Update heatmap cluster columns argument
 

 Bump version to 1.33.1
 

 fix a typo.
 

 version bump
 

 Merge pull request #161 from Huber-group-EMBL/H5Oget_info

Add H5Oget_info() 

 Version bump
 

 Add code for reading timestamps
 

 Merge pull request #3 from federicomarini/vignette_renewal

Vignette renewal 

 shortening up the text to avoid creation of extra variable
 

 temp disabling the BiocCheck, failing because of missing examples
 

 yep, using knitr and rmarkdown also in the Suggests: field
 

 removing the Sweave vignette
 

 removing marks images, replaced by the emoji codes :)
 

 so, wrapping text into the limit to have it displayed in a more pleasant way
 

 added extra missing citation (?)
 

 rework done till fully finished section 4, plus some edits ahead
 

 yaml and intro fixed
 

 updating biocViews
 

 Added a NEWS file with some preliminary entries
 

 added URL and BugReports address to simplify maintenance
 

 some typos fixed as spotted in a full pass
 

 using authors@R to specify roles as required in BiocCheck
 

 added .Rbuildignore
 

 first good stub at setting up the GHA
 

 making session info section unnumbered
 

 results set to "hide" where needed, and removed occurrency of forcing them to tex
 

 Bump version and update NEWS
 

 Force install TSE
 

 Fix test
 

 fix
 

 ok
 

 deleted GHA
 

 workflow update
 

 Merge pull request #216 from plasde/patch-1

added sep argument in read_biom2phyloseq.R 

 added sep argument in read_biom2phyloseq.R
 

 Merge pull request #214 from microbiome/clr

Clr 

 removed compositional transformation as part of clr
 

 clr
 

 ok
 

 ok
 

 Merge branch 'microbiome:master' into main
 

 test GHA
 

 Merge pull request #206 from Daenarys8/main

Fix typos in packages method functions 

 Merge pull request #361 from rformassspectrometry/phili

fix `BPPARAM` parameter passing in `peaksData()` 

 Merge branch 'main' into phili
 

 changed R version
 

 Use expect_true(is_ggplot(.)) instead of expect_s3_class(., "ggplot")
 

 Clean up messages in tests
 

 Add GenomeInfoDb to Suggests
 

 Minor fix for varImp
 

 TVTB 1.35.1: Import Seqinfo instead of GenomeInfoDb
 

 Added a README and a gitignore file.
 

 Add `Seqinfo` to dependencies and export `seqinfo` methods (#12)

 

 GenomicFiles 1.45.1: Add Seqinfo to Imports
 

 version bump in release
 

 Fix: added BiocStyle to Suggests for vignette build
 

 Reoxygenize
 

 Add markdown to Suggests
 

 Use expect_true(is_ggplot(.)) instead of expect_is(., "ggplot")
 

 Add Seqinfo to Suggests
 

 version bump 1.21.8
 

 version bump 1.3.8
 

 use .gsutil_do from GCPtools
 

 version bump 1.3.7
 

 version bump 0.99.2
 

 export gsutil_requesterpays_flag
 

 Add usage section to example data
 

 Use is_ggplot instead of is(, "ggplot")
 

 Bump cache version on GHA
 

 Ensures conda executable is found for igblast

Adds a check to verify that the conda executable is found
via `basilisk.utils::find()` before proceeding with igblast.
This prevents errors when the conda environment is not properly
set up and guides the user to install basilisk if needed.
Also improves error messaging when igblast fails.
 

 version number
 

 update namespace to add more details and add links to workpage
 

 Merge pull request #26 from RockefellerUniversity/mamba

Mamba 

 mask some functions to remove memeory wieght
 

 roxygenize
 

 fix issue with import of conda env and add mamba
 

 match the dev
 

 add mamaba functionality
 

 Bump version, update NEWS
 

 fix the multiple filters that not work for two value filter.
 

 Resolve merge conflict in DESCRIPTION
 

 Merge branch 'RELEASE_3_21' into devel 

 bumped release version
 

 removed breaking debug line!
 

 fixed clamulet for xgb>3
 

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

 Merge branch 'devel' of github.com:plger/scDblFinder into devel
 

 [U]
Changed again color scale for alluvial_plot
 

 prova
 

 implementing the 'label.prune.cutoff' parameter in the function 'ReferenceMapping()' to prune low-confidence predicted cell labels based on the confidence probability scores
 

 fix: bug in estimatePrecursorMz() ignoring parameter BPPARAM
 

 docs: explicitly mention scplainer in the man pages
 

 docs: explicitly mention scplainer in the man pages
 

 reorganize imports
 

 Try new env spec
 

 fix: #15
 

 fix: deps
 

 fix: update after basilisk dropped bioconda packages
 

 Bugfix: reduce memory foot print in functions (#122)

* Reduced memory foot print of parameter solvers

Reduced the function environment causing memory swelling

Also simplified the loops structure

* Parallelized also GDI calculations

* Fixed minor issue

* Fixed loggers

* Added extra cells' UMAP plot in examples

* Updated NEWS.md

* Reduced memory foot-print of function `getDataMatrix()`

Now the function avoid instantiating multiple matrices of the size
of the original one. Also calculation are now split across multiple
cores.

