more Bioformats formats (#52)

* pyramid formats are introduced
* claude fixes and version bump 

 Mention H5Ocopy() in NEWS
 

 Fix variable name in H5Ocopy()
 

 Bump version to 1.11.1 in DESCRIPTION file 

 update installation instructions from github
 

 fix(spectronaut): Migrate chunking from readr to arrow (#17)

Co-authored-by: Tony Wu <wu.anthon@northeastern.edu> 

 Fix(Spectronaut): Enable annotation to be added to input (#18) 

 Merge pull request #614 from lgatto/jomain

refactor: use selective imports from BiocGenerics 

 refactor: use selective imports from BiocGenerics

- Move ProtGenerics and BiocGenerics from Depends to Imports
- Use selective imports from BiocGenerics.
 

 Bump version
 

 Add warning comment to h5checktypeOrOpenLocS3()
 

 Remove h5checktypeOrNULL()
 

 Remove h5const2Factor()

This function was already unused since https://github.com/Huber-group-EMBL/rhdf5/commit/95988aeae35904b068c84aa6e4b81eb0008e8af6
 

 Install latest version of Rhdf5lib and rhdf5filters in CI
 

 Mention h5tid deprecation in NEWS
 

 Stop using H5Pset_lzf(h5tid =) arg in our own code
 

 add .gitignore for build artifacts and editor/OS files

Compiled objects under src/, R CMD build and check output, R session
leftovers, and editor/OS files were all showing as untracked after every
build, making it easy to commit them by accident. Note that .Rbuildignore
governs what goes into the built tarball, which is a separate mechanism
from what git tracks.
 

 Upgraded with visualisation functions
 

 Make objects referrable by text
 

 Add debug template
 

 Docfixes for links to functions in external packages.
 

 version up to Bioc

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

# Conflicts:
#	DESCRIPTION
 

 improve splines vignette
 

 Update NEWS to include the export of sccomp_scatterplot function for visualizing cell-group proportions against continuous covariates. Documented the function in the introduction vignette, enhancing user guidance for its application.
 

 Merge pull request #267 from MangiolaLaboratory/improvements-stefano

Fix filter scoping, quosure misuse, noisy stdout, and missing forcats import 

 Update NEWS
 

 Resolve merge conflicts with master: keep version 2.1.32 and metadata-based seed in sccomp_remove_outliers
 

 Merge pull request #284 from MangiolaLaboratory/revert-pr-272

Revert "Cohort level sccomp" (#272) 

 Merge pull request #272 from lel4011/cohort-level-sccomp

Cohort level sccomp 

 Merge pull request #282 from MangiolaLaboratory/copilot/fix-sccomp-remove-outliers

Make `sccomp_remove_outliers()` deterministic with fixed `mcmc_seed` 

 Fix CI: revert cmdstanr install to CRAN instead of GitHub
 

 Consolidate reproducibility tests into generic script
 

 Align reproducibility test iterations constant
 

 Fix sccomp_remove_outliers seed reproducibility
 

 This commit updates the package version to 2.1.33 and introduces functionality for handling smooth terms (`s()` and `t2()`) in sccomp formulas. Key changes include the addition of new utility functions for parsing smooth terms, modifications to existing functions to accommodate smooths, and the implementation of tests to ensure correct functionality. The vignette has also been added to demonstrate the use of smooth terms in modeling.
 

 Refactors the `incorporate_parameters_into_fit_object` and `incorporate_parameters_into_sccomp_object` functions to allow for optional parameter loading, enhancing flexibility in handling Stan model parameters. Additionally, it updates related tests to reflect these changes.
 

 Update scatterplot and boxplot functions to use 'linewidth' and 'median.linewidth' parameters

This commit modifies the 'plot_scatterplot' and 'plot_boxplot' functions to replace the 'fatten' parameter with 'linewidth' and 'median.linewidth', respectively. These changes enhance the clarity of the code and improve the visual representation of the plots.
 

 Add debug print statement for y values in glm_multi_beta_binomial Stan model

This commit introduces a debug print statement to output the values of y for filtered indices in the glm_multi_beta_binomial Stan model. This addition aims to assist in troubleshooting and verifying the data being processed during model execution.
 

 Enhance sccomp functions to support reproducibility and improve data handling

This commit adds a seed parameter to the sccomp_remove_outliers.sccomp_tbl function to ensure reproducibility of predictive paths based on the posterior's sampling run. Additionally, it updates the unknown_grouping variable in both sccomp_replicate and utilities functions to use a consistent representation with rep(0L, 4L) for clarity. The glm_multi_beta_binomial_generate_data Stan model is also modified to accommodate up to four random effect slots, enhancing its flexibility for modeling.
 

 Merge pull request #276 from MangiolaLaboratory/refactor_stan_association_function

Refactor stan association function 

 Enhance documentation for prior_overdispersion_mean_association parameter in sccomp_estimate

This commit updates the documentation for the 'prior_overdispersion_mean_association' parameter in the sccomp_estimate function, providing detailed information on its structure and usage. Additionally, unnecessary commented-out code has been removed from the glm_multi_beta_binomial Stan model to improve code clarity.
 

 Refactor precision parameters in glm_multi_beta_binomial Stan model

This commit updates the precision parameters for intercepts and slopes in the glm_multi_beta_binomial Stan model to utilize prior values instead of hardcoded constants. The changes enhance model flexibility and consistency by allowing the use of user-defined prior distributions for better performance in Bayesian inference.
 

 Modify sccomp_estimate function parameters

 In the sccomp_estimate function, the parameter 'exclude_priors' has been replaced with 'exclude_mean_variability_association' to clarify its purpose. The corresponding changes have been made in the function definitions, documentation, and Stan model to ensure consistency across the codebase. Deprecated parameters have also been noted in the documentation.
 

 Add ggside package support and new omit_ci parameter for interval plots

This update introduces the ggside package for enhanced plotting capabilities, allowing for side density plots in 2D interval visualizations. Additionally, a new parameter, omit_ci, has been added to the sccomp_plot_intervals_2D and plot.sccomp_tbl functions, enabling users to omit credible interval error bars from the plots. Documentation has been updated accordingly, and tests have been added to ensure functionality with the new features.
 

 Add precision parameters to incorporate_parameters_into_sccomp_object function

This update includes the addition of 'prec_intercept' and 'log_prec_sd' to the parameters block, enhancing the model's capability to handle precision-related computations more effectively.
 

 Refactor Stan model parameters and likelihood calculations for improved numerical stability

Fixed generation of quantities
 

 Use !!factor instead of .env$factor in subset_results_by_factor filter

Agent-Logs-Url: https://github.com/MangiolaLaboratory/sccomp/sessions/8874427d-1d31-4bef-b1c5-2d97851aeef2

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 

 Remove deprecated scatterplot function and its documentation from plot.R

This commit eliminates the `plot_scatterplot` function and its associated documentation, streamlining the codebase by removing unused components. The changes enhance clarity and maintainability of the plotting functions in the R package.
 

 Refactor initialization logic in fit_model function for improved clarity and flexibility

Update the initialization of parameters in the fit_model function, including changes to the precision standard deviation and mixing proportion. Simplify the logic for setting intercept and non-intercept initial values based on variability conditions, enhancing code readability and maintainability.
 

 Remove unnecessary arrangement steps in draws_to_tibble functions for cleaner output

Eliminate the sorting of data frames by `.variable` and other columns in the `draws_to_tibble_x_y` and `draws_to_tibble_x` functions. This change simplifies the output structure, focusing on essential columns and improving data handling efficiency.
 

 Update variability contrast draws handling to accommodate fewer columns

Modify the `get_variability_contrast_draws` function to handle cases where the number of columns in `draws` is less than or equal to four. This change ensures that the function can return an appropriate empty data frame when no contrasts of interest are present, improving its robustness and flexibility in processing data.
 

 streamline the contrast calculation
 

 Refactor parameter naming for consistency in incorporation functions

Update the parameter name in `incorporate_parameters_into_fit_object` and its usage in `incorporate_parameters_into_sccomp_object` to enhance clarity and maintainability. This change standardizes the terminology used for parameters, improving code readability and consistency across the functions.
 

 fixed prior

Merge remote-tracking branch 'upstream/master' into cohort-level-sccomp

# Conflicts:
#	.gitignore
#	DESCRIPTION
#	R/model_fitting.R
#	R/plot.R
#	inst/stan/glm_multi_beta_binomial.stan
#	tests/testthat/test-plot.R
 

 update docs
 

 Update version to 2.1.31 and refine alpha normalization handling

Bump package version in DESCRIPTION. Update .Rbuildignore to exclude test script. Refactor alpha normalization logic in various functions to compute values in R instead of Stan, enhancing clarity and maintainability. Introduce new tests for alpha normalization to ensure correctness in both unimodal and bimodal scenarios, reinforcing the integrity of the estimation process.
 

 Refactor sccomp_estimate and sccomp_remove_outliers for improved parameter handling

Update the `portable` parameter documentation to clarify its functionality regarding draw file management. Refactor file deletion logic to use `file.remove` instead of `unlink`, enhancing clarity and error handling. Adjust parameter lists in both functions to include `prec_coeff` and streamline the handling of Stan output files. Introduce new tests for HMC workflows to ensure robustness in parameter accessibility after file deletion, reinforcing the integrity of the estimation process.
 

 Enhance Stan model integration and update plotting functions

Add new imports for `stan_package_compile` and `stan_package_model` to improve Stan model handling. Refactor `sccomp_remove_outliers` to utilize the correct output files from the updated fit object. Clean up documentation by removing unnecessary lines in `sccomp_estimate` and `sccomp_remove_outliers` man pages, ensuring clarity and conciseness. These changes enhance the overall functionality and maintainability of the codebase.
 

 Refactor plotting functions to use new naming conventions and enhance functionality

Update `plot_1D_intervals` and `plot_2D_intervals` to `sccomp_plot_intervals_1D` and `sccomp_plot_intervals_2D`, respectively, for consistency with new naming standards. Introduce new plotting functions that improve data handling and visualization of cell-group effects. Update documentation and tests to reflect these changes, ensuring robust functionality and adherence to the new naming conventions.
 

 Add variability to composition mapping functionality

Introduce a new internal function `get_variability_to_composition_map` to match variability design columns to composition design columns based on their names. Implement error handling for missing terms in the mapping. Update the Stan model to incorporate the new mapping and adjust the model calculations accordingly. Add comprehensive tests to validate the mapping functionality and ensure robustness against missing terms.
 

 Enhance test coverage for plotting functions by updating significance checks in `test-plot.R`. Introduce a new helper function to correctly extract captions from patchwork plots, ensuring accurate validation of Bayesian FDR labels in plot outputs.
 

 Refactor Stan model parameters for mean-variability regression by consolidating intercepts into a single array structure. Update initialization logic in model fitting to accommodate bimodal associations and streamline loading of Stan models by preferring local sources. Enhance documentation for model loading function to clarify parameter usage.
 

 Update documentation for plotting functions and residuals calculation. Added missing commas in `plot_1D_intervals` and `plot_2D_intervals` documentation. Clarified description of `residuals_unconstrained` in `sccomp_calculate_residuals` to specify the calculation method and added details on residuals computation on both proportion and unconstrained scales.
 

 Refactor model fitting and plotting to use new parameter structure for mean-variability regression. Replace 'prec_coeff' with 'prec_intercept' and 'prec_slope' parameters across relevant functions and Stan models. Update tests to reflect changes in parameter names and ensure compatibility with new structure.
 

 drop prec_sd_2 from stan generation
 

 add unit test for plotting intercept-only fit
 

 update model fitting to 1 prec_sd
 

 prec_sd with sd of 1
 

 limit prec_sd to one parameter for both modes
 

 update stan and plot
 

 Merge pull request #270 from MangiolaLaboratory/optimise_draw_reading

Optimise draw reading 

 Restore three-branch fixed-effect draw extraction to avoid performance regression

Agent-Logs-Url: https://github.com/MangiolaLaboratory/sccomp/sessions/74ea79f7-4d61-4d01-8826-128a007b2f49

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 

 Refactor draw extraction in sccomp_replicate and sccomp_test

- Updated `sccomp_replicate` to conditionally extract draws from the fitted model based on available parameters, improving memory efficiency.
- Simplified the `get_abundance_contrast_draws` function in `sccomp_test` by removing redundant code and enhancing clarity in draw processing.
- Removed commented-out code to streamline the function and improve readability.
 

