Update backend to 2.0.0 with fastreeR 1.99.1
 

 Merge branch 'RELEASE_3_21' of git.bioconductor.org:packages/fastreeR into devel
 

 Remove ignoreHets, ignoreMissing and onlyHets parameters
 

 Fix docker action
 

 Fix docker action
 

 Update README and ready for v2
 

 Backend update. CLI change to check Java-11. Mem requirements in MB.
 

 correct devel version
 

 version bump in devel for bug fix
 

 Merge pull request #44 from ccb-hms/RELEASE_3_21

Release 3 21 

 revert back to 1.2.0
 

 bump version
 

 Merge branch 'main' into devel
update
 

 update images
 

 Refer to preprint
 

 remove external downloads from examples
 

 start re-writing vignette; update status check for minimap2; update plot_demultiplex for pipelines
 

 suppress minimap2 compilation warning
 

 vendor minimap2 binary; use Rsamtools when missing samtools
 

 WIP: add show method
 

 WIP: update vignette
 

 WIP: deprecate old pipline functions
 

 fix ordering in mutation_positions' output
 

 WIP: refactor bulk with S4
 

 update seqDigest()
 

 x.y.z
 

 remain x.y.z
 

 Delete image.png 

 OrganismDbi 1.51.3

Drop mirbase.db from Suggests (package got removed from BioC 3.22
after being deprecated in BioC 3.21). As a consequence, the microRNAs()
extractor and argument 'miRBaseBuild' of functions makeOrganismDbFromUCSC()
and makeOrganismDbFromBiomart() are now defunct.
 

 with full docu
 

 Also prepare a table
 

 Solvings problems in vignette and na in marks
 

 Problem with id
 

 vignette seems to build
 

 New function works for nn
 

 Revert changes to randomnested, also accounts for fixed effects, just much safer to use
 

 udpate news
 

 Require QFeatures 1.19.1 (with typeMetadata)
 

 add Léopold as contributor
 

 Merged with master
 

 fix: bug in handling missing patterns in computeSCR
 

 Merge branch 'master' into issue81
 

 Merge pull request #88 from leopoldguyot/switch_to_se

typo in GA config 

 Merge pull request #87 from leopoldguyot/switch_to_se

Use typeMetadata branch from QFeatures for Bioc Check 

 Merge branch 'UCLouvain-CBIO:master' into switch_to_se
 

 update chache version
 

 dispatch workflow
 

 Fix scp1 generation + SCP_framwork.png update
 

 update vignettes
 

 update tests to use SE
 

 change QFeatures type in readSCP + tests
 

 GenomicFeatures 1.61.3

Drop mirbase.db from Suggests (package got removed from BioC 3.22
after being deprecated in BioC 3.21). As a consequence, function
microRNAs() is now defunct.
 

 default to same beta
 

 Update README.md 

 Update README.md 

 fix/bump version and update news
 

 Remove useless comments and _dev name
 

 Update R/plotSpectra-PTM.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

 Put m/z lab at the far right of the axis
 

 adjust the xlab
 

 update documentation
 

 Update unit tests on plotSpectraPTM
 

 update vignette
 

 vignette cosmetics
 

 harmonize barebone naming
 

 Remove Rcheck artifacts and add to .gitignore
 

 Version bump and remove dependency

Updates the package version to 1.11.2.

Removes `basilisk.utils` from the list of dependencies as it's no longer required, streamlining the installation process.
 