* Extended paramters to function calling data reduction function

* Fixed remaining bugs

Made chunk division more uniform

* Fixed remaining bugs

* Changed slicing of function  \n\nNow helpers slice across genes instead of cells for improved efficiency

* Fixed minor bug

* Solved issue with error propagation in `mclapply()`

* Dropped use of `mclapply` for `getDataMatrix()`

Including dropping unnecessary new parameters in
functions calling it

* Fixed test

---------

Co-authored-by: Silvia Giulia Galfre <49807846+seriph78@users.noreply.github.com> 

 Added functions for better junction reporting.
 

 Bump version to trigger Bioconductor build
 

 it seems working.
 

 add the real code for two filters.
 

 Bump to 1.1.2
 

 Use release branch
 

 Fix R versions in action
 

 Add release to action
 

 add makeBiocFileCacheFromDataFrame example
 

 load namespace and attach to search list
 

 run runnable examples
 

 add URL to DESC
 

 expand example in convertHub doc
 

 fix: #7
 

 Update: Add current maintainer
 

 Fix: Updated outdated dataset accessor
 

 Bump version: 3.17.3 → 3.17.4
 

 Update version number
 

 Fix documentation typo
 

 updated with checks
 

 Merge pull request #44 from seanlu96/master

Merge with wejlab MeteaScope 

 Update metascope_blast.R 

 fixed update_bam with group_by species
 

 Fixed missing taxonomy issues
 

 Group by taxa (species)
 

 Update metascope_blast.R
 

 Update DESCRIPTION

Changed R version dependency 

 Merge branch 'master' of https://github.com/seanlu96/MetaScope

# Conflicts:
#	R/download_accessions.R
#	inst/WORDLIST
#	man/download_accessions.Rd
 

 fixing tests for new ggplot2 release
 

 Edit suggests
 

 Change required Python version to 3.12
 

 More development for junction in cellCounts
 

 Done realignment core function.
 

 fix cran warnings
 

 Update maintainer e-mail to lawremi@gmail.com
 

 Update maintainer e-mail to lawremi@gmail.com
 

 Update maintainer e-mail to lawremi@gmail.com
 

 Update maintainer e-mail to lawremi@gmail.com
 

 further development on a cloud compyuter
 

 Further development for junc
 

 Merge pull request #10 from wisdomadingo/patch-1

Update cfTools-vignette.Rmd 

 Merge pull request #180 from gdrplatform/GDR-2187

 

 fix: typo
 

 chore: bump version and update NEWS.md
 

 version bump 1.27.9
 

 use pkgndep to generate dependency_heatmap

Co-authored-by: Giacomo Antonello <57659689+g-antonello@users.noreply.github.com>
 

 update title
 

 update email address
 

 docs rebuild
 

 `uniprot_organisms`: access to UniProt taxonomy data
 

 version bump in devel
 

 correct dependencies for Bioconductor tests on linux platform
 

 organisms for `chalmers-gem`: added to supported names special rat common names from Ensembl
 

 Merge pull request #179 from gdrplatform/GDR-680

Gdr 680 

 Update R/fit_SE.R

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

 refactor: headers
 

 refactor: update full list of headers
 

 chore: bump version and update NEWS.md
 

 fix citation bug
 

 correct branch
 

 correct devel version
 

 add biocversion
 

 bump version to test build
 

 Remove bigbed test
 

 Update for 0.10.3
- Add support for gappedPeak, RNA elements bed files
- Raise an error for unknown files
- Replace mouse bed file in vignette
- Replace bed_type with bed_compliance
- Comment out bigBed until import fixed
 

 Update api to 0.10.1
 

 Update DESCRIPTION 

 Refactor data handling in multiple functions to replace deprecated as_matrix with column_to_rownames and pivot_wider for improved data manipulation. Enhance tests to validate handling of NA values in various scenarios.
 

 Refactor code for improved clarity and functionality. Removed deprecated functions and updated import statements. Enhanced data selection logic in `add_formula_columns` and improved conditional handling in `get_specific_annotation_columns`. Updated pivoting method in `as_matrix` for consistency.
 

 Fix documentation warnings
 

 Update DESCRIPTION 

 Update README and plot functions to enhance clarity and accuracy in visualizations. Adjusted parameter handling in plot_2D_intervals to exclude intercepts from significance coloring. Updated README figures to reflect recent changes in analysis results and improved plot aesthetics.
 

 Replace 'corrected' terminology with 'adjusted' for intercept data. Updated data processing and plotting logic to reflect this change, including the addition of a horizontal line for the adjusted intercept facet. Ensured proper labeling and ordering of parameters in the plot.
 

 Update tests/testthat/test-plot.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

 Enhance plot_2D_intervals function by adding corrected intercept as a new facet. Updated data processing to include corrected variability effects and adjusted facet ordering. Modified plotting logic to accommodate new data structure and ensure proper labeling of cell types. Improved regression line aesthetics and ensured compatibility with updated parameter handling.
 