 Update DESCRIPTION

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

 Fix docs and portable caching in sccomp_estimate/sccomp_remove_outliers

Agent-Logs-Url: https://github.com/MangiolaLaboratory/sccomp/sessions/8cab558c-2928-4a1c-9a2e-2d58a04b6361

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 

 Update R/sccomp_calculate_residuals.R

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

 update docs
 

 - Bumped package version in DESCRIPTION file.
- Deprecated `cleanup_draw_files` argument in favor of `portable` for controlling draw file cleanup in `sccomp_estimate()` and `sccomp_remove_outliers()`.
- Updated documentation and function signatures to reflect the new parameter.
- Adjusted relevant code and tests to ensure compatibility with the new cleanup mechanism.
 

 Skip draw calculation for estimate and simple sccomp_test

- Updated `sccomp_glm_data_frame_counts` and `sccomp_remove_outliers.sccomp_tbl` to utilize `sccomp_summarise_posterior_for_estimate` for improved efficiency in summarizing posterior means and intervals.
- Enhanced `sccomp_test` to support a fast path for direct covariate contrasts, reducing reliance on full posterior draw tensors.
- Added new tests to ensure correct handling of special characters in factor levels and to address a bug related to proportional fold changes.
- Introduced a new script for benchmarking significance across datasets, improving usability for performance evaluations.
 

 Merge branch 'master' into prec_coeff_bug_fix 

 Merge pull request #261 from MangiolaLaboratory/admin-installation

Enhance documentation for restricted environments 

 Enhance documentation for restricted environments

- Bumped version number in DESCRIPTION file.
- Added guidance in README.md and introduction.Rmd for using `sccomp` in restricted or read-only environments, including instructions for setting a custom cache directory for Stan models.
- Introduced `cache_stan_model` parameter in `sccomp_boxplot` function to allow explicit cache directory specification.
- Added unit tests for cache handling in restricted environments.
 

 Merge pull request #265 from MangiolaLaboratory/fix-action-dependency

Add ragg package to workflow and update pkgdown installation 

 Merge pull request #263 from MangiolaLaboratory/fix-action-dependency

Replace devtools with remotes for dependency installation in workflow… 

 drop linux devel workflow as it is the only one failing for dependency issues
 

 Add remotes package to DESCRIPTION 

 Enhance documentation for restricted environments

- Bumped version number in DESCRIPTION file.
- Added guidance in README.md and introduction.Rmd for using `sccomp` in restricted or read-only environments, including instructions for setting a custom cache directory for Stan models.
- Introduced `cache_stan_model` parameter in `sccomp_boxplot` function to allow explicit cache directory specification.
- Added unit tests for cache handling in restricted environments.
 

 fix unit  test
 

 Merge pull request #259 from MangiolaLaboratory/change-default-statistics-plotting

Modify significance statistic handling 

 Merge branch 'master' into change-default-statistics-plotting 

 Merge pull request #253 from MangiolaLaboratory/add-unconstrained-predictors

Enhance sccomp functions with unconstrained predictors 

 Merge branch 'master' into add-unconstrained-predictors 

 Merge pull request #257 from MangiolaLaboratory/fix-boxplot

Refactor sccomp_boxplot function and enhance tests for factor handling 

 Modify significance statistic handling

- Incremented package version to 2.1.26.
- Changed default value of `significance_statistic` in plotting functions from "FDR" to "pH0" for improved clarity in significance interpretation.
- Updated documentation and function parameters to reflect the new default and ensure consistency across plotting functions.
- Enhanced user messaging to inform about the change in default significance statistic for boxplots.
 

 Enhance outlier handling and testing in sccomp functions

- Improved the integration of outlier attributes in the `sccomp_remove_outliers` and `sccomp_boxplot` functions to ensure consistency across analyses.
- Added new tests to verify the correct exposure of outlier attributes and their representation in visualizations.
- Cleaned up existing test cases for better clarity and maintainability.
 

 Refactor sccomp_boxplot function and enhance tests for factor handling

- Simplified the calculation of the 'is_zero' column in the sccomp_boxplot function by removing unnecessary lines.
- Updated the ggplot data handling to ensure parameter-level statistics are used as default for user-added layers.
- Added a new test case to verify that point counts match sample counts for factors with more than two levels, addressing issue #256.
 

 Update R/plot.R

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

 Update package version to 2.1.24 and enhance outlier handling in plotting functions

- Incremented package version to 2.1.24.
- Improved outlier handling in `plot.sccomp_tbl` and `sccomp_boxplot` functions by integrating outlier data more robustly.
- Added checks to ensure outlier attributes are correctly joined or set to FALSE when absent.
- Updated `sccomp_remove_outliers` and `sccomp_test` functions to maintain outlier attributes for consistency across analyses.
 

 update stan and plot
 

 Merge pull request #252 from MangiolaLaboratory/fix-proportion-fild-change-hyphen

Fix proportion fild change hyphen 

 Fix ratio calculation in sccomp_proportional_fold_change function

- Updated the ratio calculations for mean, upper, and lower proportions to correctly compute the ratio as proportion_to / proportion_from.
- Added clarifying comments to enhance code readability regarding the arrangement of samples and the direction of fold change statements.
 

 Merge branch 'fix-proportion-fild-change-hyphen' of https://github.com/MangiolaLaboratory/sccomp into fix-proportion-fild-change-hyphen
 

 Add character column conversion to factors in sccomp_proportional_fold_change

- Introduced an internal helper function `convert_to_factors_with_levels` to ensure character columns in new data are converted to factors with levels matching the original training data.
- Updated the `sccomp_proportional_fold_change.sccomp_tbl` function to utilize this new helper function, enhancing prediction accuracy by preventing incorrect treatment of character values.
- Adjusted sample identifiers in new data creation for clarity and consistency.
 

 Add validation for factor level conversion in sccomp_proportional_fold_change

- Enhanced the `convert_to_factors_with_levels` function to check for invalid factor levels during conversion, preventing NAs and providing informative error messages.
- Stored original values before conversion to facilitate the identification of invalid inputs, improving robustness and user feedback.
 

 Add character column conversion to factors in sccomp_proportional_fold_change

- Introduced an internal helper function `convert_to_factors_with_levels` to ensure character columns in new data are converted to factors with levels matching the original training data.
- Updated the `sccomp_proportional_fold_change.sccomp_tbl` function to utilize this new helper function, enhancing prediction accuracy by preventing incorrect treatment of character values.
- Adjusted sample identifiers in new data creation for clarity and consistency.
 

 Implement parameter incorporation into fit object before cleanup

- Added `incorporate_parameters_into_fit_object` function to load all Stan model parameters into the fit object, ensuring accessibility after CSV draw files are deleted.
- Updated `sccomp_estimate.data.frame` to call this function when `cleanup_draw_files` is enabled.
- Introduced tests to verify the functionality of parameter incorporation and its handling of models with and without random effects.
 

 Add cleanup_draw_files parameter to model configurations

- Set `cleanup_draw_files` to FALSE in both `model_with_factor_association` and `model_without_association` to prevent automatic deletion of Stan draw files during analysis.
 

 Update R/clear_draw_files.R

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

 Update roxygen documentation for files return value clarity

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 

 Update R/clear_draw_files.R

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

 Enhance model loading logic to handle missing Stan files in cache

- Updated `load_model` function to check for the existence of the Stan file when loading from cache.
- Added a message to indicate when the cached model is missing the source Stan file, triggering recompilation.
- Improved error handling with `tryCatch` for better robustness in model loading.
 

 Merge pull request #228 from MangiolaLaboratory/allow-FDR-text-in-boxplot

- Added tests to ensure `sccomp_boxplot` can accept additional ggplot… 

 Merge branch 'master' into allow-FDR-text-in-boxplot
 

 Reduce MCMC draws in vignette examples to minimize file sizes

- Add max_sampling_iterations = 2000 to all sccomp_estimate calls
- Reduces Stan draw CSV file sizes from ~50-250MB to manageable sizes
- Works in combination with workflow cleanup step
- Helps prevent GitHub 100MB file size limit errors
 

 Fix pkgdown build: integrate into main workflow with cmdstanr environment

- Move pkgdown build steps into workflow_with_cmdstanr job
- Build now uses the same cmdstanr environment as tests
- Only runs on ubuntu-latest + release R on pushes to main/master
- Set install=TRUE to ensure sccomp package is installed before building docs
- Removed separate build job to avoid duplicate environment setup
 

 Solve github error for build site
 

 Merge branch 'master' into allow-FDR-text-in-boxplot 

 update vignette image sources
 

 version UP
 

 version UP
 

 Merge branch 'improve-proportional-change' of https://github.com/MangiolaLaboratory/sccomp into improve-proportional-change
 

 Enhance sccomp_proportional_fold_change function to support complex interaction categories in from/to parameters. Improved handling for both two-factor and three-factor interactions, ensuring correct new_data structure creation. Added comprehensive unit tests to validate functionality across various interaction scenarios and error handling for invalid inputs.
 

 Merge pull request #240 from MangiolaLaboratory/fix_contrasts_to_parameter_list

Fix contrasts to parameter list 

 Bump version from 2.1.18 to 2.1.19 

 improve package man
 

 Add package help man page for sccomp

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
 

 Fix contrasts to parameter list handling variables containing digitals
 

 - Added tests to ensure `sccomp_boxplot` can accept additional ggplot layers, improving flexibility for users.
- Updated vignettes to reflect changes in function usage and added examples for custom ggplot layers.
 

 Enhance sccomp_proportional_fold_change function to support complex interaction categories in from/to parameters. Improved handling for both two-factor and three-factor interactions, ensuring correct new_data structure creation. Added comprehensive unit tests to validate functionality across various interaction scenarios and error handling for invalid inputs.
 

 Add pkgdown configuration and update GitHub Actions for deployment
 

 Update README.md 

 Update README.md 

 update authors
 

 Remove automatic GitHub Bioconductor CI
 

 Reduce SPB runtime and add Linux devel CI
 

 Skip blosc tests on older rhdf5 for now
 

 Bump minimum required rhdf5filters version
 

 Add regression tests for compression on variable length
 

 Remove outbuf_size

This parameter is unused / always overwritten for BLOSC and unnecessary for LZF. It is easier to remove it to simplify our code both here and in rhdf5, and to avoid issues such as
https://github.com/Huber-group-EMBL/rhdf5/issues/168 when we cannot compute outbuf_size properly (VLEN types).

Linked to https://github.com/Huber-group-EMBL/rhdf5filters/pull/37
 

 Fix vignette headers
 

 Document outbuf_size removal in NEWS
 

 Remove outbuf_size

This parameter is unused / always overwritten for BLOSC and unnecessary
for LZF. It is easier to remove it to simplify our code both here and
in rhdf5, and to avoid issues such as
https://github.com/Huber-group-EMBL/rhdf5/issues/168 when we cannot
compute outbuf_size properly (VLEN types)
 

 use Rarr::write_zarr_group (#51) 

 Fix NEWS braces
 

 docs: replace the README screenshot, which showed the wrong-reference bam (#172) 

 fix: keep the human genomes off hgdownload, and the demo bam on hg38 (#169)

* fix: keep the human genomes off hgdownload, and the demo bam on hg38

Two problems reported against the public demo.

