bumped the package version v1.3.3
 

 Update github action
 

 bumped version
 

 `plot_dms_heatmap()`
- added function and Rd
- used function in vignette
 

 adds `feature_info` data.frame to result from eigenWeightedMean
 

 add dog to species_info
 

 Add documentation to remove y label.
 

 Update myRank and test
 

 Simplify, handle errors passing genome
 

 Merge
 

 Fix a few things.
 

 Remove the dedicated path() method for ReloadedArrays.

The method for DelayedArrays should now call the seed method directly.
 

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

 Update flag_overlap.R 

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

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

 Update extract.probe.regions.Rd 

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

 Update extract.probe.regions.Rd 

 Update DESCRIPTION 

 Update extract.probe.regions.Rd 

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

 Update calc.probe.coords.Rd 

 Update DESCRIPTION 

 bumped to 0.99.7
 

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

 Update flag.overlap.Rd 

 Update check.for.cc.switch.Rd 

 Update check.for.cc.switch.Rd 

 Update DESCRIPTION 

 Update extract.probe.regions.Rd 

 Update calc.probe.coords.Rd 

 Update check.for.cc.switch.Rd 

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

 Update identifying_probe_SNPs_introduction.Rmd 

 Update DESCRIPTION 

 Merge branch 'devel' of https://github.com/pachterlab/voyager into devel
 

 replaced `is` with `inherits`
 

 Update DESCRIPTION 

 Update extract_probe_regions.R 

 Update extract.probe.regions.Rd 

 Update calc.probe.coords.Rd 

 Update manifest_anno_object.Rd 

 Update CpG_probe_bed.Rd 

 Update CpG_SNP_intersection.Rd 

 Update manifest_anno_object.Rd 

 Update extract.probe.regions.Rd 

 Update calc.probe.coords.Rd 

 Update CpG_probe_bed.Rd 

 Update CpG_SNP_intersection.Rd 

 version bump up
 

 add RUnit to Suggests
 

 fix warnings
 

 Release 1.3.3
 

 bump to 1.3.2
 

 fixed NEWS.md so it shows up on website
 

 added hexsticker to readme
 

 devtools::document
 

 version bump
 

 replace sapply with vapply
 

 adapt plot_ORA to restructured ORA_hypergeometric
 

 color coding inside plot_ORA instead of ORA_hypergeometric
 

 bug fix
 

 re-structured get_ORA_annotations + adding Sys.sleep to avoid KEGG API errors
 

 re-structrue fit_dynamics_model()
 

 Merge branch 'devel' of github.com:KatjaDanielzik/MetaboDynamics into devel
 

 Update README.md 

 Update CITATION.cff 

 bug fix
 

 style changes
 

 shorter examples
 

 re-structured estimates_dynamics and added tests
 

 Update authors
 

 Fix missing meme_path and verbose argument
 

 Update examples
 

 use pre-calc tree for sorting taxa
 

 update cutadapt: add --minimum-length
 

 remove extdata
 

 - crissCrossValidate works with AUC performance metric.
 

 doc: version bump
 

 feat: add try catch for charge
 

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

 Deprecate WrapperArraySeed in favor of DelayedUnaryIsoOp.

Now ReloadedArraySeed directly inherits from DelayedUnaryIsoOp, which already
implements all of the trivial methods that forward the operation to the seed.

The only operation that isn't supported is the dedicated coercion methods from
to dgCMatrix. Turns out it wasn't that useful anyway, because there is no
longer a dedicated fast path from CSC_H5SparseMatrixSeeds to dgCMatrix.
 

 Improvements for phylogenetics

 Changes to be committed:
	modified:   DESCRIPTION
	modified:   R/AlignSeqs.R
	modified:   R/Clusterize.R
	modified:   R/DistanceMatrix.R
	modified:   R/FindSynteny.R
	modified:   R/StaggerAlignment.R
	modified:   R/Taxa-class.R
	modified:   R/TreeLine.R
	modified:   man/AlignPairs.Rd
	modified:   man/DistanceMatrix.Rd
	modified:   man/Genes-class.Rd
	modified:   man/MODELS.Rd
	modified:   man/TreeLine.Rd
	modified:   src/ClusterML.c
	modified:   src/DECIPHER.h
	modified:   src/DistanceMatrix.c
	modified:   src/PairwiseAlignment.c
	modified:   src/R_init_decipher.c
	modified:   vignettes/ClassifySequences.Rnw
	modified:   vignettes/DesignPrimers.Rnw
	modified:   vignettes/DesignProbes.Rnw
	modified:   vignettes/FindingNonCodingRNAs.Rnw
	modified:   vignettes/GrowingTrees.Rnw
	new file:   vignettes/NucleotideModels.pdf
	modified:   vignettes/RepeatRepeat.Rnw
 

 version bump
 

 code styling
 

 restructure compare_metabolites
 

 input check for triplicate measurements
 

 input check for triplicate data
 

 remove cat()
 

