HDF5Array 1.35.9

Some refactoring of inst/scripts/make_timings_table.R
 

 add revised normalization & PCA timings for kjohnson3
 

 some improvements to inst/scripts/run_benchmarks.sh and associated scripts
 

 bumped version,  updated plotP
 

 Merge pull request #141 from ncborcherding/dev

v2.2.3 

 grouping handling

#139 Fixed how data is split and handled during escape calculation
 

 hexbin installed
 

 fix testthat
 

 testthat pass
 

 import Matrix t()

#132 fix issue with t.default() error
 

 v2.2.1
 

 Merge pull request #122 from ncborcherding/master

update pull request for dev branch 

 Merge pull request #112 from kew24/master

update GSVA function with new name 

 update GSVA function with new name 

 Merge branch 'master' of https://github.com/calebclass/NanoTube
 

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

 Merge pull request #6 from calebclass/devel

Devel 

 Chore: Package-wide man page2
 

 version bump 1.33.8
 

 version bump 

 fixed BiocCheck warning
 

 add checks for j, ... arguments in `[[` MAE method
 

 Fix plotting based on FDR
 

 add deployment configuration for shinyapps.io
 

 version bump 1.7.3
 

 get ready for 2.0.0
 

 Merge pull request #171 from MangiolaLaboratory/fix-cmdstanr-depedency-2

change the way I check package 

 change the way I check package
 

 fix CHECK ERRORS
 

 add check if the acgumwnt have factors that did not exist in the original data
 

 keep factor ordering
 

 add cartoon
 

 update README and Vignettes
 

 no need to remove this c==1 because it is an effect too. Also otherwise if C is size 2 it gives error
 

 fix test for random effects if there is no contrasts
 

 Merge pull request #162 from MangiolaLaboratory/fixes-for-HCA

Fixes for hca 

 fix contrast of kind (...) /2
 

 add commented resaving of the fit for portability, it takes too much memory for big models.
 

 add LICENSE
 

 regularise the last component
 

 some updates and fixes
 

 fix contrast of kind (...) /2
 

 add commented resaving of the fit for portability, it takes too much memory for big models.
 

 pull

Merge branch 'fixes-for-HCA' of github.com:stemangiola/sccomp into fixes-for-HCA

# Conflicts:
#	LICENSE
 

 add license
 

 Merge branch 'boxplot-with-removed-effects' of https://github.com/MangiolaLaboratory/sccomp into boxplot-with-removed-effects
 

 add parameter, tests and docs
 

 some updates and fixes
 

 fix CHECKs
 

 add parameter, tests and docs
 

 Create LICENSE 

 Merge branch 'master' of github.com:stemangiola/sccomp
 

 Merge pull request #161 from MangiolaLaboratory/deprecate-RUV-terminology

version UP 

 Merge branch 'master' into deprecate-RUV-terminology 

 version UP
 

 make test one core
 

 skip colouring
 

 Merge with bioconductor
 

 Update ATAC-seq path
 

 Fixed a typo in query.Rmd

Typo was found in line 182: "#Only seelct the first 5 patients"

Was changed to "#Only select the first 5 patients" 

 version bump 1.19.8
 

 install node
 

 version bump 

 refactor(getSubnetworkFromIndra): Create separate helper function to get correlation matrix (#34)

* refactor(getSubnetworkFromIndra): Create separate helper function to get correlation matrix
 

 feat(getSubnetworkFromIndra): Add correlation metrics into INDRA results (#32)

* feat(getSubnetworkFromIndra): Add correlation metrics into INDRA results
 

 feat(getSubnetworkFromIndra): Add additional filters (#30)

Add statement type, paper count, and evidence count filters 

 fix(getSubnetworkFromIndra): Fix bugs related to multiple matches for an HGNC ID (#28)

* fix(getSubnetworkFromIndra): Fix bugs related to multiple matches for an HGNC ID
 

 refactor: Make changes from feedback from HUPO (#26)