The browser sat on an empty panel with a spinner for tens of seconds
before drawing anything. A stock genome is requested by bare id, so
igv.js resolves it against genomes3.json, where every hg19 and hg38
asset - 2bit sequence, cytobands, chrom.sizes and the RefSeq annotation
- lives on hgdownload.soe.ucsc.edu. That annotation is whole-genome and
unindexed, so igv.js downloads all of it before the first gene appears,
and the host itself was answering a 1 kB range request in 35 s, with
60 s timeouts and a 503 alongside. Pin our own reference for the two of
them instead: sequence and cytobands from igv.org, alias and the
tabix-indexed RefSeq from the igv.org.genomes bucket. Startup drops from
about 30 s to about 3, and no longer depends on UCSC at all.

Pinning by reference is not quite enough on its own: igv.js merges the
registry entry by id, so a reference carrying only fastaURL keeps the
registry twoBitURL and the sequence still comes from UCSC. getSequence()
then never resolves and any alignment track spins forever - which is how
this was found. twoBitURL is therefore pinned explicitly.

mm10 stays on the registry id on purpose: the bucket has its indexed
RefSeq but no cytoband file, and losing the ideogram to gain startup
time is the worse trade.

The demo BAM was 1000 Genomes phase 3, which is GRCh37, loaded into a
browser running hg38. It drew every read as a wall of mismatches against
a reference it was never aligned to. It now loads NA19240 from the igv.js
structural-variant tutorial, which is hg38, 150 kB and carries its index.

Closes #167
Closes #168

* chore: re-pin the Connect demo to the commit that fixes the genome hosts

* test: assert the pinned twoBitURL for both human genomes 

 Merge pull request #146 from myushen/add-donor-id-metadata

Add donor id metadata 

 add donor id to metadata. clean up internal metadata column descriptions on website
 

 seurat return correct assay name
 

 version bump
 

 skip missing sct files helper
 

 Merge pull request #140 from myushen/polish_readme_website

update pseudobulk download id 

 Add repository links to README

Added links to R API, Python API, and article code in README. 

 Update README by removing logos and author name

Removed author name and several logo images from the README. 

 provide pseudobulk direct download link, update citation, tidy style
 

 Merge branch 'master' into pseudobulk-select-column-dynamically 

 Merge pull request #135 from myushen/master

fix: add CZI r-universe to R repos for pkgdown CI 

 Merge pull request #132 from myushen/handle_metadata_atlas_naming

Handle metadata atlas naming 

 handle metadata versions internally as a dictionary.
 

 Enhance `get_pseudobulk()` and `get_metacell()` to retain consistent metadata columns across files. Introduce `coldata_columns` parameter for both functions, ensuring identical `colData` schema during aggregation. Update tests to validate new functionality for metacell grain keys.
 

 Merge pull request #124 from myushen/master

add additional repo path pkgdown 

 add additional pkgdown repo path
 

 update default version
 

 version bump
 

 README
 

 rename metadata
 

 conditionally skip suggest dependencies for windows os
 

 Merge pull request #123 from myushen/master

Reference and documentation 

 update cell communication default metadata
 

 version bump
 

 description
 

 census table not load to disk
 

 Merge pull request #120 from myushen/get_sce_sct_assay_message

Update SCT assay warning message 

 warning message handling NULL returned in file ids in SCT
 

 Merge pull request #118 from myushen/filter_qc_internally_for_pseudobulk

Apply QC automatically for pseudobulk, and warn users 

 Apply QC automatically for pseudobulk, and warn users
 

 move Seurat to Suggests
 

 Give get_foldchange_matrix the display_id family

The other fold-change functions let a caller work in symbols; this one
took identifiers only, so anyone holding symbols had to convert first and
convert the result back.

`genes` is now accepted as display labels and the returned matrix is
labelled with them, resolved through the same helpers the heatmap uses.

Symbols are not unique, and duplicated rownames are not a cosmetic
problem in a matrix: `m["SYM", ]` would return whichever row R found
first and silently hide the other. Duplicates are made unique with a
warning naming them, no row is dropped, and the row order is untouched.

Rows keep the object's identifiers unless display_id is supplied, so no
existing call changes. An unresolvable display_id errors rather than
quietly returning identifiers, matching get_foldchange_heatmap() -- a
silently skipped relabelling is worse than a clear failure.
 

 Close the last harmonization gaps, and the bugs they were hiding

Routing the remaining plots through the shared resolvers surfaced three
defects that the duplicated code had kept out of sight.

get_foldchange_heatmap(annotate_columns = TRUE) drew nothing. Its columns
are comparisons, but it filtered colData by `sample %in% colnames(fc_mat)`
-- an intersection that is always empty -- so the annotation was built from
an empty frame and rendered a track with no levels and no colours. It now
annotates by comparison, seeded from the object's comparison palette so the
heatmap agrees with every other comparison-coloured plot, and gains
column_anno_colors via .resolve_heatmap_annotation_colors() to match
get_expression_heatmap().

.map_gene_ids() failed with "missing value where TRUE/FALSE needed" for a
display_id supplied without a display_orgdb: `to_type == from_type` is NA
when from_type is NA and logical(0) when it is NULL, and `||` can evaluate
neither. It now reports the missing argument.

get_expression_lineplot accepted display_from and display_orgdb and ignored
them -- its inline copy of the mapping only handled the rowData path.

Three near-identical copies of that mapping had drifted apart; all now call
.resolve_foldchange_gene_ids(), and a test greps the sources so a fourth
cannot appear (3 matches before, 0 after).

get_expression_boxplot adopts .resolve_expression_plot_facet() without
changing behaviour: it passes the requested gene count, since `genes = NULL`
draws every gene and faceting all of them was never what "auto" meant, and
keeps its own "group" answer for pooling. All nine facet cases verified
identical to the pre-change baseline.
 

 Make embedding snapshots invariant to eigenvector sign

PCA and MDS axes come from an eigendecomposition, and the sign of an
eigenvector is arbitrary -- prcomp() and cmdscale() may return v or -v for
identical input, decided by the LAPACK/BLAS build. A runner image update
negated both MDS axes and turned this suite red with nothing in VISTA
changed: the magnitudes in the CI diff match the stored ones exactly, only
the signs and the resulting sort order differ.

The old digest rounded coordinates, which handles numeric noise but not a
sign flip. Canonicalise each axis instead -- orient it so its
largest-magnitude coordinate is positive -- then sort, so row order cannot
inherit the flip either. Applied only to embeddings; negating an axis of a
barplot or heatmap would be wrong, so those keep layer_digest().

Snapshots regenerated for PCA and MDS only.

Also pins the property directly: negating both axes must not change the
digest, while moving a single coordinate by 1 still must. Verified the old
digest fails the first check and the new one passes both.
 

 Publish the changelog on the pkgdown site

pkgdown generates news/index.html from NEWS.md automatically, but the
navbar `structure.left` was overridden to [intro, reference, articles],
which drops `news` from the default set -- so the page was never linked.
All twelve version headings already parse correctly; only the link was
missing.

Adds release links back to the Bioconductor landing pages, so readers can
tell which version the notes describe.

Verified on a tracked-only tree: check_pkgdown() clean, build_news()
renders 1.1.3 back to 0.99.1, and Changelog appears in the navbar.
 

 bump version
 

 Add Claude Code GitHub Workflow (#50)

* "Claude PR Assistant workflow"

* "Claude Code Review workflow" 

 igblastr 1.3.18: Add built-in germline db for mouse C57BL/6J

This new germline db is named '_OGRDB.mouse.C57BL_6J.IGH+IGK+IGL.202410'
and is based on the following OGRDB germline sets:
- 'C57BL/6 IGH' version 5
- 'C57BL/6J IGKV' version 1
- 'C57BL/6J IGLV' version 1
- 'IGKJ (all strains)' version 1
- 'IGLJ (all strains)' version 1
 

 fix(qc-plots): Fix plot title for all proteins to generalize to metabolites (#216) 

 Update README with MSstatsBioNet reference

Added a new reference for MSstatsBioNet publication in the README. 

 Remove Bioconductor Devel Build badge

Removed the Bioconductor Devel Build badge from README. 

 Update Codecov badge to point to devel branch 

 refactor: Removed deep-copy data.table ops from the dataProcess pipeline (#208)

Authored-by: Rudhik1904 <rudhikshah50@gmail.com> 

 Freed heavy fit objects and large dataProcess intermediates early (#207) 

 chore(c++): Upgrade c++ compiler from c++11 to c++14 (#205) 

 docs(impute): Update documentation w.r.t. censoredInt and MBimpute (#204) 

 Streamlined search for external methods in saveObject's generic.

Also bumped version and date for a new release.
 

 Mention examples and C formatting in NEWS
 

 Add example for H5Sunlimited()
 

 Add example for H5Tset / get stringpad
 

 Add h5writeAttribute example
 

 Fix plotForest tiplab matching (#229) 

 Run devtools::document()
 

 add logo
 

 Update Dockerfile (#876) 

 Keep p-value annotations working under ggpubr 1.0.0

ggpubr 1.0.0 turns `label = "p.format"` into an expression calling its
package-internal create_p_label(). VISTA supplies its own aes(group = ),
so the merged mapping carries VISTA's environment, where that internal is
not visible -- the plot constructed fine and then died when drawn with
`could not find function "create_p_label"`. Nothing caught it because the
failure is in ggplot_build(), not in the call that adds the layer, so no
tryCatch at construction could ever see it.

Name the statistic's own computed columns via after_stat() instead of
delegating label construction to ggpubr. Rendered text is identical on
0.6.3 and 1.0.0, verified for p.format and p.signif. An unrecognised
p.label still falls through to ggpubr rather than dropping the annotation.

Six call sites, not the three a truncated grep first showed:
get_expression_boxplot/violinplot/barplot/raincloud and
get_foldchange_boxplot/raincloud.

This is user-facing, not just a vignette failure: any caller using
stats_group = TRUE with the default p.label hit it after upgrading ggpubr.

Verified by rendering all seven articles against ggpubr 1.0.0, and by
mutation -- restoring the old delegation reproduces the failure.

Version 1.1.3.
 

 Catch the two documentation failures CI could not see

Both of today's pkgdown failures were invisible until a 20-minute site
build had already run, and one of them only after the first was fixed.

pkgdown.yaml: run check_pkgdown() before build_site(). It fails in
seconds on a man page missing from the reference index, or on an index
entry naming a file that is not committed. Verified by injecting each
fault into a tracked-only tree: the unindexed topic reports "1 topic
missing from index", the phantom article reports "failed to evaluate".

R-CMD-check.yaml: new `articles` job rendering vignettes/guides/*.Rmd
and vignettes/workflows/*.Rmd. Only vignettes/*.Rmd are package
vignettes, so R CMD check structurally cannot see these seven files --
the pkgdown build was their only test. Each renders in its own process,
matching pkgdown, so a package attached by one article cannot decide
whether the next one passes. The loop continues after a failure so every
broken article is reported in one run, and annotates each with
::error file= so it surfaces on the file in the PR diff.

The job runs in parallel with the check itself, so it adds no wall time.
 

 Fix the pkgdown site build

Two independent causes, both of which abort build_site():

1. This branch added VISTA-show, VISTA-subset, updateObject,VISTA-method,
   as_deseq_dataset, counts and VISTA-deprecated, but _pkgdown.yml uses an
   explicit reference index and hard-errors on any documented topic that
   is not listed. R CMD check has the opposite policy -- it only flags
   undocumented objects -- so every package check stayed green while the
   site build failed.

2. guides/VISTA-reference.Rmd was never added to the articles index.
   pkgdown validates articles after the reference index, so this would
   have failed the next run even with (1) fixed. Same root cause as the
   README link to it that 404'd: the file is maintained but was never
   rendered. It is now published and linked.

Also set url:, which was ~. That made check_pkgdown() itself abort, so
neither problem could be caught locally. It now reports no problems and
is usable as a guard.

Docs only -- no package code changed.
 

 Import the base functions the code calls unqualified

R CMD check listed callNextMethod, na.omit, as.dist, hclust,
getFromNamespace and head as undefined globals. They resolved only
because methods/stats/utils happen to be attached. callNextMethod is
used by the new [ method, so this branch introduced that one.
 

