Add scrapper to Depends
 

 Add scrapper to Depends
 

 Remove manual install of system dependencies

Since this should now be handled by r-lib/actions/setup-r-dependencies (via pak)
 

 Use ubuntu- and windows-latest images
 

 Merge branch 'devel' into marlene_dev 

 corrected NEWS file from rebase
 

 distToCells finished
 

 updating param descriptions
 

 changed metric to statistics
 

 Merge branch 'devel' into brunop 

 Merge branch 'marlene_dev' of https://github.com/BodenmillerGroup/imcRtools into marlene_dev
 

 Merge branch 'devel' into marlene_dev 

 testing works
 

 working on testings
 

 working on testing
 

 started working on test_distToCells
 

 Merge pull request #137 from BodenmillerGroup/fix_devel_branch_github_actions

changed installation of dependencies in github actions 

 fixed typo in yaml
 

 changed installation of dependencies in github actions
 

 first version of interaction_abundance method
 

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

 plot_isoform_reduced_dim: add aes params
plot_demultiplex backward compatibility
 

 remove unused dependencies
 

 fix showing expect_cell_number for MultiSampleSCPipeline
 

 refactor entropy function
 

 remove txdb
 

 WIP: drop txdb
Seems to produce Error in x$.self$finalize() : attempt to apply
non-function when using inside functions
 

 Create an optimised Dockerfile
 

 update README: warn against conda
 

 fix: specify bash incase sh is linked to dash
 

 fix typo in pipeline figure
 

 fix flexiplex stopping at empty read
similar to https://github.com/DavidsonGroup/flexiplex/issues/61
 

 update flexiple: use multthreaded BGZF output
 

 update find_barcode: keep all cutadapt output, remove outdated tests
 

 Add cpuonly
 

 fetch from bioconductor upstream
 

 correct the doc
 

 remove unused dplyr in vignette
 

 edited documentation
 

 fix typo in README
 

 changes manually propagated from release to synchronize
 

 error fix in plotCrossHeatmap
 

 Bioconductor does not like remotes
 

 remove zzz.R
 

 Remove Risa dependency from DESCRIPTION
 

 remove remotes description
 

 Update DESCRIPTION
 

 Efficiency improvement to precisionPathwaysPredict and change of return value to flowchart.
 

 - Made default colours of strata plot and flowchart of precision pathways consistent.
- Criss-cross-validate plot default axes text is black instead of grey for better contrast with white background.
 

 Precision pathways documentation updated for new mode parameter.
 

 - Harmonise crissCrossValidate's crossValidate calls with recent changes to crossValidate parameters.
 

 SVMpredictInterface updated for model matrix trained model.
 

 - clincal spelling fixed to clinical.
- SVM now uses model matrix interface, can handle factors.
- samplesMetricMap also does row ordering, in addition to previous column ordering.
 

 - Improved documentation of nFeatures to be more precise.
- If nFeatures is a vector and the user didn't change tuning mode from "none", it is automatically changed for them.
 

 reduce long-check time
 

 Merge branch 'devel' of github.com:edyp-lab/Pirat into devel
 

 Update author
 

 Delete tests/.DS_Store 

 Delete R/.DS_Store 

 1st revision
 

 Merge pull request #18 from fmicompbio/add-vignette-workflow

Add vignette workflow 

 Define methods for hausdorffDistPlot example
 

 Fix vignette
 

 Run coverage tests on ubuntu
 

 Add dimred plots to workflow vignette
 

 Add packages used in vignette to Suggests
 

 Add chunk labels to vignette, remove package qualifiers
 

 Ignore R, BioC versions when using the BioC containers in CHECK.
 

 update TODO
 

 igblastr 0.99.12

install_IMGT_germline_db() now tries to fail a little bit more
informatively when the zip of the latest release is not yet available.

Also connection timeout is now 20s instead of 10s when querying
https://www.imgt.org. This is to accomodate the intermittent
sluggishness of the IMGT website. It can be controlled via global
option 'IMGT_connecttimeout'.
 

 update to use GCPtools
 

 update wideFormat docs
 

 update 17
 

 add some oarfish quant info
 

 add README to sticker
 

 changed size of package sticker
 

 Update GitHub workflow cache and fix NEWS file
 

 Merge branch 'devel' into devel 

 Update DESCRIPTION

update psi-ms.obo to v4.1.199 

 bump version for bioconductor re-build
 

 library instead of devtools load_all
 

 Fix BiocCheck Notes - pre-Air formatting
 

 Adjust dependencies
 

 Change and condense previous vignettes
 

 rerun documentation
 

 Merge pull request #8 from imbeimainz/bioc_review

Bioc review

* fixing camelCase naming
* using the output of setClass() instead of new() inside the constructor function

 

 Merge branch 'bioc_review' of github.com:imbeimainz/DeeDeeExperiment into bioc_review
 

 Merge branch 'devel' into bioc_review 

 adopting camelCase naming for methods & generics names
 

 version bump
 

 update
 

 update bioc version
 

 update bioc version
 

 Added Gut-Brain modules database
 

 update DESCRIPTION
 

 update parallel computing
 

 Addressed reviewer comments
 

 Updating rcpp error
 

 typo and version bump
 

 version bump
 

 styleR
 

 reduce code repetition by setting constant variables, and helper functions for setter and getters
 

 add rownames=T for better ouput
 

 change access via @ by slot functions and add dependencies to importfrom
 

 change 1:n by seq_len(n)
 

 replace sapply by vapply
 

 Add installation and motivation section to vignette
 

 add NEWS file
 

 version bump 0.99.3, to reflect changing the method names
 

 updating methods name in the anatomy figure
 

 renaming generics & methods to be more consistent
 

 Response to Bioconductor review: naming, formatting, and metadata updates

- Wrapped Description and biocViews fields to fit 80-character width
- Added URL and BugReports fields to DESCRIPTION
- Renamed loadPretrainedModel() → loadQuantInaccuracyModel()
- Removed unavailable citation from vignette
- Added chunk labels to all vignette code chunks
 

 removing unicode symbols
 

 Merge branch 'devel' of https://git.bioconductor.org/packages/ontoProc into devel
 

 Fixed comparator logic
 

 Added missing namespacing
 

 Fixed get_cgi_t2t export
 

 Updated tests
 

 Updated file type guessing method
 

 Fixed t2t export
 

 Modified CMakeLists.txt
 

 Further updates to tatami, scran_variances; added new topicks library.
 

 Missing some important export notes. Documentation still needs to be
done
 

 implementing slice for plyxp objects
 

 Update NEWS
 

 minor updates
 

 update vignette subsetting explanation, closes #342
 

 bump
 

 fixing warnings + biocdevel email
 

 trying to get example exec time down
 

 Delete src/Makevars 

 feat(getSubnetworkFromIndra): Include capability to add any node not in the dataset (#54)

 

 drop example in infercdr
 

 problem with thrust and cub
 

 Revert "chore: delete LICENSE for LICENSE.md"

This reverts commit adf2349f55418a8c319af14ec06f07b686327512.
 

 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.