BiocGenerics 0.55.4: Small tweak to updateObject(data.frame)
 

 Updated version of scran_markers and topicks.
 

 v1.99.2
 

 calculate FDR from all p-values at once
 

 Merge pull request #235 from lmweber/python-reticulate

Update Python interoperability to use Miniconda, Conda, and reticulate 

 update text to clarify re-using an existing Python installation
 

 add GenomeInfoDb manually as dependency due to changes to GenomicRanges
 

 revert eval=FALSE now with correct BS dependencies
 

 skip plot
 

 pause imcRtools
 

 install BS from GitHub
 

 comment and wording
 

 reorganize python interoperability chapter to start with conda and reticulate
 

 rmv caching
 

 revise intro; reformat plot
 

 +Imports:SpaceTrooper
 

 decon/Visium HD revision

 

 increase png rendering size
 

 hlc revision
 

 spatialFDA HLC revision
 

 remove tidyverse from load libraries
 

 add tidyverse to DESCRIPTION, needed in VHD chapter
 

 update plot title'
 

 Merge branch 'sandbox' into vhdcell
updates from last night
 

 changes so far
 

 new version of spatialFDA
 

 Bump version: 1.99.1 → 1.99.2
 

 Merge pull request #127 from rformassspectrometry/jomain

docs: extend documentation for use of external similarity functions 

 docs: extend documentation for use of external similarity functions

- related to issue #126: expand the documentation of `CompareSpectraParam()` and
  add examples to the vignette describing how e.g. *msentropy* spectra
  similarity calculations can be used instead of the default.
 

 Merge branch 'main' into devel
Fixing Herve deletion of data?
 

 Update README.md 

 update vignette and testthat with smaller mock data
 

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

 v1.0.0
 

 refactor: small performance improvements for longForm
 

 v1.99.1
 

 handle clusters NULL
 

 increased a length threshold for exon extraction test
 

 fixed preprocessing part2
 

 v1.5.1
 

 docs: fix download shield
 

 chore: move to codeberg.org
 

 Remove exclude-lib in Makevars, update version.
 

 version bump
 

 fix(dataProcessPlots, groupComparisonPlots): Migrate away from deprecated functions for ggplot (#175)

 

 Add MIT License to the project 

 minor text edits to msstatsplus vignette
 

 Merge pull request #173 from Vitek-Lab/tony-feature-model_weights

test(anomaly_scores): Add unit tests for dataProcess and groupComparison for anomaly score feature 

 Add more granular unit tests for data summarization subfunctions
 

 test(anomaly_scores): Add unit tests for dataProcess and groupComparison for anomaly score feature
 

 fix(groupcomparison): Fix .countMissingPercentage for custom contrast matrices (#171)

 

 changed default to topN with 100 features
 

 added manual converter example
 

 bug fix
 

 minor bug fixes
 

 bug fix
 

 anomaly score to column validator
 

 fixed anomaly bug
 

 anomaly weighted summarization
 

 added weights to groupComparison
 

 UPDATE
 

 feat: add color customization to plotUpSet()
 

 faster example cases
 

 just bump
 

 still trying to reduce example times and small fix to imports
 

 Better document where the alpha value is saved.
 

 Thighten the dependency on ggplot2

This is because we use the `@` S7 accessor.
 

 Roxygen
 

 Merge pull request #128 from ferenckata/export_tss

CAGEfightR enhancer calling extension 

 be very explicit
 

 debugging
 

 fix rowSums as suggested
 

 addressing comment about both tpm and count assay, tested alrigth now
 

 fix confusion with assay/assays
 

 add score again
 

 update docs
 

 addressing #128 #132 and #133
 

 Merge pull request #135 from charles-plessy/correlationMethodsBrushup

Brushup of CorrelationMethods.R 

 Fix Error in if (samples == "all") { : the condition has length > 1
 

 Consolidate corVector in .correlationMatrix
 

 Streamline the setMethod statements.

It required to move some code so that accessory functions are found.
 