 Rewrite the README: fix dead links, use badges that resolve

Dead links removed or corrected:

- Four article links pointed at articles/.html, but the vignettes
  live in vignettes/guides/ and vignettes/workflows/, so pkgdown renders
  them one level deeper. VISTA-comparison, VISTA-colors and
  VISTA-deconvolution now use their real paths.
- VISTA-reference was linked but is not in _pkgdown.yml's articles list,
  so it 404s on the site. Replaced with the function reference index.
- Four published articles were missing entirely (code-economy,
  input-preparation, chord, raincloud); all four are now listed.

Badges: Bioconductor publishes no version shield -- the two
shields/version/... URLs in the previous badge block 404'd. Replaced
with endpoints that exist and self-update: build status for release and
devel, platform availability, download rank, and time in Bioconductor.
Added coverage and pkgdown workflow badges alongside R-CMD-check.
Dropped the posts shield (reads 0/0) and did not add the dependency
count (201) -- neither tells a reader anything.

Every URL in the file was checked; all resolve.

Also refreshed the body: accessor table, collapsible plot catalogue,
the harmonized argument grammar from this branch, and the retained raw
counts marked as development-only.
 </pre>
    </div>
  
    

      Package: VISTA

      Commit: 7d784c164d5d317897be6b3edd959bc66e910d68

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 15:51:38 +1000

      Commit message:


	  
		
 Declare the base packages the code already uses

R/ calls grDevices::, graphics::, stats::, tools:: and utils:: 145 times
between them; none were in Imports. R CMD check flags undeclared `::`
usage, and nothing guarantees these stay attached.
 
    
  
    

      Package: VISTA

      Commit: fb911127e7ae85ecf60a9303a539468d000f210e

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 15:51:25 +1000

      Commit message:


	  
		
 Harden the DE-table alignment helper against label/value drift

.align_de_to_counts() reindexes every comparison onto the counts matrix,
so a fault here separates values from gene labels package-wide -- the
1.0.0 failure mode. Two ways it could:

- A duplicated ref_rn made R de-duplicate the returned rownames
  ("g2" -> "g2.1"), leaving them disagreeing with the gene_id column
  they were built from. Now rejected, along with empty/NA references.

- A tibble silently ignores `rownames<-`, so every gene read as absent
  and was replaced by an NA row: correct labels, no data. Non-plain
  data frames are now demoted before rownames are touched. No shipped
  path reached this -- all ten callers go through .tidy_de_results(),
  which already returns a plain data.frame -- but the next caller that
  skipped it would have got a silently empty table.

Both were found by the new tests. A post-condition now asserts the
function's own contract (rownames and gene_id both equal ref_rn), so a
future regression fails loudly instead of returning plausible garbage.

Coverage of the function goes 45.5% -> 98.7%: identifier resolution and
its fallbacks, DESeq2/edgeR/limma column canonicalisation, type-
preserving NA padding across numeric/integer/character/logical/factor/
Date/POSIXct, and the reordering guarantee itself.
 
    
  
    

      Package: VISTA

      Commit: 58246f5c107eb23218c386b3a326e3b5a83ab6f2

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 14:42:04 +1000

      Commit message:


	  
		
 Extract a testable seam for enrichment identifier detection

Installing covr surfaced a defect in one of my own tests that neither
pkgload::load_all() nor R CMD check could: covr instruments the
installed package, and the B9 test introspected
deparse(body(run_vista_report)) with a regex, which instrumentation
rewrites.

Re-reading it, the test was weak for a second reason. Its behavioural
half exercised a local reimplementation of the resolution rule rather
than the real code, so reintroducing `%||% cfg$display_id` in
reporting.R would not have failed it. It was close to vacuous.

The fix is a seam rather than a better regex. The detection was an
inline expression buried in an 800-line function that needs Quarto to
reach; it is now .vista_detect_id_type(ids), which the test exercises
directly. The guard against the original bug is now structural --
display_id cannot reach the detector, because the function takes only
identifiers, and the test asserts that from its formals.
 
    
  
    

      Package: VISTA

      Commit: 577499e923c5f3683db8f285df1bc5c1040f64fa

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 14:21:45 +1000

      Commit message:


	  
		
 Add label/value integrity tests across the gene-taking API

The 1.0.0 row-mislabelling defect survived a passing test suite because
every test asserted SHAPE -- is.matrix(), nrow(), class -- and the broken
output satisfied all of them. A matrix of the right dimensions with the
right row names, holding the wrong numbers, is indistinguishable from a
correct one unless something recomputes the answer.

Of the 27 exported functions that accept a gene set, only two had any
invariant coverage. This adds it for the rest, asserting two properties
the defect violated:

  - permutation invariance: reversing or shuffling the genes passed in
    must not change the result;
  - label/value correspondence: the value reported for gene G is G's own
    value, checked against assay(x, "norm_counts") or the DE table rather
    than against another VISTA function that could share the bug.

Covered: eight expression plots, three fold-change plots, the three
embedding/correlation plots, both heatmap matrices, both matrix
extractors, sample ordering across all three sample_order modes, and
group summarisation.

Also asserts that asking for fewer genes returns the same values for
those genes, which is where a positional subset would diverge from a
name-keyed one.

Validated by mutation rather than assumed: reintroducing the exact 1.0.0
defect fails five tests across three files, and swapping
get_foldchange_matrix() to positional indexing fails nine. Both were
green before the mutation and green again after reverting it.

Suite goes from 1005 to 1267 assertions.
 
    
  
    

      Package: VISTA

      Commit: 58edff93f6de29686f291231921f616839ce86f3

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 14:13:01 +1000

      Commit message:


	  
		
 Update the identifier type in the xCell2 SYMBOL retry

Found in the original audit and not fixed until now.

run_cell_deconvolution() retries scoring with a SYMBOL-keyed matrix when
the first attempt fails, but built the retry arguments with
`dots_symbol <- dots`, which carried over the gene_id_type set for the
first attempt. So the retry handed xCell2 symbol rownames while telling
it they were Ensembl IDs. Depending on the installed xCell2 version that
either errors -- masking the original failure behind the generic abort
below it -- or silently scores against a near-empty gene overlap and
returns meaningless fractions.

The retry now declares "symbol" to match the matrix it is passing.

Verified on the argument-assembly logic rather than end to end, because
the xCell2 runtime is skipped in this environment.
 
    
  
    

      Package: VISTA

      Commit: 40bf2649b4dfdb1794c2eacf5c54204a9c5ec62a

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 13:34:18 +1000

      Commit message:


	  
		
 Require label identity when aligning deconvolution scores (layer 4)

The last live instance of the defect class behind the 1.0.0 row
mislabelling: trusting that a matching count implies matching identity.

.normalize_xcell2_scores() aligned by name when it could, but otherwise
fell through to `nrow(df) == length(sample_names)` and stamped the
object's sample names onto the scores. That branch fired even when the
scores carried real labels of their own that simply disagreed --
contradictory evidence, silently overridden. The consequence would be
every sample's cell fractions attached to the wrong sample, with no
warning, in a matrix of exactly the right shape.

Alignment is now attempted by name in either orientation first. A count
mismatch is an error rather than a warning that returns unusable data.
When the count matches but the labels do not, VISTA refuses: guessing by
position there is precisely the wrong move. Position is used only when
the scores carry no labels to contradict it -- absent, empty, or R's
positional defaults -- and says so.

.deconv_long_table() has the same fallback but is only reachable when
there are no rownames at all, so position is genuinely the only option;
it now reports that rather than doing it silently.

Tested against the helper directly rather than through
run_cell_deconvolution(), because the xCell2 runtime is skipped in CI and
these guards need coverage that actually executes.
 
    
  
    

      Package: VISTA

      Commit: 6268979bc1745b2d4405c5b9ec3f388743e775cc

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 12:59:58 +1000

      Commit message:


	  
		
 Remove order dependence from pathway gene capping; seed the vignette

Follow-up to the 1.0.0 row-mislabelling defect: that bug was an instance
of trusting an ordering nothing guarantees, and the same assumption was
still live in two places.

get_pathway_heatmap(max_genes) and get_enrichment_chord(max_genes)
truncated the pathway gene set with [seq_len(max_genes)] -- a positional
head of a SET. Verified empirically that clusterProfiler returns the
genes of a term in an order that differs between R sessions: the same
seed, same data and same code produced "ENSG00000004799/ENSG00000003402"
in one process and the reverse in another. Confirmed this is not RNG
(two different seeds give byte-identical output), so set.seed() cannot
fix it. The consequence was that the same call could plot a different
subset of genes on different runs.

Both now select deterministically and more meaningfully: the heatmap
ranks by expression variance, which is what makes a heatmap row worth
showing, and the chord by pathway participation, each breaking ties on
the gene identifier.

The airway vignette gains a seed. GSEA estimates p-values by permutation
and ComplexHeatmap's row k-means is unseeded, so the published document
changed on every render; measured drift between two runs on identical
input was up to 0.07 in p-value and 0.05 in NES. The GSEA chunks re-seed
so they stay stable if chunks above them are edited.

Its pathway preview also sorted before head(): showing "the first five
genes" of an unordered set is not meaningful even when it is stable.

Adds test-order-independence.R, which asserts results are invariant
under permutation of the inputs rather than merely checking shape --
the property that would have caught the original defect.
 
    
  
    

      Package: VISTA

      Commit: 58febfa3402d79ed791585e18528d455d171fbf5

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 12:08:11 +1000

      Commit message:


	  
		
 Fix a silent typo the ... validation caught in the airway vignette

Building the vignettes -- the gate none of my earlier checks exercised --
failed at the heatmap-annotated chunk:

  get_expression_heatmap() received unknown argument in `...`.
  x cluster_row_slice (did you mean `cluster_row_slices`?)

That is the new argument validation doing its job on VISTA's own
documentation. cluster_row_slice is not a ComplexHeatmap argument, so
the vignette has been passing a setting that silently did nothing since
it was written; the rendered heatmap never had slice clustering
disabled. Corrected to cluster_row_slices.

Scanned every vignette for the same class of problem rather than fixing
only the reported chunk. Three other hits, classified:

- get_pathway_heatmap(value_transform, display_id, ...) -- false
  positives. That function keeps its original blocked-argument guard
  rather than .vista_check_dots(), and all five names are real
  get_expression_heatmap formals it forwards to.
- get_expression_raincloud(value_transform) -- a real formal there, not
  the alias deprecated on violinplot/lineplot.
- get_expression_heatmap(cluster_by) -- the real column-name argument,
  not the value deprecated on get_corr_heatmap().

Also modernized the three genuinely deprecated calls so the vignette
teaches the current API instead of emitting deprecation warnings:
col_up/col_down -> colors, show_corr_values/col_corr_values ->
label/label_color, top_n_genes -> top_n.

The airway vignette now renders end to end.
 
    
  
    

      Package: VISTA

      Commit: 8ba7ab90afcccf0c3942bef8b0835e459d50a8f1

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 11:01:35 +1000

      Commit message:


	  
		
 Stop linking to undocumented internal helpers in roxygen

devtools::document() emitted five "Could not resolve link to topic"
warnings. All five were mine: I used roxygen's [] link syntax to
cross-reference .vista_defaults(), .vista_deprecate_arg(),
.vista_convert_ids() and .map_gene_ids(), which are internal helpers
marked @noRd and therefore have no Rd topic to link to.

Replaced the links with plain code formatting. The cross-references read
the same and document() is now silent.

No generated Rd changed, and the suite is unaffected.
 
    
  
    

      Package: VISTA

      Commit: 447867f4cf2b99f6a4d9e03143fb42473bda9bde

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 10:56:25 +1000

      Commit message:


	  
		
 Scope the GSEA and importer entries in NEWS, and correct an overstatement

Both entries described their defect without saying who was exposed, which
leaves a reader unable to decide whether to re-run anything.

