DMRcate_2.17.1
 

 bump
 

 update transformerList constructor according to the latest scales package
 

 fix: typo in description version
 

 bug fix: added https to biomart command
 

 Version bump
 

 fix: remove extdata on project root
 

 Fix build errors
 

 feat: initial implementation of new data generation workflow
 

 C++17 Updated
 

 Fix: RI corrected binary format compatibility

RI files generated with TargetSearch after 2.4.0 allow for empty
spectra (ie, no fragments). This is incompatible with earlier
TargetSearch versions, so we remove such spectra before passing
them to the C code.
 

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

 fix merge
 

 update rainfallplot with correct pyrimidine classification of substitutions
 

 Update README.md 

 remmoved additional parameters settings section from vignette
 

 Merge pull request #3 from ErasmusMC-CCBC/devel

fix reading of synonymous variants in .maf files, git issue #2 

 Remove unnecessary imports
 

 Add more comments
 

 Merge pull request #303 from stemangiola/de-no-forking

De no forking 

 fix vignette
 

 add argument to avoid forking
 

 bumped the package version v0.99.36
 

 bumped the package version v0.99.34
 

 docs: add missing entry for lysarginase
 

 docs: replace sweave vignette to rmarkdown html format
 

 chore: include new contributors and update vignette rendering
 

 a change in process_reaction (all columns preserved)
 

 bump dev version (1.1.7)
 

 dev version bump (1.1.6)
 

 highlight_entities accept named numeric vector
 

 add diff threshold to UpDown Cluster and summary.getCluster()
 

 Updated vignette
 

 Fix version number in latest NEWS
 

 Revert "Version bump to 1.17.1"

This reverts commit 45b1233255145fe891ff6d9e4c7bc4affab50694.
 

 Update NEWS file
 

 Transfer cluster_by_groups option to HMM when running in samples mode to allow running the HMM on "all_observations".
 

 Fix for plotting with dynamic_resolution enabled when the png size limit of cairo is hit to not have parts of the plot that try to be plotted outside the limit.
 

 Update to work with Seurat v5 object changes.
 

 Fix typo in CLI script for one of the arguments.
 

 Add a "no_" at the start of CLI script options that flip a boolean from a default TRUE to FALSE so that it is clearer that it disables the option.
 

 Merge branch 'master' into devel
 

 add a new vignette
 

 version bump
 

 Merge branch 'RELEASE_3_18'
 

 ci: update workflows
 

 Bump version
 

 Merge pull request #4 from wenjie1991/devel

Devel 

 Announce R/Biocondutor package & contribution
 

 Fix some bugs
 

 Merge remote-tracking branch 'upstream/devel'
 

 Delete commented test as we never save empty rowRanges.
 

 No need to extend StrType size by 1 for HDF5 attributes.
 

 Merge pull request #3 from wenjie1991/main

Update BugReports and URL of package 

 Merge pull request #2 from wenjie1991/main

Merge branch 'wenjie1991-master' 

 Update r.yml 

 Merge pull request #1 from wenjie1991/devel

Update workflow R version 

 remove hidden files
 

 updating recommendations and requirements from reviewer
 

 adding NEWS.md
 

 revised and fixed following reviewer's requirement and recomendation
 

 ridgeplot supports passing a vector of selected pathways, #193
 

 Merge pull request #260 from huerqiang/treeplot

Fix treeplot() 

 Merge pull request #47 from YuLab-SMU/devel

merge 

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

 update
 

 Fix missing comma
 

 Cope with Ns in start codons
 

 Fix another instance of str_detect()
 

 Add export tag to the function make_ext_fasta()
 

 fix typo in data frame column name
 

 dplyr NSE removed
 

 Trigger bioc build
 

 use textconnection for readTrailer and readIndex
 

 refactor: address Sebastian's comment

- Bump version of Spectra object.
- Update bundled Spectra object.
- Disable parallel processing in vignette.
 

 docs: fix comment from Andrea
 

 refactor: address Phili's comments
 

 docs: fix version
 

 feat: enable chunk-wise processing for peaks data operations

- Add and modify functions to enable default chunk-wise processing of peaks
  data (issue #304).
- Split the documentation for chunk-wise (parallel) processing into a separate
  documentation entry.
 

 refactor: move function
 

 Do not run all examples
 

 Relaxed numeric precision in tests to pass CHECK on Arm Macs.
 

 version bump in devel
 

 update
 

 update installation
 

 Merge pull request #15 from noriakis/sc_dot

Implementation of `sc_dot` method 

 update news
 

 cluster.idents and feature.groups
 

 update sc-dot.R param description
 

 set default group.by
 

 implementation for Seurat object
 

 split.by in SCE
 

 retrieve embedding without FetchData
 

 Merge pull request #13 from xiangpin/master

fix the issue for Seurat object 

 adjust the legend name when density = TRUE
 

 Merge remote-tracking branch 'upstream/devel'
 

 ignore document source branch
 

 Bumped version and date for BioC-devel.
 