 Merge pull request #129 from ferenckata/correlation_heatmap

Function to calculate correlation matrix 

 Merge branch 'devel' into correlation_heatmap 

 Merge pull request #130 from ferenckata/automatic_alpha_passing

Store power law parameters in the plot's metadata 

 devtools::document()
 

 Merge branch 'devel' into export_tss 

 fix sample name selection
 

 Merge pull request #134 from ferenckata/import_bigwigs

fixing score import 

 Merge branch 'automatic_alpha_passing' of github.com:ferenckata/CAGEr into automatic_alpha_passing
 

 Merge branch 'charles-plessy:devel' into automatic_alpha_passing
 

 devtools::document()
 

 adding new param in ggplot object
 

 trying to fix doc error
 

 typo
 

 fixing roxygen about input, removing comment - sorting done at getctss
 

 fix namespace
 

 fix input params again
 

 fix order
 

 testing addition of new metadata
 

 fix docs
 

 address comments: get str1 file expect str2, move examples
 

 remove unnecessary (duplicated code), issue remaining that bigwigs are two files instead of one for each sample
 

 biocthis::use_bioc_github_action(biocdocker = 'devel', covr = F, pkgdown = F, testthat = F, RUnit = F)
 

 attempt to pass CI
 

 reintroduce whitespaces
 

 remove whitespace
 

 attempt at bigwig import integration
 

 a simple function to calculate correlation matrix and let the user plot it
 

 add full enhancer calling function, try to fit into s4
 

 fix typo
 

 bump version
 

 Merge pull request #668 from xiangpin/gheatmap_update

update gheatmap to be compatible with ggplot2-4.0.0 

 update gheatmap to be compatible with ggplot2-4.0.0
 

 update readme
 

 shortened example runtime
 

 fix test
 

 fix some final errors
 

 fix fprintf issue
 

 version bump
 

 data_provenance.R is finalized
 

 Vignette Finalized
 

 Data Provenance Finalized
 

 Delete #config.log# 

 accomodate multiple summaries
 

 change to include neg epsilon
 

 Further edits
 

 Add 1 column to .pat auto in Spock 

 Finalized generateTCGAMatrix function
 

 Merge github.com:rockwillck/CBN2Path into HEAD
 

 fixed bioconductor dependencies
 

 variable camelCase refactoring and parallelization using BiocParallel
 

 Citation to the F1000Research paper
 

 Create CITATION.cff 

 Revert "v2.0.0"

This reverts commit c9cf98b3f81a39b1caefed7b260432b652a35b8d.
 

 change of the output column names
 

 improve class assertion
 

 code cleaning
 

 batch size for parallel computing
 

 require at least 5 metacells
 

 small improvements and bug fixes
 

 Merge branch 'revert-bd76fcb8' into 'devel_2.0'

Revert "Adding clusters"

See merge request scwg/gene-transcriptional-network/activity-inference/Epiregulon!22 

 Adding clusters 

 do not filter connections during metacell number optimization
 

 correct tests
 

 set default cellNum
 

 documentation update
 

 deterministic clustering
 

 conversion to spare matrix
 

 Merge branch 'CellNumSol' into devel_2.0
 

 message when optimization issue is detected
 

 documentation update
 

 Revert "resample cells to increase metacell size"

This reverts commit 5b0910a574f2c3488407b889e479724b6a0e7bc9.
 

 modification of optimization defaults
 

 guessing the solution form the cell number
 

 add documentation
 

 resample cells to increase metacell size
 

 Merge branch 'deterministic_kmeans' into devel_2.0
 

 Calculation of the epirical p-value and FDR.
 

 Spearman method as default
 

 sparse activity output
 

 preserve sparsity of activity matrix
 

 reference to the final publication added
 

 Fix an issue for the corrdinates changes of GRCh37 annotation.
 

 Update vignette
 

 Update calculateEvents.R 

 Update NEWS.md 

 Bump version: 0.99.4
 

 Remove commented code
 

 Update Python to version 3.12.3
 

 Ignore Jujutsu files
 

 Add spell check and vignette links (#366)

* Add spell check

* Add links between vignettes

* Fix typo

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Update tests/spelling.R

* Update tests/spelling.R

* run air

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> 

 Use `BiocFileCache` in Python vignette (#361)

* Use BiocFileCache in Python vignette

* Fix BiocFileCache package prefix

* Lint 

 Avoid creating character datasets with LZF filter (#356)

* Avoid creating character dataset with LZF filter

* Enable LZF writing test

* Update NEWS 

 Add reticulate backend (#322)