The GSEA entry also overstated the damage. It said "any real dataset was
affected", which reads as all of get_gsea(). Tracing the pre-fix code and
measuring it shows only set_type = "kegg" was affected in practice: that
path always converts to ENTREZID and real data always contains
identifiers with no ENTREZ mapping, so the name vector always shortened.
set_type = "msigdb" converted an identifier type to itself, which
short-circuits before touching the annotation database and cannot
shorten -- verified at 22/22 on an input deliberately seeded with two
identifiers absent from the OrgDb, against 20/22 for "kegg". The "go"
branch never reassigned names at all; in the pre-fix source the
assignments sit at lines 43 and 56 of the function, and the go branch
spans 47-52. Users of MSigDB and GO GSEA do not need to re-run anything.

The importer entry now states that only a vector of two or more STAR,
HTSeq or RSEM file paths was affected, and only when those files did not
already share a gene order. Single files, data frames, matrices,
featurecounts and tximport all take a name-keyed path -- confirmed by
running each. It also names the realistic trigger: mixing files from
different pipeline runs, where HTSeq's trailing __no_feature rows or
STAR's leading N_* rows differ.
 
    
  
    

      Package: VISTA

      Commit: 07a827110d47d7973b04a11ae9ac6d6e7682f5be

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 10:46:24 +1000

      Commit message:


	  
		
 State the blast radius of the get_expression_matrix fix in NEWS

The entry described the defect and how to detect exposure but not its
scope, which is the part a reader actually needs: "rows were mislabelled"
invites the question "so were my heatmaps wrong too?" and invites
re-running everything.

An exhaustive search finds no caller of get_expression_matrix() anywhere
in the package -- no direct call, no do.call/match.fun/get() indirection,
and nothing in the R code the report generator emits as strings. Internal
group averaging goes through norm_counts(summarise = TRUE), which labels
rows from the matrix itself. So no plot, table, export or report was
affected; only direct calls could be wrong.

The entry now says that, states the three conditions that had to coincide,
notes that ranked inputs such as get_genes_by_regulation(top_n = ) are
normally not in row order and so were affected, and records that the bug
reaches back to the first release.
 
    
  
    

      Package: VISTA

      Commit: aa6d13050776af1f6cbbb6dc21bf0e535abfead2

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-04 10:25:05 +1000

      Commit message:


	  
		
 Unify the return_type vocabularies (3f)

VISTA had three incompatible spellings for the same choice of "give me
the picture, the numbers behind it, or both":

  c("heatmap","clusters","both")  get_expression_heatmap, get_foldchange_heatmap
  c("plot","matrix","both")       get_celltype_heatmap
  c("heatmap","both","genes")     get_pathway_heatmap  (with "both" in the middle)

All four now use c("plot","data","both"). The legacy values still work
and warn through a new .vista_deprecate_value(), which is separate from
the argument registry because that is keyed on argument *names* and this
is a value rename.

Deliberately untouched: get_pathway_genes(), get_genes_by_regulation(),
read_vista_counts() and derive_vista_metadata() select the SHAPE of a
purely tabular result and have no plot component, so folding them into
plot/data/both would have been wrong.

Two functions gained the argument they were missing:

- get_foldchange_lineplot() always returned a list with no way to ask
  for just the plot. Default stays "both" so existing code is unaffected.
- get_enrichment_chord() drew to the active device and returned its
  table invisibly, so its output could not be saved. Default stays
  "data"; "plot" returns a recorded plot and save_vista_plot() gained a
  replay path for base-graphics output.

That last one exposed a trap worth calling out: png() and pdf() keep
their display list disabled, so recordPlot() returns a recording that
looks valid, replays to nothing and writes a zero-byte-or-absent file.
VISTA now enables the display list before drawing and rejects an empty
recording with an actionable message instead of handing back a plot that
silently saves nothing.

Also fixes a guard I would otherwise have broken: the heatmaps skip
k-means computation when only the plot is wanted, and that test compared
against the pre-resolution value "heatmap", which would have made the
condition always true.
 
    
  
    

      Package: VISTA

      Commit: 683088d20a4c594246329964c15067e5c258bd5d

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-01 01:10:05 +1000

      Commit message:


	  
		
 Remove closure mutation introduced by this branch

BiocCheck flagged five uses of `<<-`, all of them mine: the show()
summary builder, updateObject()'s back-fill helper, and the report's
parameter reconciliation. Each mutated a variable in an enclosing frame
from inside a local helper, which is harder to follow than the
straight-line alternative and is discouraged by the Bioconductor style
guidance.

All three are now data-driven: show() assembles a named list of fields
and filters it, updateObject() diffs a defaults list against the stored
metadata, and the reconciliation walks a config-key-to-cutoff map.
Behaviour is unchanged -- show() output is byte-identical and the full
suite passes.
 
    
  
    

      Package: VISTA

      Commit: b739e2a60938104103c19e8705966bc7c6832c89

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-01 00:52:24 +1000

      Commit message:


	  
		
 Drop the Rd-time \Sexpr and finish the renamed-argument docs

The ?VISTA-deprecated page rendered its table by executing
VISTA:::.vista_deprecation_rd() through \Sexpr at Rd-build time. That
produced "stack imbalance in ':::'" warnings in two R CMD check sections
-- executing package code during documentation rendering is fragile and
buys little. The page now explains how to inspect the registry, and the
example prints it, so the authoritative list still lives in one place
and cannot drift.

Also adds the label_type/label documentation to both circular DEG plots;
the earlier substitution had matched only one of the two.
 
    
  
    

      Package: VISTA

      Commit: 9d4f04d89bd0d48185cd92ab621b7164af45ffe5

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-08-01 00:45:50 +1000

      Commit message:


	  
		
 Fix R CMD check warnings from the new methods and renames

Four issues the first full check surfaced:

- exportMethods(show) had no corresponding function because the generic
  was never imported; added @importFrom methods show.
- man/VISTA-subset.Rd lacked the four-element siglist alias R CMD check
  expects for `[` ([,VISTA,ANY,ANY,ANY-method), so the method counted as
  undocumented.
- The renamed arguments errorbar, label_type, top_n_genes and max_genes
  had no @param entries; several of my doc substitutions had not matched.
- get_chromosome_plot() still carried a requireNamespace("viridis")
  guard even though nothing in the package calls viridis:: any more, so
  it demanded a package it did not use and left an undeclared dependency
  after viridis was dropped from Imports.
 
    
  
    

      Package: VISTA

      Commit: 646e1c49f14999182f646ffa467c834c5f7bf070

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 13:15:36 +1000

      Commit message:


	  
		
 Document 1.1.2 in NEWS and bump the devel version
 
    
  
    

      Package: VISTA

      Commit: c4a5cfe91ce177a73b6b1db786db3dca52957021

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 13:14:13 +1000

      Commit message:


	  
		
 Unify "how many", "linewidth" and gene-cap naming (3d)

The same concepts carried different names across the package:
top_n_genes on the three embedding plots versus top_n everywhere else,
and line_size on the lollipops versus ggplot2's own linewidth (renamed
upstream in 3.4). Both canonical names are now available with the old
spellings kept as warning aliases.

.filter_genes() also gains an explicit max_genes argument, replacing the
hardcoded 20-gene abort that only the embedding plots enforced, and its
own top_n_genes parameter is renamed to match.

Tests assert the deprecated and replacement spellings produce identical
ggplot build output.
 
    
  
    

      Package: VISTA

      Commit: 4fae9e4b6b33b99e8135bff47ea379cab4bef663

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 13:09:08 +1000

      Commit message:


	  
		
 Rename four colliding arguments, keeping the old names working (3c)

Four argument names meant different things in different VISTA functions,
which is the failure mode users cannot reason their way out of.

`label` is logical in roughly ten functions but was a character enum
c("both","count","percent","none") on the pie and donut plots, so
label = TRUE silently did nothing there. The enum moved to `label_type`;
`label` still works, warns, and TRUE/FALSE translate to "both"/"none".

`cluster_by` names a colData column in the heatmap functions but was an
ordering strategy in get_corr_heatmap(). Renamed there to `order_by`.

`error` is the logical abort-or-report switch in validate_vista() but
selected an error-bar statistic in get_celltype_group_dotplot().
Renamed there to `errorbar`.

`comparisons` is an exported accessor returning DE contrasts, and
`sample_comparisons` means DE contrasts throughout the package -- yet on
four expression plots `comparisons` meant group pairs for ggpubr
significance brackets. Renamed to `stat_comparisons`.

All four keep the old formal on the standard deprecation timeline, and
tests assert that the deprecated and replacement spellings produce
identical ggplot build output. The plot-stability snapshots are
unchanged.
 
    
  
    

      Package: VISTA

      Commit: 1e1604ac6e6a960a4cc34f1ff0871cd9acc0814f

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:58:29 +1000

      Commit message:


	  
		
 Reject unknown arguments passed through ... (3b)

Twelve exported functions forward ... to a third-party plotting or
enrichment engine, and only get_pathway_heatmap() checked what it was
being handed. Those engines ignore names they do not recognise, so
get_expression_heatmap(v, gene = my_genes) -- singular "gene" instead of
"genes" -- silently plotted the default top-50 variable genes rather
than the requested set, and the user had no signal at all.

.vista_check_dots() is now wired into get_volcano_plot(),
get_expression_heatmap(), get_foldchange_heatmap(),
get_deg_venn_diagram(), get_go_enrichment(), get_kegg_enrichment() and
save_vista_plot(), each validating against the downstream function's own
formals so genuinely forwarded arguments keep working. Names the wrapper
manages itself (matrix, toptable, filename, ...) are blocked with a
distinct message rather than being silently overridden.

Unknown names produce a did-you-mean suggestion, so `kmeans_kk` points
at `kmeans_k`.

This is a behaviour change, not purely a bug fix: a typo that previously
produced a plausible-looking wrong plot now errors.
 
    
  
    

      Package: VISTA

      Commit: 4340a3c1c552ff81b69e40bba41d310f3d69b467

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:52:42 +1000

      Commit message:


	  
		
 Warn on the previously-silent argument aliases; expose the gene caps (3a, 3e)

Eight argument aliases changed behaviour without saying anything:
show_corr_values, col_corr_values, col_up/col_down/col_other/col_others,
lab_size, sample.seed, facet_scale and value_transform. Only
use_vista_colors warned. Each now routes through .vista_deprecate_arg()
and has a registry row, so the timeline is documented in
?VISTA-deprecated and the registry test guarantees it keeps warning.

.resolve_plot_label_flag() -- which existed for exactly this purpose and
had zero callers -- needed its precedence corrected before adoption. It
implemented "new wins, warn only on disagreement" while get_corr_heatmap
implemented "legacy wins, silently". Adopting it as written would have
silently flipped behaviour for anyone passing both, so it now
implements "legacy wins, always warn" and get_corr_heatmap uses it.

get_expression_lollipop() only ever had facet_scale, never facet_scales,
so the rename that reached the other expression plots had stopped
half-way. It now has both, with the old one warning.

Separately, three undocumented hard gene caps (20 for embeddings, 15 for
lollipop, 25 for barplot) are now the `max_genes` argument with their
existing values as defaults, so the limit is discoverable and
overridable instead of an opaque abort.

Behaviour is unchanged throughout: the plot-stability snapshots taken
before this commit still match, and passing an alias produces the same
build output as passing its replacement.
 
    
  
    

      Package: VISTA

      Commit: e02cb7116a7488885a70f1f251b4d6e8172627f0

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:46:34 +1000

      Commit message:


	  
		
 Pin plot layer data before the API harmonization

Phase 3 adds argument aliases and renames across ~60 plotting functions.
Every one of those changes is supposed to be a no-op for existing calls,
but "supposed to be" is not a test.

These snapshots capture the built layer data (positions, extents, fill,
colour, group) for eight representative plots spanning the embedding,
correlation, DEG-count, MA, expression and fold-change families, taken
now that all the correctness fixes have landed and before any renaming
starts. A rename that accidentally changes what is drawn will show up
as a snapshot diff instead of passing silently.

Values are rounded and row-ordered so the snapshots survive BLAS and
platform noise while still catching real movement.
 
