empty directories
 

 update clean directories scripts
 

 Merge branch 'devel' of https://github.com/gkanogiannis/fastreeR into devel
 

 Update fastreer recipe from bioconda-recipes
 

 Remove ignored files
 

 Change check command
 

 version
 

 update directories
 

 Bumped version to trigger recompilation.
 

 fix permissions
 

 fix path
 

 update path for cleaning empty directories
 

 Ran on Windows 11

- Updated installation of recommended packages
- Added info that .bridge file should be in current working directory.
@egonw
 

 Merge branch 'main' into devel
 

 version
 

 version
 

 checking devel branch for redirect strategy
 

 update .Rd file placeholder
 

 version
 

 update vignette stub
 

 update .Rd file placeholder
 

 clean doc
 

 version
 

 fix vignette notes
 

 remove invalid biocViews
 

 shorter filenames
 

 update gitignore files
 

 update Rbuildignore
 

 fix vistas reference
 

 version bump 2.37.1
 

 v13
 

 v bump and maintainer email
 

 corrected the min_cell_count slider
 

 Added ce11 to UI and server
 

 Added ce11 data to documentation
 

 Added ce11 C. elegans gene annotation
 

 Fixed problem of not updating scExp when changing parameter (norm, component,...) + colSums / rowSums raw mat
 

 corrected num_cell_after_QC_filt_scExp
 

 Added requirements of installing flexdashboard for report generation
 

 Corrected verbose for create_scExp
 

 Added ',', '-' and '_' to file separator and improved format tests
 

 Merge branch 'main' into devel
 

 edition of function documentation
 

 Merge branch 'main' into devel
 

 Add NEWS and v2 of pre-print
 

 Add CITATION file
 

 Merge branch 'main' into makeAdjacancyMatrix 

 Merge branch 'main' into plotSpectraPTM 

 Add unit tests USI parameter
 

 Add USI parameter to plotSpectraPTM
 

 Remove showDetails
 

 Remove split from adjacencyMatrix method
 

 Add reference to examples and specify the importance of splitting
 

 Missing argument documentation
 

 fix wrongly introduced arg
 

 fix typo in man page
 

 Merge branch 'main' into PSMatch-labelFragments 

 Add selenocysteine and pyrrolysine
 

 Remove R plots pdf
 

 Merge pull request #27 from guideflandre/PSMatch-vignette

PSMatch Fragments vignette update 

 Update vignette based on PR review
 

 Add NEWS message and correct the description warnings
 

 Correct plot output vignette
 

 remove unnecessary conflict
 

 update vignettes
 

 update vignettes again

Merge branch 'PSMatch-vignette' of https://github.com/guideflandre/PSMatch into PSMatch-vignette

# Conflicts:
#	vignettes/Fragments.Rmd
 

 update vignette
 

 update vignette
 

 Merge branch 'PSMatch-vignette' of https://github.com/guideflandre/PSMatch into PSMatch-vignette
 

 Update vignette
 

 update readGeoMx to fix a bug when reading multiple negprobe and remove
 

 AlphaMissenseR 1.5.3: Add S4Vectors and Seqinfo to Suggests
 

 VplotR 1.19.1: Add Seqinfo to Imports
 

 OGRE 1.13.1: Add Seqinfo to Imports
 

 ldblock 1.39.1: Add Seqinfo to Imports
 

 remove complete.cases call
 

 Merge pull request #17 from BorchLab/dev

Update for immApex changes 

 Adding immApex to remotes
 

 Merge branch 'main' into dev 

 updating immApex integration
 

 minor DESCRIPTION adjustment
 

 removing basilisk from the picture
 

 crupR 1.1.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.
 

 SpatialFeatureExperiment 1.11.1: Update old serialized objects with updateObject::updatePackageObjects()
 

 QDNAseq 1.45.1: Add Seqinfo and BiocGenerics to Imports
 

 Forgot version bump
 

 InPAS 2.17.1: Add Seqinfo to Imports
 

 epigraHMM 1.17.2: Add GenomeInfoDb to Suggests
 

 gmapR 1.51.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.
 

 RiboProfiling 1.39.1: Fix imports

- Replace GenomeInfoDb with Seqinfo in Imports;
- Add methods to Imports.
 

 Fix in documentation
 

 update Dockstore version 1.17.2
 

 Merge branch 'main' into devel
 

 cleaning parameter calls for summary.fun and scale.counts
 

 sequenceDecoder doucmentation
 

 update all unit tests
 

 make sure to reformat atchley everywhere
 

 Update immApex.so
 

 Update getIR.R

fix handling of NA and multichains
 

 update unit tests for sequenceEncoder dim names change
 

 Update immApex.Rmd
 

 sequenceEncoder outputs names
 

 Moving geometricEncoder into sequenceEncoder