* layout(visualizeNetworks): Set up cose layout for network viz

* refactor(getSubnetworkFromIndra): Add input validation

* fix visualizeNetwork tests

* Add validation tests for hgncID column being missing 

 Deprecate
 - unresponsive
 

 Improve specificity of detection of missense mutations in `TFinfluence` (#134)

* Fix mutation_available column

* run tests, update NEWS, DESCRIPTION

* switch to rasp as default in TFinfluence

* Correct MAF filtering

---------

Co-authored-by: Anna Melidi <your@email.com>
Co-authored-by: Matteo Tiberti <matteo.tiberti@gmail.com> 

 Fix mutation_available column (#130)

* Fix mutation_available column

* run tests, update NEWS, DESCRIPTION

---------

Co-authored-by: Anna Melidi <your@email.com> 

 added variable legend.position
 

 small bug fix in calcCrossMetricPerFov
 

 removed automatic creation of ID variable - adjusted examples
 

 fix bug in by variable
 

 tests: complete unit test coverage
 

 Updated version that uses Bioconductor MultiAssayExperiment infrastructure
 

 Merge remote-tracking branch 'origin' into devel
 

 Update non-code docs

Wrote NEWS, updated links in DESCRIPTION and README, some formatting, 
spelling and clarification in vignette and README.
 

 Merge pull request #6 from MetaboComp/fix-build-bug

Export S4 generics 

 edgeR 4.5.2
- Updating citation for Chen et al (NAR 2025).
 

 version number bump
 

 add -lz to Makevars.win
 

 Repair package on Windows after PR #2 broke it

This commit fixes the linking error on Windows (undefined references
to 'gzopen', 'gzread', and 'gzclose'). See full error output at:
https://bioconductor.org/checkResults/3.21/bioc-LATEST/affyPLM/palomino7-install.html
 

 remove prerequisites element from response
 

 GenomeInfoDb 1.43.4

Register 3 genome assemblies for Gadus morhua (Atlantic cod):

- GadMor_May2010 (NCBI): https://www.ncbi.nlm.nih.gov/assembly/311358/

- gadMor1 (UCSC, same as GadMor_May2010 but uses UCSC-style chromosome
  names): https://genome.ucsc.edu/cgi-bin/hgGateway?db=gadMor1

- gadMor3.0 (NCBI):
  https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_902167405.1/
 

 version bump 1.17.4
 

 Fix package anchors
 

 remove pkgdown.yaml in devel
 

 Updated all the functions previously dependent on the SurvMetrics package to remove the dependency on SurvMetrics, Resolved issues with the NAMESPACE file, updated NEWS.md and DESCRIPTION file, version bump to 0.99.5
 

 Delete inst/NEWS.Rd 

 Add files via upload 

 Add files via upload 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Update DESCRIPTION 

 Update DESCRIPTION 

 version bumpt
 

 Chore: Reduce time testing and examples
 

 More robust path comparisons in the tests to pass CHECK on other platforms.
 

 bug fix in POMA and plot_boxplots
 

 BiocCheck
 

 bug fix
 

 new utility: get_ag_summary, documentation and bump
 

 interface to infomap GCD
 

 bump
 

 1.15.141  `fit_limma`  drop args `ftest` and `plot` from doc (check)
 

 1.15.139  Add ggtext to Suggests (check warning)
 

 1.15.137  `which.medoid`  use simple centroid when spatial median fails
 

 1.15.135  Drop `default_coefs`. Use `coefs` instead.
 

 1.15.133  `fit_xxx`  `PF~global~limma` (instead of `p~F~limma`)
 

 1.15.131  `fit`_limma`  pass `coefs` to plotting functions
 

 1.15.129  `fit_lmer`  record `t~Fsubgroup` and `p~Fsubgroup`
 

 1.15.127  `fit_lm`  record `t~Fsubgroup` and `p~Fsubgroup`
 

 1.15.125  `fit_limma`  : `t~F~limma` (new!)
 