    
  
    

      Package: VISTA

      Commit: ea0e2cccf76147e1afbbdad4867a1a118e015db4

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:45:19 +1000

      Commit message:


	  
		
 Replace placeholder @return text with real documentation (A9)

Eighteen exported functions carried the literal string "An object
returned by this function." injected through
R/bioccheck_roxygen_fixes.R. That satisfied BiocCheck's requirement for
a non-empty \value section while telling the reader nothing -- notably
for the two heatmap functions and get_foldchange_lineplot(), whose
return type actually varies with return_type or is a list rather than a
plot.

Each now documents what it really returns, including the return_type
branches and the ggmatrix/gseaResult/enrichResult cases.
 
    
  
    

      Package: VISTA

      Commit: 10bb7deb9558e5514899554d1c4a82921334853f

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:44:08 +1000

      Commit message:


	  
		
 Restrict generic dispatch, resolve ?VISTA, update DESCRIPTION (2e-2g)

None of the nine setGeneric() calls passed signature=, so every formal
joined the dispatch signature. norm_counts(v, summarise = stop("boom"))
raised at dispatch rather than in the method body, and enrichMsigDB
dispatched on all ten of its arguments. Added signature = "object" to
the eight accessors and signature = "x" to enrichMsigDB, which is the
Bioconductor idiom and stops non-class arguments being forced early.

Also dropped the methods:: prefix from standardGeneric. It is a base
primitive that methods does not export, so methods::standardGeneric
errors if evaluated; it worked only because setGeneric rewrites the body.
tools:::.check_packages_used flagged it as a missing object.

?VISTA returned character(0) because man/VISTA-class.Rd carried only
\alias{VISTA-class}. Added \alias{VISTA} and @docType class there, plus
a "_PACKAGE" sentinel generating man/VISTA-package.Rd. The alias lives
on the class page only -- duplicating it on both pages is an R CMD check
error, not a warning.

DESCRIPTION: Depends bumped to R (>= 4.6.0) to match Bioconductor 3.23+,
which BiocCheck was noting.

The maintainer ORCID that BiocCheck also notes is deliberately not
added: it is a real-world identifier and must be supplied by the
maintainer rather than invented.
 
    
  
    

      Package: VISTA

      Commit: 45db04f1649acd93bfe86e0cce21275d0ecbe9b9

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:42:20 +1000

      Commit message:


	  
		
 Retain raw counts as a second assay; add counts() and as_deseq_dataset() (2d)

A VISTA object kept only normalized counts, so a package whose entire
purpose is wrapping DESeq2/edgeR/limma threw away its own input.
counts(v) failed outright, and DESeq2::DESeqDataSet(v, design) picked up
the first assay -- norm_counts -- and died on "some values in assay are
not integers". There was no way back into the tools VISTA wraps.

All three backends already held the filtered raw matrix at the point
they assembled their result list, so this is plumbing rather than
recomputation. It is registered as assay "counts" AFTER norm_counts, so
an unqualified assay(x) is unchanged; the preceding commit made every
internal read site name its assay explicitly precisely so this addition
could not silently repoint them.

- create_vista(keep_raw_counts = TRUE) by default, documented as roughly
  doubling the assay footprint, with FALSE as the opt-out.
- as_vista(raw_counts =) accepts and realigns a raw matrix, erroring if
  it does not cover the same genes and samples.
- counts() on BiocGenerics::counts. On an object without the assay it
  explains that pre-1.2.0 objects store only normalized counts and that
  updateObject() cannot recover them, because normalization is not
  invertible -- a rebuild is required.
- as_deseq_dataset() is explicit rather than making DESeq2::DESeqDataSet
  work implicitly, since the implicit path would depend on assay order.

Schema bumped to 1.1.0 to record the new layout, and the cached example
object regenerated so it carries the assay.
 
    
  
    

      Package: VISTA

      Commit: 73dcd91aad6de5da1c76e4dd8fb0bd5be7f087db

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:30:35 +1000

      Commit message:


	  
		
 Add a show() method; remove the uncallable print.vista (2c)

existsMethod("show", "VISTA") was FALSE, so display fell through to
SummarizedExperiment's method and every VISTA object introduced itself
as "class: SummarizedExperiment". None of the analysis state -- the
grouping column, the comparisons, which DE source is active, the
thresholds, the schema version -- appeared anywhere in the default
display, so inspecting an object told you nothing about the analysis it
carried.

setMethod("show", "VISTA") prints the inherited SE header with the class
corrected, then a short VISTA block. print.VISTA is kept as a registered
S3 that forwards to show(), because knitr and rmarkdown call print()
rather than auto-displaying; the two routes now produce byte-identical
output, which the tests assert.

print.vista (lowercase) is removed. No object in the package can carry
class "vista" -- setClass("vista", ...) has not existed for several
releases and nothing assigns that class -- so the method was uncallable
and its removal cannot break user code.
 
    
  
    

      Package: VISTA

      Commit: b7f42355c8f8ca9dd69757dc38d3ae2e6aab1b78

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:28:05 +1000

      Commit message:


	  
		
 Add a [ method so subsetting keeps metadata consistent (2b)

VISTA inherited SummarizedExperiment's `[` unchanged. Row subsetting
shrank the assay and rowData but left every DE table in metadata()
describing all the original genes, and setValidity() -- which checks
structure but not the DE contract -- reported the result as valid.
Measured on the packaged example: v[1:10, ] produced a 10-row object
whose comparisons()[[1]] still had 123 rows, validObject() returned
TRUE, and get_deg_count_barplot() charted counts for 123 genes.

Column subsetting was worse because it was completely silent: even
validate_vista(level = "full") passed, while group colour maps still
named groups with no remaining samples.

setMethod("[", c("VISTA","ANY","ANY")) now reindexes de_results,
de_summary and every de_results_by_method/de_summary_by_method entry to
the retained genes in the new row order, and recounts DEG summaries from
the rows that survived. Column subsetting deliberately leaves DE tables
intact -- they are model results, not per-sample data -- but prunes
orphaned group and comparison colours and warns by name when a
comparison's groups are no longer represented, since its plots no longer
describe the object. Every subset is recorded in
provenance$subset_history.

The DE-rownames check moved from .validate_vista_full() into
.validate_vista_core(), so the stale state is caught at the core level.
It deliberately stays out of setValidity(), which runs on every new() and
slot assignment and must remain cheap and structural; putting it there
would make existing v[i, ] calls in vignettes and saved pipelines error
at construction.
 
    
  
    

      Package: VISTA

      Commit: 4b04bf7ef100ddc8b1b8d94741754e6d646d0623

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:22:07 +1000

      Commit message:


	  
		
 Compare and migrate the metadata schema version (2a)

metadata(x)$vista_schema_version was written by the constructor and then
never read. Nothing compared it to .VISTA_SCHEMA_VERSION and there was
no migration path, so an object serialized under an older layout
deserialized silently and could be missing keys the current code
expects. Verified beforehand: setting the tag to "0.0.1" still passed
validate_vista(level = "full") with zero issues.

Adds .vista_schema_compare() and a BiocGenerics::updateObject() method.
Migration back-fills absent metadata keys with their documented
defaults, stamps the current schema, and records what it did in
provenance$updates. validate_vista() now informs when an object is older
and points at updateObject(); a *newer* schema is reported as an issue,
because newer metadata may carry semantics this version would misread.

updateObject() deliberately refuses to touch a newer object -- the fix
there is to upgrade the package, not to rewrite the object.

This is prerequisite infrastructure for the raw-counts assay: counts()
on a pre-1.2.0 object cannot be back-filled (normalized counts are not
invertible) and needs the schema machinery to say so coherently.
 
    
  
    

      Package: VISTA

      Commit: de660307bd935965110b14358d80cb8902c528b4

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:18:55 +1000

      Commit message:


	  
		
 Name the assay explicitly at every read site

17 call sites read SummarizedExperiment::assay(x) with no assay name,
relying on norm_counts being the first (and only) assay. That is fine
today but silently repoints every one of them the moment a second assay
is added, which the next commit does.

Behaviour-neutral: the full suite passes unchanged.
 
    
  
    

      Package: VISTA

      Commit: ad47851a1037aefdf0e95c157a6860505a52333c

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:13:00 +1000

      Commit message:


	  
		
 Report the analysis that actually ran, not config defaults (B8, B9)

Two independent ways run_vista_report() could describe an analysis that
never happened.

B8: cutoffs(vista_obj) was never read anywhere in reporting.R. When a
prebuilt object was supplied through `vista_rds`, create_vista() was
never called, so cfg$de_method / log2fc_cutoff / pval_cutoff /
p_value_type kept the hardcoded defaults deseq2 / 1 / 0.05 / padj -- and
those were printed verbatim in the analysis summary and the executive
summary. An object built with edgeR at LFC 2 and raw p < 0.01 produced a
report claiming DESeq2 at LFC 1 and padj < 0.05, while every plot and
gene list reflected the real settings.

The object is now the authority: its stored cutoffs override the config,
a conflicting explicit config value warns rather than being silently
applied, and the summary table gained a `source` column recording
whether each parameter came from the object or the report.

B9: enrich_from fell back from `from_type` to `display_id`. Those are
different things -- display_id names a rowData column used for labels,
from_type describes what the gene identifiers are. The common config
pairing of Ensembl identifiers with `display_id: SYMBOL` therefore
declared the IDs to be symbols, every ID lookup failed, and the report
rendered an empty enrichment section that reads as a real negative
result. display_id is out of the chain; detection now falls straight
through to inspecting the identifiers, and reports what it detected.
 
    
  
    

      Package: VISTA

      Commit: 5117dcacdc47dcd348c32e621bf7e9ea6df537c5

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:09:48 +1000

      Commit message:


	  
		
 Fix no-op gene ID mapping in get_expression_lollipop (B7)

The OrgDb branch called

    .map_gene_ids(genes, from_type = display_from, to_type = display_from)

with source and target key types identical, which .map_gene_ids() short
-circuits as a no-op. Symbols supplied via `genes` were therefore never
translated to the object's own identifiers, and the function aborted
with "None of the specified `genes` were found" even though the mapping
was available. Only the rowData branch worked, so the failure appeared
exactly when a user had no SYMBOL column and reached for an OrgDb --
which is when they needed the mapping most.

Replaced the hand-rolled block with .resolve_foldchange_gene_ids(),
which already implements both branches correctly, including the
display_id/display_from swap. This also removes one of the duplicated
gene-resolution implementations flagged in the API audit.
 
    
  
    

      Package: VISTA

      Commit: ea4028fcfb0c2f38db61b39bcbd32cb20531e729

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:06:05 +1000

      Commit message:


	  
		
 Fix GSEA ranked vector sliding scores onto the wrong genes (B2)

get_gsea() built its ranked vector then reassigned the names:

    rank_vec <- sort(setNames(fc, rn), decreasing = TRUE)
    names(rank_vec) <- .vista_convert_ids(names(rank_vec), ...)

.vista_convert_ids() ends with unique(out[!is.na(out) & nzchar(out)]),
so its result is shorter than its input whenever any identifier fails to
map or two map to the same target. R does not error on a short names<-
assignment; it pads with NA. Every score after the first gap therefore
slid onto a different gene, and the trailing genes were left unnamed.

On the packaged example this silently corrupts 123 ranked genes into 121
mapped identifiers with 2 NA names. In a five-gene reproduction with two
unmappable symbols, BRCA1 received the score belonging to an unmapped
entry and EGFR received BRCA1's. Since the KEGG branch always maps to
ENTREZID, unmapped identifiers are guaranteed in any real dataset, so
the resulting NES values and leading-edge gene lists were meaningless.

Added .vista_map_ids_strict(), which returns a vector the same length as
its input with NA for unmapped entries, and .vista_build_rank_vector(),
which drops name and score together, resolves many-to-one mappings by
keeping the largest absolute score, re-sorts, and reports what it
dropped or collapsed. All three set_type branches now use it.

.vista_convert_ids() is deliberately left alone: its de-duplication is
correct for its other callers, which want a gene set rather than keys.
.map_gene_ids() is deliberately not reused either -- it falls back to the
input identifier when unmapped, which is right for display labels and
would trade this bug for a silent key mismatch against gseKEGG.
 