 Bump version
 

 Remove ..Rcheck/ files and ignore future check artifacts
 

 Merge pull request #15 from JohanLassen/main

Perf: faster retention time grouping using tree structures 

 noRd fixed
 

 Author description updated
 

 Merge branch 'main' of github.com:JohanLassen/MsFeatures
 

 ci: fix cache version
 

 Merge remote-tracking branch 'upstream/devel'
 

 requested changed made
 

 Resolved merge conflict in windowlayoutstate.pper
 

 Delete .Rproj.user directory

pushed by mistake 

 performance improvements on retention time grouping
 

 docs: update README
 

 Update readme
 

 docs: use devel branch for codecov badge
 

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

 ci: update to R 4.2 BioC 3.16
 

 fix: pkgdown url
 

 README: fix
 

 Re-add logo
 

 Update README
 

 Merge remote-tracking branch 'upstream/master'
 

 Merge pull request #12 from rformassspectrometry/jomaster

Add logo and update CI 

 Merge remote-tracking branch 'upstream/master'
 

 Remove ..Rcheck/ files and ignore future check artifacts
 

 Update for Bioconductor submission - version 0.99.9
 

 v1.1.90: Preliminary version of new features

- Add options to generate violin plots instead of boxplots
- Add support for Jenks natural breaks and custom grouping to  step7TopGenesSurvival
- Add support for custom regions and MotifDb filtering options to step7LinkedDNAMethylationSitesMotifSearching
- step7TopGenesUserPeakOverlap now accepts peak names, generates results for each individual peak rather than each peak file, and accepts multiple input objects or directories
- Fix TENETSavedSizePlot bug that caused warnings and failure to respect an explicitly specified size
- Fix TENETCacheAllData to fail if any dataset does not exist on the hub
 

 use 1.17.1 rawrr assembly
 

 make for loop more CS like #84
 

 Merge remote-tracking branch 'bioc/devel' into merge_devel
 

 Update version and fix license (#103)

* update license and docs 

 Merge pull request #102 from gagneurlab/oht_bump_version

Introducing OHT and bump version 

 Update NEWS 

 Version bump to trigger rebuilding/propagation of Windows and Mac binaries
 

 update to version 2.0.0
 

 Update README.md 

 Merge pull request #92 from andrearaithel/OHT

Optimal Hard Thresholding to determine optimal encoding dimension 

 Update helper-functions.R 

 update bioc versions
 

 Merge pull request #95 from gagneurlab/DelayedSubset

 

 add updateSeqlevelsStyle & tests
 

 make loadFraserDataSet compatible with really old versions of FRASER
 

 add singular value plots to visualize OHT
 

 use GHA checkout V4 & R 4.4 for mac and windows
 

 remove unused denoiseR package
 

 add OHT tests
 

 change optimHyperParams function to use OHT as default and rename it to estimateBestQ
 

 Version bump 1.99.4 

 fix error when intron not on same chr as any genes in the txdb (issue #74)
 

 Merge remote-tracking branch 'bioc/RELEASE_3_21'

# Conflicts:
#	.github/workflows/check-bioc.yml
#	DESCRIPTION
#	NEWS
 

 Merge pull request #77 from gagneurlab/oht_bump_version

Oht bump version 

 Update DESCRIPTION 

 use txdbmaker instead of GenomicFeatures for makeTxDbFromGFF
 

 Version bump to trigger rebuilding/propagation of Windows and Mac binaries
 

 label adjustments
 

 Merge pull request #75 from andrearaithel/oht_bump_version

Merge search methods for optimal encoding dimension into estimateBestQ function 

 add singular value plot
 

 combine grid-search and OHT in estimateBestQ function
 

 Merge pull request #74 from gagneurlab/AtaJadidAhari-patch-bioc

Bioc new version 

 add highlight.label.size to docs 

 fix highlight.label.size 

 Update plotFunctions.Rd 

 Update README.md 

 Optimal Hard Thresholding to determine optimal encoding dimension (#69)