 Refactor DESCRIPTION and README for sccomp package

- Updated package title and description to reflect comprehensive capabilities in differential composition and variability analysis for single-cell data.
- Enhanced author list in DESCRIPTION to include additional contributors.
- Revised README to provide a clearer overview of package functionalities, key applications, and installation instructions.
- Added new visualizations and examples in the README to illustrate the package's features and usage.
- Removed outdated README.Rmd file to streamline documentation.
 

 Merge pull request #211 from MangiolaLaboratory/sum-to-zero-variable

Sum to zero variable 

 Update model_fitting.R
 

 Enhance NEWS.rd with details on version 2.1.11 improvements

- Introduced a new sum-to-zero variable constraint method, enhancing model efficiency and reliability.
- Explained the rationale behind the change, highlighting the previous method's limitations.
- Clarified user benefits, including faster convergence and increased effective sample size (ESS).
- Summarized the improvement in ESS across various datasets, demonstrating significant gains in analysis robustness and reproducibility.
 

 Enhance compare_branches_job.R with renv integration and improved data handling

- Added setup_renv and cleanup_renv functions for isolated environment management using renv.
- Streamlined package installation within the run_branch function to utilize renv.
- Introduced prepare_data function for data loading and preparation, ensuring clarity in data processing steps.
- Launched comparison jobs in the main execution section, providing clear instructions for users.
- Improved comments and structure throughout the script for better readability and usability.
 

 Update R/utilities.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

 pass fit
 

 update branch comparison
 

 drop try catch for fitting
 

 Refactor random effect handling in glm_multi_beta_binomial_generate_data.stan to use regular vectors instead of sum_to_zero_vector for improved floating-point precision. Adjusted array dimensions for random effects and their corresponding sigma parameters to ensure consistency across the model. Applied manual sum-to-zero constraints where necessary.
 

 Update random effect initialization in model fitting and Stan files to accommodate changes in dimensions. Adjusted matrix sizes for random effects and their corresponding sigma parameters to ensure consistency across the model. Enabled debugging output for better traceability during inference.
 

 Refactor random effect handling in Stan models to use arrays instead of matrices for improved flexibility. Updated related functions to accommodate changes in dimensions and ensure proper sum-to-zero constraints for random effects. Adjusted model calculations to reflect these updates, enhancing overall consistency across the codebase.
 

 version UP
 

 Add compare_branches_job.R script for parallel branch comparison

This new script allows users to launch background jobs for two branches, install the selected sccomp branch, and run a lightweight model fit on test data. It includes a function to compare results after job completion, enhancing workflow efficiency for model evaluation.
 

 Correct beta_raw matrix dimensions and improve error handling during HMC inference. Adjusted verbosity for exception display and refined error reporting for model compilation issues.
 

 Fix random effect
 

 Update priors and random effects in glm_multi_beta_binomial Stan model to use correct scaling for sum-to-zero constraints. Adjusted normal distributions for random effects and their corresponding sigma parameters to enhance model accuracy and consistency.
 

 Update README and code to require cmdstanr version 0.9.0 or higher for new features; remove deprecated QR-based sum-to-zero functions and replace with new implementation. Add error handling for cmdstanr version checks. Include new figures in vignettes.
 

 Update repository URLs in check_and_install_cmdstanr function to include new Stan Dev repository
 

 Update DESCRIPTION 

 Update documentation to reflect function name change for consistency
 

 Remove deprecated old framework

- Bumped package version to 2.1.12.
- Completely removed the deprecated old framework (methods_OLD_framework) and all its associated functions and files.
- Updated NAMESPACE to reflect the removal of deprecated methods.
 

 Refactor GitHub Actions workflow to separate build and deploy jobs for pkgdown site
 

 Add deployment step for GitHub Pages in workflow_with_cmdstanr.yml
 

 Merge pull request #213 from MangiolaLaboratory/adapt-to-ggplot2-S7

Adapt to ggplot2 s7 

 Refactor theme handling in plotting functions

- Replaced the deprecated `create_multipanel_theme` function with `sccomp_theme` across all relevant plotting functions.
- Updated the NAMESPACE file to export the new `sccomp_theme` function.
- Removed the old `create_multipanel_theme` function and its documentation.
- Enhanced the README to reflect the changes in theme usage for ggplot2 compatibility.
 

 Add pkgdown workflow for R package deployment

- Introduced a new job in the GitHub Actions workflow to build and deploy the pkgdown site.
- Configured steps for R environment setup, installation of dependencies, and CmdStan.
- Added deployment steps to upload the generated site artifacts to GitHub Pages.
 

 fixed import issues
 

 merge master
 

 Merged master

Merge branch 'master' into devel

# Conflicts:
#	DESCRIPTION
 

 Improved star mapping
 

 replaced = with <- in example doc
 

 add names to attributes
 

 Development for cellCounts + junc detection
 

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

 mbest package is back on CRAN again
 

 update docs and fix import of GenomeInfoDb
 

 Add air config files
 

 version bump 1.11.2
 

 bug fix
 

 Import GenomeInfoDbData
 

 bump v
 

 version bump 

 Bug fix long tests ieugwasr