    
  
    

      Package: VISTA

      Commit: 1b94e70ce6c47f75b6e8cd8f2612c9cfb391bbac

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:03:30 +1000

      Commit message:


	  
		
 Bind multi-file count imports by gene identifier (B6)

The STAR, HTSeq and RSEM importers each built their count matrix with
vapply(FUN.VALUE = numeric(length(genes))), taking gene identifiers from
the first file only. vapply enforces that every file returns the same
number of values; it never checks that row i describes the same gene.
Any file whose rows were ordered differently was silently pasted onto
the first file's gene labels, and the whole matrix for that sample was
wrong.

This is not hypothetical. HTSeq output follows GTF order and its
trailing __no_feature/__ambiguous rows vary by version; STAR output is
often post-processed to strip the four leading N_* rows. Two files with
equal row counts and different content were accepted without a word.

Added .bind_count_files(), used by all three importers so the semantics
cannot drift apart again. It takes the reference gene set from the first
file, keeps the fast positional path when every file already lists the
same identifiers in the same order (which also preserves support for
repeated identifiers), and otherwise indexes each file with match().

A file that does not cover the reference set is now an error naming the
file and up to five missing identifiers, rather than a silent zero-fill
-- a silent zero is the same class of bug being fixed here. Extra
identifiers are dropped with an informational message.

This can surface an error where a script previously appeared to work. It
was producing wrong numbers.
 
    
  
    

      Package: VISTA

      Commit: ffff6ed3cd8dd846652ae2d5acb66fa2fb35d350

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 12:00:46 +1000

      Commit message:


	  
		
 Fix corr heatmap triangle mask ignoring the clustered axis order (B3)

get_corr_heatmap() built the tile data from as.table(cor_mat), applied
the `triangle` and `show_diagonal` masks by comparing factor codes, and
only afterwards re-levelled the axes to the hclust order. Since
cluster_by = "correlation" is the default, the retained cells described
the input order while the axes showed the clustered order.

The result looked plausible but was not a triangle: on the packaged
example, cells kept per axis row were 3,6,1,2,4,5 instead of 1..6. Some
sample pairs were missing entirely and others appeared in the half a
reader would not look for.

Axis levels are now resolved first and the masks compare codes in that
same coordinate system. Tests assert the retained-cell counts are
strictly 1..n (lower) or n..1 (upper) across all four cluster_by modes,
and spot-check that each tile's value still belongs to its own sample
pair after re-levelling.

Also drops viridis from Imports. It became unused when the dead
.plot_corr_heatmap() helper was removed in the previous release commit;
get_corr_heatmap()'s viridis_option/direction/begin/end arguments are
served by ggplot2::scale_fill_viridis_c and are unaffected.
 
    
  
    

      Package: VISTA

      Commit: cd2a9304b6b6b2371b67b863cc315d05517bcf15

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:58:27 +1000

      Commit message:


	  
		
 Fix YAML and filename escaping in report/asset generation (B10)

Two related escaping bugs, both reachable from ordinary config values.

esc_yaml() in run_vista_report() escaped a double quote by emitting
backslash-backslash-quote, which YAML reads as an escaped backslash
followed by an unterminated string. A report_title containing a quote
therefore corrupted the front matter, and a title containing a backslash
("C:\project") emitted an invalid escape. Verified: of four
representative titles, the old escaper round-tripped only the one with
no special characters.

The filename sanitiser used "[^A-Za-z0-9_\\-]+". Inside a bracket
expression the backslash is literal, so the class whitelisted it -- a
comparison name containing a backslash survived into every asset
filename. exporting.R carried an identical copy of the same regex.

Both helpers are now package-level internals, .vista_escape_yaml() and
.vista_sanitize_name(), used by reporting.R and exporting.R alike, and
covered by direct tests that round-trip five awkward values through
yaml::yaml.load(). Extracting them removes the duplicate definition that
let the sanitiser bug exist in two places at once.
 
    
  
    

      Package: VISTA

      Commit: a27faf125c6b840f1360797c6c728402b0723686

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:55:45 +1000

      Commit message:


	  
		
 Drop empty factor levels when summarising by group

split() on a factor grouping column keeps levels that no longer have any
samples, so rowMeans() over an empty selection produced an all-NaN
column. Both group-summarisation paths were affected:
norm_counts(summarise = TRUE) and get_expression_matrix(summarise =
TRUE).

This is reachable today with any user-supplied colData whose grouping
column is a factor carrying unused levels, and it is also what makes
column-subsetting an object return NaN. Fixing it here means the
upcoming `[` method does not have to paper over it.
 
    
  
    

      Package: VISTA

      Commit: 5baac3c24326a06935d78ca4177f84a7d37707d4

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:54:53 +1000

      Commit message:


	  
		
 Fix comparison colour fallback returning character(0) (B5)

.vista_comparison_colors() narrowed the stored colour map with
`cols[intersect(comps, names(cols))]`. When nothing matched, that yields
character(0) rather than NULL -- and both the helper's own fallback and
every one of its six call sites branch on `is.null(cols)` to decide
whether to generate a palette. The zero-length vector walked past all of
them.

get_foldchange_lineplot() then died with "subscript out of bounds" at
`pal[[1]] %||% "black"`; %||% cannot catch a subscript error, so the
documented "black" fallback was unreachable. Any object whose stored
comparison colours have drifted from its comparison names -- hand-edited
metadata, an object round-tripped from an older schema, or comparisons
added after construction -- crashed instead of falling back.

Added the `if (!length(cols)) cols <- NULL` guard that
.vista_group_colors() has always had, so the two siblings behave
identically. No caller changes needed: NULL[[1]] returns NULL, so
`pal[[1]] %||% "black"` now yields "black" as documented.
 
    
  
    

      Package: VISTA

      Commit: 11a01e739f2334dd28aa2be8219935065697ddb4

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:52:09 +1000

      Commit message:


	  
		
 Fix deconvolution crash on ENSEMBL:SYMBOL rownames (B4)

.collapse_ensembl_symbol_ids() piped its argument straight into
tibble::rownames_to_column(), but its only caller passes
assay(x, "norm_counts") -- a matrix, not a data.frame. Every call failed
with "is.data.frame(df) is not TRUE".

This was not an edge case. gene_id_type defaults to "auto", and
.infer_gene_id_type() returns "ensembl_symbol" for the common
ENSG...:SYMBOL rowname convention, which routes directly into the
collapser. run_cell_deconvolution() was therefore unusable for any
object built with those identifiers.

Coerced with as.data.frame() before the pipe. Added tests that exercise
the collapser directly, including the symbol-averaging behaviour, so the
path is covered on platforms where xCell2 itself cannot run.
 
    
  
    

      Package: VISTA

      Commit: 0179ec258b3ca1270b2e4562ad4d555ae1c4a873

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:51:22 +1000

      Commit message:


	  
		
 Fix get_expression_matrix() relabelling summarised rows (B1)

When `genes` was supplied together with `summarise = TRUE`, the matrix
was subset in assay order but its rownames were then overwritten with
`genes[genes %in% rownames(mat)]`, which preserves the caller's argument
order. Whenever those two orders differed, every row was labelled with a
different gene's identifier and the returned values were silently wrong.

On the packaged example, requesting five genes in reverse order reports
801.10 as the control mean for ENSG00000000971, whose true mean is
4769.98 -- it had been handed ENSG00000000003's row. A marker-panel call
such as get_expression_matrix(v, genes = c("MYC","CD8A"), summarise =
TRUE) returns MYC labelled with CD8A's expression, and everything
downstream (tables, exports, hand-built heatmaps) inherits the error.

The row identifiers are now captured immediately after the subset and
assigned back verbatim, so labels always travel with their own data. As
a side effect duplicated entries in `genes` no longer produce a
"length of 'dimnames' not equal to array extent" error, because the
replacement vector is derived from the matrix rather than the argument.

The unsummarised path was never affected and is unchanged.
 
    
  
    

      Package: VISTA

      Commit: 3bf16fed02e5bc0b2ab7e364eddc143d36dc37ff

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 11:49:31 +1000

      Commit message:


	  
		
 Add deprecation and shared-default infrastructure

VISTA has accumulated six argument aliases that change behaviour silently
(show_corr_values, col_corr_values, col_up/col_down/col_others, lab_size,
facet_scale, sample.seed, value_transform). Only use_vista_colors warns.
Nothing prevented the next alias from being just as quiet.

R/deprecation.R adds .vista_deprecate_arg(), .vista_defunct_arg() and
.vista_check_dots(), all driven by a single registry table that records
the deprecated/defunct/removed release for every alias. The registry has
three consumers: the warning helpers read timelines from it so no call
site hardcodes a version, roxygen renders it into ?VISTA-deprecated, and
test-deprecation-registry.R iterates every row asserting the old formal
still exists and still warns. Adding a silent alias now fails CI.

Warnings carry class c("vista_deprecated_arg", "deprecatedWarning"). The
base class matches .Deprecated() so suppressWarnings and Bioconductor
tooling behave as expected; the subclass is what the tests assert on.
They are throttled per session so a deprecated argument inside a loop
cannot emit hundreds of warnings; options(vista.deprecation_frequency =
"always") disables the throttle and the test helper sets it.

.vista_check_dots() generalizes the guard that existed only in
get_pathway_heatmap(), including a did-you-mean suggestion. It is not
wired into any function yet.

R/defaults.R collects the cross-function default values in one place. No
value changes here; this only makes the planned 1.4.0 default
harmonization a single atomic edit instead of ~60 scattered constants.
 
    
  
    

      Package: VISTA

      Commit: c47f2ff38ee3e873ef92725d2d4a00f3197a5dbf

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 10:17:38 +1000

      Commit message:


	  
		
 Merge fix/audit-2026-07: cutoff consistency, consensus p-values, backend filtering

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: VISTA

      Commit: eb3e11269ac17e198dbe2a7f42ab4f0e27d71861

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-07-31 10:15:06 +1000

      Commit message:


	  
		
 Fix cutoff consistency, consensus p-values, and backend filtering

Addresses defects found in a full-package audit of 1.1.0.

get_volcano_plot() hard-coded the raw pvalue column at a fixed 0.05
cutoff, so it coloured a different gene set than deg_summary(),
get_deg_count_barplot(), and get_genes_by_regulation() reported for the
same object (69/59 vs 76/71 Up/Down on a 3000-gene airway subset). It
now inherits log2fc_cutoff, pval_cutoff, and a new p_value_type argument
from cutoffs(x), and labels the y-axis accordingly. Explicit arguments
still override, so p_value_type = "pvalue" restores the old behaviour.

Consensus tables built with method = "both" overwrote pvalue and padj
with exactly 1 for every gene not called by both backends -- 95.1% of
genes on the same subset -- collapsing consensus volcano/MA plots. Each
gene now carries the less-significant of the two backend values. DEG
calls are unchanged; per-backend columns were already preserved.

The edgeR and limma backends ignored min_counts when filtering and used
a hard-coded cpm > 1, so identical arguments produced different feature
sets per backend. They now share the DESeq2 predicate and filter before
calcNormFactors(), per the edgeR user's guide. The benchmark harness
mirrors both changes, and benchmark_vista_equivalence() still reports
exact agreement with matched standalone runs.