* changed estimateBestQ to use OHT

* edit estimateBestQ error messages and variable names

* add unit tests for OHT

* update OHT tests

* add denoiseR package to Suggests

* add xcolor package for vignette building

* added my name

* update vignette

* add if statement to transpose zScores if aspect ratio larger than 1

* replace small latent space error by warning

* fix estimateBestQ test error

* Use GHA checkout V4 & R 4.4 for mac and windows

---------

Co-authored-by: AtaJadidAhari <atajadidahari@gmail.com> 

 Merge pull request #7 from neurogenomics/encode_peak

Update to v1.1.1 

 Add rust install to rworkflows
 

 Switch rworkflows repo
 

 Update CITATION
 

 Update news for 1.27.2
 

 Update copyright year for README
 

 remove markdown as a suggest
 

 reduce package size
 

 comments and update documentation for hpaDownload
 

 fix ontology test
 

 Merge pull request #15 from Bioconductor/html_ref_mans

add functions to build html reference manuals 

 rename build_html_mans to build_dbs
 

 create manuals/pkg/man/ dir
 

 add details section
 

 rename src_base to src_destDir
 

 add functions to build html reference manuals
 

 whitespace and version bump

- rename CITATION.txt as CITATION, as per 'Writing R Extensions'
 

 Merge branch 'main' into devel
git merge main -m "Merge main into devel to sync latest changes.
 

 update title
 

 Update backend and CLI. Preparing for major version upgrade
 

 Configure Linguist for language detection
 

 Updated NEWS.md and bumped-up version
 

 Use umap functions from Seurat (#111)

* Used `Seurat::RunUMAP()` as algorithm to calculate the UMAP

Used appropriate accessors on Seurat objects instead of direct access

* Fixed minor issues with call to function `Seurat::RunUMAP`

* Moved genes' section to separate function

Now genes' selection has been move to a separate function
`genesSelector()`

split clustering's UMAP plots are now outside
the Seurat clusterization function

The function `cellsUMAPPlot()` now uses the same number of features
as the clusterization

* Separated genes selection from Seurat clustering

Now in the split stage the three results of the `seuratClustering()`
function are separated:
- `genesSelection()` this function has been unified with the
  already existing genes selector that was part of the function
  `cellsUMAPPlot()`
- `suratClustering()` now simply returns the new clusterization and
  the `PCA` used to obtain it
- The creation of the PDF output is now done directly in the
  function `cellsUniformClustering()` via calls to the
  function `UMAPPlot()`

Reduced the maximum point size of the `UMAPPlot()` dots

Solved a few bugs and aligned the tests to the new slightly
different output in the cluster names

* Minor improvement of the `seuratClustering()` function

* Expanded choices for `dataMethod` of the `cellsUMAPPlot() function

Added new choices: BinarizedDiscrepancy, DerivativeLogLikelihood and
SignedLogLikelihood

Added shorcuts strings for all choices

Extended calculate function `calculateLikelihoodOfObserved()` to
get a formula parameter and return all likelihood related data matrices

* Now `cellsUMAPPlot()` scales the data matrix along the genes' direction

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

* Fixed bug in `calculateLikelihoodOfObserved()`

In case of DerivativeLofLikelihood the formula was wrong

Updated NEWS.md 

 Minor refactoring from other branches (#109)

* Moved `lambda` and `nu` estimates out of `clean()` method

* Standardized maybe access to estimated values

* Restored nu estiamtion in the `clean()` function

* Minor refactoring of `dropGenesCells()`

* Fixed minor issues

* Aligned writing of `lambda`, `nu`, `dispersion`

Both in documentation and in error messages 

 update title Intro
 

 feat: add parameter matchedPeaksCount to CompareSpectraParam

- Add parameter `matchedPeaksCount` to `CompareSpectraParam` to allow counting
  and reporting the number of matched peaks in the result object.
 

 version bump devel 1.1.2
 

 Version bump in devel
 

 pumping verstion
 

 Group is now passed as a param
 

 cleanup
 

 version bump
 

 Updates for the latest versions of the underlying C++ libraries.
 