 1.15.123  `fit_limma`  contrast_coefs (not model_coefs) to ensure meaningful F
 

 1.15.120  Accomodate `coefs` hardcoding in examples
 

 1.15.118  `fit_wilcoxon`  hardcode `coefs`
 

 1.15.116 `fit_lme` : hardcode `coefs` and `ftest`
 

 1.15.114 `fit_lmx` : hardcode `coefs` and `ftest`. Use pF (not p) for ftest pvalue.
 

 1.15.112  `fit_linmod`  softcode `volcanoargs$coefs` and `exprargs$coefs`
 

 1.15.110  `fit_survival` Softcode plot (width|height)
 

 1.15.108  `plot_survival` flag dropouts
 

 1.15.106  `fit_survival` run survdiff and coxph (in that order)
 

 1.15.104  `plot_survival`  unclash labels
 

 Marked Windows as unsupported
 

 change Free to free in c code
 

 Fix getChromInfoFromNCBI("panpan1.1")

On January 9, 2025, someone added a duplicated MT entry to the "Full
sequence report" for the GCF_000258655.2 assembly (panpan1.1), which
broke getChromInfoFromNCBI("panpan1.1").

getChromInfoFromNCBI() now removes this new MT entry (GenBank accession
KT153251.1) and keeps the original one (RefSeq accession NC_001644.1).
The latter is more useful because it matches chrM in UCSC genome
panPan2 (panPan2 is based on panpan1.1).
 

 Merge remote-tracking branch 'bioc/devel'
 

 added required packages & bump ver
 

 require protein in real_se & updated manual
 

 use all input samples when sampleids is not provided
 

 add a threads option to colPermIPL
 

 make sure pltmat and cldt have brc in the same order
 

 add rna_n_sd option to ppRealInp
 

 add a function to setup PARADIGM run
 

 add an option to add runPrd output file tag
 

 add an option to add runPrd output file tag
 

 add an option to add runPrd output file tag
 

 add n_sd option to def RNA state; increase default n_perms from 3 to 100
 

 incr scaling dummy for fitting very small numbers
 

 add doc on CN meaning
 

 add doc on input CN matrix
 

 increase default n_random_runs
 

 added a getSignifOvrOnCl func
 

 use as_edgelist instead of get.edgelist for igraph 2.0
 

 correct examples
 

 del trailing space
 

 add func to plot ovr heatmap
 

 refactor: sort vector
 

 test: add unit tests
 

 Chore: Version Bump2
 

 bump version
 

 Merge pull request #23 from ccb-hms/devel

merge devel 

 Merge pull request #66 from ahl27/master

fix: minor bug 

 Merge pull request #65 from ahl27/master

feat: multiple clustering support for ExoLabel 

 add examples to man page
 

 adds multiple clustering support
 

 Fixed missing package: BiocStyle
 

 Fixed missing package: BiocStyle
 

 version bump 1.33.6
 

 rename longFormat to longForm in vignettes
 

 use r-devel for test-coverage.yml
 

 set actions/cache to v4
 

 export longFormat generic
 

 update NEWS.md
 

 update script to re-write ref version line
 

 version bump 1.19.6
 

 bump version to 1.7.1
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update test_function_calculateMetrics_from_Spectra.R
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Change vignette to use default host in useMart. Bumping version number.
 

 doc: update docs
 

 Merge pull request #142 from gdrplatform/GDR-2798

Gdr 2798 

 build: trigger build
 

 refactor: change default regexes for separator and batch substring
 

 chore: add more examples
 

 chore: change 'v' param to 'drug_vec'
 

 Update R/utils.R

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

 Update R/utils.R

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

 doc: docs fixes
 

 chore: update tests
 

 feat: evaluate three function for gnumber batches removal
 

 Fixed citation
 

 GenomeInfoDb 1.43.3

Repair unit test broken (again) by yet another change to NCBI MonDom5
assembly. This time someone sneakily removed 3900 sequences from the
assembly, and of course, like last time, the RefSeq accession, GenBank
accession, and Date were not changed on the assembly page at
https://www.ncbi.nlm.nih.gov/assembly/237648/
Looks like the goal is to be as opaque as possible with these changes.
Interesting approach to data management!
 