 Save the representation's version for RSE's saveObject.
 

 Allow saving/reading of SummarizedExperiments with no 'assays' subdirectory.
 

 Transition (R)SE savers and loaders to the new simplified world. (#2)

This aligns with the new takane validators in alabaster.base. 

 Skip loading of mcols/metadata if the corresponding paths are NULL.
 

 Bumped version and date for BioC-devel.
 

 Avoid expansion of nested objects as DF columns.
 

 Updated takane with the latest array validators.
 

 Bugfix to drop dimensions when reading atomic vectors.
 

 Exported the missing placeholder name variable.

Also split up HDF5-related transformation/placeholder utilities.
 

 Remove extraneous internals for the base list HDF5 saver.
 

 Updated takane  validators and accompanying R bindings.

This adds validation support for various genomic ranges classes, such as the
genomic_ranges itself, sequence_information and various compressed lists.

We also transition to saving factor codes as unsigned integers. This is, on
the whole, more sensible, as downstream consumers don't have to check whether
the codes are negative (which would make no sense outside of missing
placeholders, and we don't need half the integer space for that).
 

 Validate all on-disk representation immediately after saving. (#20)

This uses the latest takane C++ validators to check the contents of the
directories created by saveObject. This enforces consistency in the
representations across all frameworks that use the same validators.
Extension developers are now expected to register their own validation
functions, either directly in R or by adding an appropriate C++ validator. 

 Remove unnecessary rownames from the mcols when staging.

These will get overridden by the names on the Vector object itself
anyway, so there's no need to waste a column storing them again.
 

 Merge remote-tracking branch 'upstream/master'
 

 Updated the user's guide.
 

 Bugfix for correct dimnames reading in dense arrays.

Also extended tests for arrays inside DFs to the new world.
 

 Added simplified saving methods for DelayedArrays.

Currently these just divert to the dense/sparse savers; support for
preservation of delayed operations via chihaya will be added later.

Also unlocked the sparse tests so that they check the block processing.
This also involved some bugfixes.
 

 Might as well depends on alabaster.base.
 

 Migrated the saving/loading of sparse matrices to the simple approach.
 

 Use optimized types when saving a dense array.

Also switch to direct writes of blocks via low-level rhdf5 functions
instead of relying on writeHDF5Array; this is because we need to
substitute NAs for placeholders on the fly to save memory.
 

 Tighted DelayedMask behavior to align with missing value policies.

The major change is that, if 'is.na()' is TRUE for a placeholder, we will mask
all values for which 'is.na()' is TRUE; this includes NaNs that were previously
not masked. This aligns with the takane policy of not trusting NaN payloads.

Another change is that, if we see an integer dataset with a NA and the
placeholder is not NA, we throw an error because the dataset's NA was likely an
attempt at -2^31, which we just can't represent as a regular integer in R.
 

 Fix spacing
 

 Make tests shorter
 

 Merge pull request #135 from grimbough/issues-from-LTLA

Fixing issues from LTLA 

 Fix leaking reference to dataspace
 

 Update NEWS
 

 When reading zero elements from integer and float datasets immediately return an appropriatly shaped R array and skip trying to actually read anything.  We alread do this for strings. Fixes #134
 

 Unit test for reading fixed then string attributes
 

 Be explicit about BiocSyle functions in vignettes
 

 Update version

Merge branch 'scverse-hackathon' into devel

# Conflicts:
#	DESCRIPTION
 

 Remove unused import
 

 Comment out class for now
 

 Add TODO
 

 Add option to read anndata nullable arrays
 

 Add function to get the values from an enum datatype
 

 More updates for handling enum datatypes
 

 Bumped version and date.
 

 version bump
 

 test fix, version bump
 

 Merge remote-tracking branch 'upstream/master'
 

 Transition to the simplified on-disk layout that doesn't use schemas. (#1)

This eliminates the involvement of schemas, allowing each reader and saver to
handle its own affairs without coordination with a separate metadata schema. 