 Finalize Bioconductor submission: removed network/DA modules, updated vignette and DESCRIPTION
 

 Trim down functions for Bioconductor compliance (per ISME feedback)
 

 fix S3/S4 signatures
 

 Merge pull request #42 from mciach/devel

numerical stabilization of sgmix() 

 merge Bioc 3.21 release
 

 v2.9.3 sgmix() bugfix
 

 v2.9.2 improved sgmix()
 

 refactor sgmix_stepE() and sgmix_stepM() into separate functions
 

 rm mu from stepsize limits in sgmix()
 

 version bumped
 

 fix: moved from the deprecated longFormat() to longForm()
 

 doc: fixed readSingleCellExperiment example (see #94)
 

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

 update cache versions
 

 version bump 1.43.3
 

 Fix weird Taishan OS build issues
 

 version update for trigger
 

 bugfix

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

 Simplify code and speedup
 

 fix: correct indentation and formatting in GitHub Actions workflow for consistency
 

 fix: streamline pak installation and dependency handling in Dockerfile
 

 feat: add Dockerfile for PharmacoGx package with system dependencies and installation steps
 

 fix: update Docker Hub credentials in GitHub Actions workflow
 

 fix: remove run_docker
 

 ci: streamline Docker build and push steps in GitHub Actions workflow
 

 ci: refactor Docker build and push steps for clarity and maintainability
 

 chore: remove outdated R and Bioconductor versions from workflow matrix
 

 download 3d DIM plot
 

 Version 1.6.1
 

 documentation
 

 update
 

 update version for devel
 

 add pkgdown page
 

 lazy data loading
 

 update bioconductor check action
 

 update vignettes
 

 add updated histology dataset names to v23
 

 Update download function and update built-in data
 

 Update documentation
 

 downloadList = NULL to list dataset
 

 fix problem where downloading other versions doesn't work
 

 Fix problem with loading built-in dataset
 

 Create hpa_download_list internal table
 

 Update lookup_df
 

 version bump 1.3.2
 

 .Rbuildignore .httr-oauth
 

 version bump 2.49.3
 

 remove avstop_for_status import
 

 removing old unit tests
 

 refactor basilisk for keras import
 

 start conversion to basilisk
 

 update getChromInfoFromNCBI() and getChromInfoFromUCSC() man pages
 

 GenomeInfoDb 1.45.4

Start to include a small "chrominfo db" in the package with chromosome
info for the most commonly used NCBI and UCSC genome assemblies e.g.
GRCh38.p14, GRCh38.p13, GRCm39, hg38, mm39, etc...
This makes calls like getChromInfoFromNCBI("GRCh38.p14") or
getChromInfoFromUCSC("hg38") work offline, plus now they are fast
and reliable.
 

 version bump
 

 Update maintainer to Anthony Wu 

 docs(vignette): Add instructions on how to download FASTA (#111)

 

 chore(docs): Fix documentation on fragpipe parameters (#108)

 

 Merge branch 'RELEASE_3_20' into devel 

 Update DESCRIPTION 

 Merge branch 'devel' into deril-dev-plotly-PTM 

 docs(fragpipe): Update vignette to include label free example (#105)

 

 Update DESCRIPTION 

 Merge branch 'feature-multi-label' of https://github.com/Vitek-Lab/MSstatsPTM into feature-multi-label
 

 bug fix
 

 fix ggplot heatmap
 

 fix heatmap numProteins and remove dplyr
 

 fix continous profile plots
 

 heatmaps
 

 code push
 

 profile plots for tmt
 

 push
 

 fix lf
 

 developing profile plot
 

 Update DESCRIPTION
 

 v2.5.1 unit test fix
 

 version bump
 

 Merge branch 'devel' of https://github.com/Vitek-Lab/MSstatsLiP into devel
 

 bug fix: Update test files to fix unit tests
 

 Merge branch 'RELEASE_3_20' into devel 

 Merge pull request #38 from Vitek-Lab/deril-dev-plotly-LiP

Adding Plotly feature to MSstatsLip with Error Handling 

 add sequence to plots
 

 pca half done
 

 structual barcode
 

 use plotly parameter from PTM plots
 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Merge branch 'RELEASE_3_18' into main 

 fix greater than issue
 

 update
 

 update
 

 Remove browser()
 

 Update DESCRIPTION to force the use of basilisk 1.18.0
 

 New test