Also fixes get_ma_plot()'s threshold fallback, which read the
non-existent metadata(x)$cutoffs key; corrects the min_replicates docs
(it counts samples experiment-wide, never per group); removes a README
reference to the non-existent get_enrichment_network(); drops duplicate
definitions of .prepare_sample_metadata()/.filter_genes() that collation
order was silently resolving; and deletes six unreachable helpers whose
generated man pages were still shipping.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: ZarrArray

      Commit: 6248f3d9f4241b93eef86234ead999b3ccb3f62c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-08-04 18:49:17 -0700

      Commit message:


	  
		
 ZarrArray 1.1.5: Implement group() method for ZarrSparseMatrixSeed objects
 
    
  
    

      Package: ZarrArray

      Commit: 0a525033f99a42b16cbf9741c43534439c5ae80b

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-07-21 10:16:49 -0700

      Commit message:


	  
		
 Bump version to 1.1.4
 
    
  
    

      Package: EMTscore

      Commit: 66ca8aebe6cfdea9e287c9751594618ade19c4a8

      Author:  wenmm <hudie.luoluo@gmail.com> 

      Date: 2026-08-04 16:30:00 -0500

      Commit message:


	  
		
 Bump to 0.99.10: final review fixes (message wording, vignette assignments)

Addresses the two remaining items from the Bioconductor review:

o R/Pathway_score_correlation.R: the cor.test() error handler now reports
  "Invalid correlation for ..." instead of "Error in correlation for ...",
  clearing the BiocCheck note about redundant 'stop'/'warn*' wording in signal
  conditions (as suggested in the review diff).
o vignettes/EMTscore.Rmd: use <- for the two remaining top-level assignments
  (colors, line 267; emt_names, line 342), clearing the lintr
  assignment_linter output. Named function arguments keep =.

No functional changes.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
 
    
  
    

      Package: rhdf5

      Commit: 45ee7bdb3227bc364fffebf735876849a513a961

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-03 16:36:47 +0200

      Commit message:


	  
		
 Bump version
 
    
  
    

      Package: rhdf5

      Commit: 761690770fea499ffcbafb0e3683950fe543a440

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-03 16:36:04 +0200

      Commit message:


	  
		
 Document XLENGTH fix
 
    
  
    

      Package: rhdf5

      Commit: 604361639b540d8c6e9b36e347cd3c4db1273b80

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-03 16:34:38 +0200

      Commit message:


	  
		
 Use XLENGTH() where relevant
 
    
  
    

      Package: rhdf5

      Commit: c545e27ee65b94428c111fae91f9e6b65c9e6323

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-03 15:55:32 +0200

      Commit message:


	  
		
 Document changes in C code
 
    
  
    

      Package: rhdf5

      Commit: d594fe906b1d9f7f495537256ce401e85c368b55

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-03 10:50:24 +0200

      Commit message:


	  
		
 Print ssize_t with zd
 
    
  
    

      Package: rhdf5

      Commit: 2a07e9b4e895b51bdf23b978457083e590abcc96

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-29 23:51:50 +0200

      Commit message:


	  
		
 Fix typo
 
    
  
    

      Package: rhdf5

      Commit: 8b3f917582b8c250be6e651a85f0500c5f99e41e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-29 23:44:28 +0200

      Commit message:


	  
		
 Use bool rather than int where possible
 
    
  
    

      Package: rhdf5

      Commit: 88da2b1486343085f7807c59fabd732247b7f9fc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-28 09:37:55 +0200

      Commit message:


	  
		
 Remove if/else from loop
 
    
  
    

      Package: rhdf5

      Commit: 22d050e546f3ea7213a5629694cc4ce14163487e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-28 08:55:15 +0200

      Commit message:


	  
		
 Fix rchk
 
    
  
    

      Package: rhdf5

      Commit: 0b9abd4523507fa20df48bef41c0171d90d6173a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-28 08:53:58 +0200

      Commit message:


	  
		
 Use dev lintr
 
    
  
    

      Package: rhdf5

      Commit: 1832f0ab70805fbddef11233e66fda57c559d0f0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 20:25:17 +0200

      Commit message:


	  
		
 Simplify NA_character_ setting
 
    
  
    

      Package: rhdf5

      Commit: 16db9dcc51fd9ab7b761e70f2252a5655b336284

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 20:24:52 +0200

      Commit message:


	  
		
 Avoid unnecessary conversions
 
    
  
    

      Package: rhdf5

      Commit: 54d83da0bd7cedd5a9879c811e9b8fc8df405afa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 20:09:53 +0200

      Commit message:


	  
		
 Run - 1L on shorter vector
 
    
  
    

      Package: rhdf5

      Commit: cf9b5b3288370c2489bfa42f36d039746b4daf82

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 20:02:29 +0200

      Commit message:


	  
		
 Fix linter and compiler warnings
 
    
  
    

      Package: rhdf5

      Commit: f40ecd63367936d942d41680dc39d07cb07cbc47

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 17:36:10 +0200

      Commit message:


	  
		
 Remove unnecessary non zero check
 
    
  
    

      Package: rhdf5

      Commit: 3cd46b2abc3eb706c950a65799972e8bbe120742

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 17:32:40 +0200

      Commit message:


	  
		
 Avoid redeclaring functions in .c file
 
    
  
    

      Package: rhdf5

      Commit: 73234b599696fca0b2aa6547840a81d1d320762d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 17:30:18 +0200

      Commit message:


	  
		
 Rewrite read_string_datatype with memset() and memcpy()
 
    
  
    

      Package: rhdf5

      Commit: a7e91347025d544ff11c0d8ead570f14386d7447

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 17:12:46 +0200

      Commit message:


	  
		
 Do not redefine a new var just for casting
 
    
  
    

      Package: rhdf5

      Commit: 97ea4579b1d5a7f78780dff4e45495cadd445533

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 17:12:29 +0200

      Commit message:


	  
		
 Use INT_MAX instead of magic number
 
    
  
    

      Package: rhdf5

      Commit: 6b958117edff88360a13d51a16daf7ff89410863

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 16:47:59 +0200

      Commit message:


	  
		
 Factor out code shared between if/else branches
 
    
  
    

      Package: rhdf5

      Commit: dfd1c736a5629628f1374832f5c74b717262eb7c

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 15:09:39 +0200

      Commit message:


	  
		
 Use && and || where possible
 
    
  
    

      Package: rhdf5

      Commit: 6c80ef6a3b147020658887cf2984dceb8a1895a3

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 14:13:40 +0200

      Commit message:


	  
		
 Use R_BlankString where appropriate
 
    
  
    

      Package: rhdf5

      Commit: b327b5e4a0ee21f1f424d8df5b78390bccd5dffb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 11:35:04 +0200

      Commit message:


	  
		
 Avoid unnecessary coercing to int in ENUM
 
    
  
    

      Package: rhdf5

      Commit: abbfaa21c0e3cd2a7a58ce3417e4c5ea525c2198

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 11:29:35 +0200

      Commit message:


	  
		
 Use memcpy() when relevant
 
    
  
    

      Package: rhdf5

      Commit: 6ef1b9a9a605e13e4e863defc38441f54303b7b9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 11:26:08 +0200

      Commit message:


	  
		
 Avoid allocVector() for scalars
 
    
  
    

      Package: rhdf5

      Commit: 3ef86e0225d0713aaafebf2815e81710eadf9bb0

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-07-27 11:25:27 +0200

      Commit message:


	  
		
 Use mkNamed() where possible
 
    
  
    

      Package: rhdf5

      Commit: 42200cf08868c60c3d0331505ef6639f61ccff24

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-08-01 09:52:12 +0200

      Commit message:


	  
		
 Run autoreconf
 
    
  
    

      Package: alabaster.matrix

      Commit: 250d6159795464b9493d99208dee8fc665dc443e

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-08-05 00:34:19 +1000

      Commit message:


	  
		
 Directly save HDF5-backed arrays without using the DelayedArray method.

This avoids generated unnecessary delayed_array-related files, which don't do
anything as all of the data ends up in the seed anyway.
 
    
  
    

      Package: lcmsPlot

      Commit: 8a8f3efdc1343b0f15c37076e582e1159c10dac9

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-08-04 14:36:31 +0100

      Commit message:


	  
		
 fix: lp_peak_density(simulate = TRUE)
 
    
  
    

      Package: mia

      Commit: 0daba061aadba5a000c79551e8c51fd004e19824

      Author:  Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

      Date: 2026-08-04 16:26:37 +0300

      Commit message:


	  
		
 Add unit tests for RPCA (#841) 
    
  
    

      Package: geneslator

      Commit: 617c6060cb00824f6d23d81f5b0deb03d4bdabab

      Author:  GMicale <gmgmicky@gmail.com> 

      Date: 2026-08-04 13:11:35 +0200

      Commit message:


	  
		
 Version 0.99.8, added check gene symbol, updated README
 
    
  
    

      Package: gDRcore

      Commit: bdf82647546e327a79629555fc63d2925b974c33

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-08-04 12:15:15 +0200

      Commit message:


	  
		
 Merge pull request #200 from gdrplatform/GDR-3484

fix: remove checkerboard artifact on combo single-agent arms 
    
  
    

      Package: gDRcore

      Commit: 4816344419d710aea3fe2acdfcd13cde612896a8

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-07-31 12:14:44 +0200

      Commit message:


	  
		
 fix: guard NA in arm subscripts and shorten NEWS line
 
    
  
    

      Package: gDRcore

      Commit: 07e53b05804eaddc96d335fe0bde8fabd084b4fc

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-07-20 15:06:53 +0200

      Commit message:


	  
		
 fix: remove checkerboard artifact on combo single-agent arms
 
    
  
    

      Package: HDF5Array

      Commit: 66a898c96681fe549d4b9591f98e44d137dc12e4

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-08-04 02:26:51 -0700

      Commit message:


	  
		
 Implement group() method for HDF5ArraySeed objects
 
    
  
    

      Package: MatrixQCvis

      Commit: d305b3c3d441a16f4ff082350f98d84956e7ec9d

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2026-08-04 11:21:59 +0200

      Commit message:


	  
		
 bump version to 1.21.1
 
    
  
    

      Package: MatrixQCvis

      Commit: f26c0dbc4c3a9c4a824927bde875f16f855466d0

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2026-08-04 11:19:46 +0200

      Commit message:


	  
		
 bug fix: add namespace to shiny::testServer
 
    
  
    

      Package: MatrixQCvis

      Commit: 423587791a411a8e3dbd3375d78511074050cac3

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2026-08-04 10:10:55 +0200

      Commit message:


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

      Package: MatrixQCvis

      Commit: 2cac72306f5ec83315edcfa6d7003da58ceccd49

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2026-02-13 15:19:28 +0100

      Commit message:


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

      Package: MatrixQCvis

      Commit: 75f7e0e625177449e20c770d92cefde5bce99585

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2025-06-26 17:09:32 +0200

      Commit message:


	  
		
 update check-bioc
 
    
  
    

      Package: HDF5Array

      Commit: 8cd8d37161c27547db9c4110c0e3c8732cb2e5ed

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-08-04 02:04:13 -0700

      Commit message:


	  
		
 HDF5Array 1.41.1: Implement group() method for H5SparseMatrixSeed objects
 
    
  
    

      Package: DelayedArray

      Commit: ec741b7f836da0197e9ef8ec73fa10f1be7260ce

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-08-04 02:00:29 -0700

      Commit message:


	  
		
 DelayedArray 0.39.4: Implement group() method for DelayedOp objects
 
    
  
    

      Package: rprimer

      Commit: f1615e1f6f374acc34246051cf670ec6eb9de68d

      Author:  Sofia Persson <anna.sofia.persson@slu.se> 

      Date: 2026-08-04 10:24:49 +0200

      Commit message:


	  
		
 Update version references in README and vignette
 
    
  
    

      Package: rprimer

      Commit: b7b6ebdc83264a5f12a22bac8a664c8e44bf8ff4

      Author:  Sofia Persson <anna.sofia.persson@slu.se> 

      Date: 2026-08-04 10:19:03 +0200

      Commit message:


	  
		
 Roxygenize package, fix CITATION and DESCRIPTION issues

- Add descriptions to @describeIn tags for S4 methods
- Regenerate documentation with roxygen2 8.0.0
- Modernize CITATION (bibentry, ASCII, doi)
- Remove non-standard biocType field
- Bump version to 1.17.2
 
    
  
    

      Package: BiocGenerics

      Commit: ab1ed78aa824420480afa1fa329df844d41f6dab

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-08-04 01:09:40 -0700

      Commit message:


	  
		
 small edit to man page of new group() function
 
    
  
  


</div>

</div>