 Matched bump2 verison to 2.9
 

 Merge pull request #101 from adugourd/master

Update README.md 

 Updated tf bulk vignette
 

 added `bump2version` config
 

 `utils-omnipath`: added static table fallback
 

 fixed old OmnipathR warning message + merged duplicte code
 

 Changed versioning of glmnet
 

 Made ulm faster
 

 `inst/doc` into `.Rbuildignore`
 

 typo
 

 github action: install qpdf and do not fail on R CMD check warnings
 

 Rbuildignore: removed end of string anchors from directory names
 

 `nproc` based on available cores
 

 minor updates on github action
 

 `docs` into `.Rbuildignore`
 

 docs rebuild
 

 removed `.data` usage
 

 cleaned up some R CMD check warnings
 

 Fixed typo
 

 Fixed omnipath issues for collectri
 

 Merge pull request #82 from smuellerd/master

Fixed translation to mouse 

 Version Bump to repush to Bioconductor
 

 Version Bump
 

 Version Bump to repush to Bioconductor
 

 version bump
 

 add dag_permutate_children()
 

 Fix vignette (#24)

 

 C++17 Updated
 

 bump to 0.99.1
 

 feat: rm pdf rendering for now
 

 Attributes are so annoying
 

 Exclude all attributes in graph tests; attributes I want are tested separately. Closing #17
 

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 

 Import DropletUtils

Merge branch 'RELEASE_3_18' of git.bioconductor.org:packages/SpatialFeatureExperiment

# Conflicts:
#	DESCRIPTION
 

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 

 Updated NEWS and minor changes
 

 Pass existing unit tests, except for mysterious arrow segfault
 

 Removed the missing methods that clutter documentation pages. The default arguments should preserve behavior from users' point of view
 

 Need to update _pkgdown.yml to manually create the sections. Truly addressing #7
 

 Allow predicates in crop, closing #6
 

 Merge branch 'saveterrards'
 

 imgData is DF with 0 cols and 0 rows rather than NULL
 

 For the release version, to foreshadow what's to come in devel
 

 imgData is DF with 0 cols and 0 rows rather than NULL
 

 Merge branch 'saveterrards' into devel
 

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 

 Two additional bugs I discovered when writing tests for #1: Visium graph not added in read10xVisiumSFE when there's 1 sample, and function to determine spot spacing doesn't work when there're singletons outside tissue.
 

 Use devel version
 

 Added citation
 

 Fixed embarrasing documentation error
 

 Haven't updated README for ages
 

 Delete inst/.DS_Store 

 unitest bug
 

 delete html
 

 updated vignette
 

 Update comment in realize() method for SummarizedExperiment objects
 

 Reverted version
 

 Updated NEWS and version after file renaming
 

 Deleted output
 

 Pass result of realize() thru DelayedArray() constructor

This is to make sure to always produce a DelayedArray object or derivative,
even after the following planned change for the default realize() method.

Planned change for the default realize() method: The plan is to change
what 'realize( , BACKEND=NULL)' does. Instead of returning an ordinary array
wrapped in a DelayedArray object like it does at the moment, it will return
a **naked** ordinary array. This change is planned for DelayedArray 0.29.1.
 

 Fixing MAF for BEATAML #573
 

 Fix bowtie parameters
 

 Revert "Revert "Renamed BPPARAM""

This reverts commit 41a46e6cedb6c97bd967556a5fa24454c4d6b293.
 

 Revert "Experienced error when pushing"

This reverts commit 5ea1fecce433e658780ba868a6f8050e6a1d221a.
 

 Renamed BPPARAM
 

 chore: sync main with devel branch
 

 Merge branch 'master' into devel
 

 chore: sync master with devel branch
 

 Merge pull request #123 from gdrplatform/GDR-2226

Gdr 2226 

 Merge pull request #124 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 

 fix: asserts
 

 doc: update documentation
 

 feat: add support for unifying duplicates in combo matrix data
 

 chore: sync master with devel branch
 

 Merge pull request #72 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 

 chore: sync main with devel branch
 

 Merge pull request #71 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 

 Merge pull request #99 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 

 chore: sync main with devel branch
 

 Merge pull request #97 from gdrplatform/GDR-2278

Gdr 2278 

 chore: bump version and update NEWS.md
 

 Merge pull request #96 from gdrplatform/GDR-2222

Gdr 2222 

 CI
 

 Merge branch 'master' into GDR-2222 

 fixed linter
 

 Merge branch 'GDR-2222' of github.com:gdrplatform/gDRutils into GDR-2222
 

 added asserts and tests for gemoetric_mean
 

 Merge pull request #95 from gdrplatform/GDR-2250_2

Gdr 2250 2 

 refactor: switch into numeric types in predict_efficacy_from_conc
 

 rebased
 

 updated documentation
 

 Merge pull request #93 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 

 Work with Seurat objects with split layers
 

 chore: sync main with devel branch
 

 Merge pull request #62 from gdrplatform/GDR-2222

Gdr 2222 

 Update NEWS.md 

 Update check.R 

 Minor fix
 

 merge with master
 

 add dag_random
 

 update website
 

 update
 

 merge
 

 Fix citation list
 

 addresses bug introduced in 1.20, fixes #80
 

 Update get_depmap_plot_data.Rd
 

 version bump0
 

 edit man file
 

 version bump
 

 version bump & some editing
 

 Updated to C++ 17