* remove anndata (the R package) as a dependency

* add ReticulateAnnData class

* add tests

* rename functions and files

* rename helpers

* rename test helper function

* update class diagram

* add vignette

* add entry to NEWS

* check python dependencies

* to import r_to_py and py_to_r I guess we'll need to bump reticulate to imports

* get rid of as_AnnData.anndata._core.anndata.AnnData

* simplify class

* update namespace

* update vignette

* update ignores

* fix linting issues

* install dummy_anndata

* Apply suggestions from code review

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

* apply suggestions from review

* simplify the py_to_r and r_to_py conversions

* simplify reticulate helpers

* update docs

* try with py_require mudata

* Update NEWS.md

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

---------

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> 

 Add citation (#351)

* Add CITATION file

* Add citation to README

* Add citation to main vignette

* Update NEWS

* Revert accidental changes to read_hdf5_helpers.R

* Actually update NEWS 

 Refactor obs/var_names handling (#328)

* fix error message

* don't try to use s3 functions which aren't actually implemented

* add missing compression arguments

* use pipe notation

* add comment

* add news

* fix missing value

* expand varm coming from seurat

* update test

Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>

* fix warnings

Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>

* don't store obs/varnames on structs, but do return them from struct getters

* fix tests

* fix linting issues

* update news

* Apply suggestions from review

* Update tests/testthat/test-from_Seurat.R

* Update R/from_Seurat.R

Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>

* fix warning

* fix warnings

* Adjust varm expansion regex in test-from_Seurat

* Suppress Seurat uwot warning in test-from_Seurat

---------

Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com>
Co-authored-by: Luke Zappia <luke@data-intuitive.com> 

 Fix note about missing man page section (#321)

 

 improve handling of SummarizedExperiment MLearn
 

 fix doRNG
 

 Remove GenomeInfoDb to suggests list
 

 Add GenomeInfoDb to suggests list
 

 fix jrf
 

 onload c
 

 fix internal jrf
 

 fix dynlib
 

 ren html vignette
 

 fix pbDS() filtering test
 

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

 v1.23.1 -> .2
 

 fix SerialParam arg name
 

 fixed typo
 

 Merge branch 'YuLab-SMU:devel' into devel
 

 Remove python
 

 Merge pull request #261 from MingLi-929/devel

update environment function 

 explicit call item
 

 update environment function
 

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

 update
 

 update bioc version
 

 bump version to 1.31.1
 

 update citation in README
 

 fix addCovToGR() to make use correctly of Seqinfo functions
 

 fix DESCRIPTION file
 

 update badges in README
 

 remove windows from CI
 

 update badges in README
 

 update doc by roxygen2 version update
 

 Update workflows to use devel bioconductor
 

 Update check-bioc workflow
 

 Update check-bioc workflow
 

 bump version
 

 Merge branch 'devel'
 

 spicyR 1.21.9

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 tidySingleCellExperiment 1.19.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 Statial 1.11.7

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 SPIAT 1.11.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 spatialHeatmap 2.15.2

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 sosta 1.1.2

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 scReClassify 1.15.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 scMerge 1.25.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 scds 1.25.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 scDD 1.33.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 RegionalST 1.7.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 peco 1.21.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 miaTime 0.99.13

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 MGnifyR 1.5.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 lemur 1.7.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 Ibex 0.99.32

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 distinct 1.21.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 cytomapper 1.21.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 clusterExperiment 2.29.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 clustSIGNAL 1.1.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 CHETAH 1.25.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 CellTrails 1.27.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 CellBench 1.25.1

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 Banksy 1.5.9

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 blase 0.99.4

Update Seqinfo-holding serialized object(s) to reflect new location of
Seqinfo class definition (the class was recently moved from GenomeinfoDb
to the new Seqinfo package).
 

 cleanup contrastTest merge
 

 Pulled all requireNamespace checks for lme4, emmeans, and lmerTest into a .checkContrastRequirements method and moved the check to happen sooner.
 

 Renamed ContrastResults to ContrastResultsList for better consistency with ResultsList and added require around lmer and emmeans usages.
 

 rename contrast to contrastTest
 

 Merge pull request #64 from sslakkimsetty/master

Resolved typo about MSImagingArrays inheriting from SpectralImagingArrays 

 Fixed issue where printing contrast results object coerced names incorrectly
 

 edited the way contrast names are constructed to preserve weird characters and spaces for easier understanding
 

 Added ability to do contrasts on lm models and fixed/updated tests
 

 Adding lme4::lmer as an option for running mixed effects models.
 

 update Description for release
 

 reduced time of an Example to remove R CMD check warning about time limit
 

 Merge branch 'wejlab:devel' into devel
 

 Updated limma to allow for 1 covariate