 Updates the workflow
 

 BSgenome 1.75.1

Formally deprecate BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg.
All these functions are now defined in the BSgenomeForge package.
 

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

 Merge pull request #38 from sneumann/feature/pkgdown

Feature/pkgdown 

 HDF5Array 1.35.8

Now depends on new h5mread package.
 

 Start using pkgdown for web documentation
 

 Start adding NIST isotope values provided by Roberto Canteri
 

 Pass sample_id to constructor in readCosMX, closing #61
 

  bumped version fro, 1.29.0 to 1.30.0
 

 v 3.19.3
 

 version 3.21.1
 

 removed contraint (max = 3)
on nb of plotly tool_tips variables (`pDataForAdditionalLabelling`)
 

 0.99.16
 

 0.99.14
 

 0.99.14
 

 0.99.14
 

 update to version 0.2.1
 

 Merged with bioconductor
 

 transfer daisybio
 

 Update README.md 

 page updated
 

 documentation updated seealso tag
 

 resolved conflict
 

 chore: update notes.json
 

 ignore Rproj
 

 Man pages
 

 Add package references for external links
 

 Introduced array.dedup.* arguments to deduplicate all arrays.

This extends the deduplication machinery from DelayedArray seeds to all arrays
that pass through alabaster.matrix's saveObject methods. The aim is to allow
deduplication of arrays outside of DelayedArrays, e.g., if a SE contains a
non-delayed array and a DelayedArray wrapping the first array, we can now
deduplicate the seed in the latter when a dedup session is supplied for the SE.

This change involves migrating many of the deduplication functions over to
alabaster.base for more general use. We also add a DelayedArray.force.external=
argument to make it easier to deduplicate DelayedArray seeds.
 

 Substitued std::binary_function which has been removed with c++17
 

 bumped version, updated citation, updated plotP
 

 Merge pull request #84 from fmicompbio/fix-legend-order

Ensure heatmap bin legend is ordered in the same way as the heatmap columns 

 Make sure heatmap bin legend is ordered in the same way as the heatmap columns.

Closes #83
 

 update documentation.
 

 Version bumped
 

 Hopefully fix adjacency tests
 

 Version bumped
 

 Version bumped
 

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

 Version number changed
 

 Defined R_NO_REMAP for build. Changed aliased functions to their Rf_*
versions.
 

 Added utilities for deduplicating objects within saveObject.

Most of this was migrated was alabaster.matrix and generalized for use outside
of DelayedArrays. The idea is that a saveObject method developer can check if
their object was already saved during a user-defined "deduplication session".
If so, they can just copy/link/symlink from the existing on-disk representation
instead of re-saving the object, reducing compute time and storage costs.

Also added a utility to get an absolute path without requiring normalization,
as the latter could resolve symlinks that a user might want to preserve.
 

 update example avoid httr2 suggests
 

 add .DS_Store
 

 label all code chunks in "HDF5Array performance" vignette
 

 Added listPaths to discover availble paths in a dataset version.

This allows us to throw a less cryptic error when someone calls fetchDataset
without a path= argument when it is required for a given dataset.
 

 Added more elaborate search examples with gsc().
 

 Updated NEWS.md
 

 Updated NEWS.md and bumped-up version in DESCRIPTION

Fixed typo
 

 Improved `"AdvancedGDIUniformityCheck"` (#97)

Now it also includes the same check about 99% quantile as the
`"SimpleGDIUniformityCheck"`

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

 Clean parameters for `proceedToCoex()` (#95)

Added possibility to specify `clean()` thresholds in the functions
`proceedToCoex()` and `automaticCOTANObjectCreation()` 

 corrected error in example
 

 add back DESCRIPTION after rebase from bioc
 

 DelayedArray 0.33.4

Small tweak to DelayedArray() method for DelayedOp objects.

Fix https://github.com/Bioconductor/DelayedArray/issues/121
 

 fix CPP11 issue
 

 bug fix
 

 bug fix