 `simplify()` keeps the most informative term if there exist multiple terms that meets the criteria (2024-11-29, Fri, #744 )
 

 update
 

 update citation
 

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

 update readme
 

 v. 0.99.4 bumped version
 

 Dear reviewer,

We think we have followed most of your recommendations to fit best practices as possible. We hope we will satisfy bioconductor expectations now.
We try to resume what we have done in the next part of the text to help the reviewing process.
Thanks for your advice.
Kind regards.

BulkSignalR
We now consider interoperability with the Bioconductor matrix-type classes. Counts can be extracted from SpatialExperiment or SummarizedExperiment depending on the workflow in the input integration (see prepareDataset function in dataPrepare.R)
S4 generics have now explicit list of arguments. (Signature parameter added)
All examples are now runnable and NOT wrapped in if (FALSE). This has been a huge improvement in fact and a lot of work to make it work in a reasonable amount of time (R CMD check)..
Description
We changed rappdirs  to tools::R_user_dir("BulkSignalR", which="cache")
Namespace
We considered using more descriptive names (colA/B is now colClusterA/B …e.g., cmpName is comparisonName, etc). We removed unexplicit shortcut names and tried to give better definitions for function names as suggested.
We have considered the removal of Biobase::testBiocCConnection and we now use  curl::has_internet() function.
Vignettes
We Include package: BulkSignalR in the YAML front matter and remove the package version note in the Load packages section.
We removed any commented code from the vignette (BulkSignalR-Differential.Rmd)
We now only use one worker for the vignette.
We do not use static images anymore in the vignette. We use evaluated code to generate plots.
We rewrite the spatial workflow and now show a use case starting with a spatial experiment object from STexampleData and we mention VisiumIO.
We removed png and dev.off calls from the vignette and use only the functions in our package. We do not use static images anymore.
R
We do not use print in the example code for getComplexes
We avoid using get.
As mentioned before, we do not use if (FALSE) in examples anymore. BSRClusterComp-class.R).
We use more descriptive slot names for the BSRClusterComp class.
We now avoid conditionally defining generics and use setGeneric directly.
We use your own accessor and setter functions in learnParameters rather than obj@SLOT.
.getEmpiricalNull internal code is more user friendly and do not require extensive call to names that are present in obj@param extensive
For the allocate and fill method, we now create a list of finite length, e.g., in BSRDataModel-class.R: use vector("list", length(ligands(sig))) instead of vapply(x, length, integer(1))
We change the use of  as.BSRDataModelComp to the as method (SetAs) for S4 classes.

We did not avoid using a method to create a class and keep our approach in (defineClusterComp,BSRDataModelComp-method for creating a BSRClusterComp class; intialInference,BSRDataModelComp-method) but we are open on this point for discussion if it’s a real problem to do as we did.
We still want to keep the graphing functionality in the package.
We did not change the assign calls in the .onLoad function because it’s the only way we found to create env variables, in order to potentially modify them in another script outside BulkSignalR and pass them to another package we develop that will work with S4 classes from BulkSignalR .Very sincerely this is for me the most blocking point for everything you ask. These variables should be able to be called outside the library, be modified by the user, and these modifications should be taken into account in another dependent package we are developing.
We removed verbose package startup messages in .onAttach.
Tests
We set up the framework for unit testing with testthat for further development later. We have made a real effort to make examples runnable and also to execute the functions in the vignette in an acceptable time. We clearly do understand why but we also think that Unit testing should be incorporated in the flow of development and, in my opinion, it makes less sense to include them after.They will be added when bug correction is needed. That said, if it’s mandatory to have a minimum level of coverage, we will do it but we expect your leniency on this point : )

We tested the package under R Under development (unstable) (2024-11-03 r87286) with Bioc21. Rdevel CMD build run in 2:30 min and the Rdevel CMD check –no-build-vignettes in almost 10mins. We think this fits a normal behavior.
 

 indention biocheck
 

 change colA,colB,stats,etc...to more verbose and clean function names...no shortcut anymore
 

 Remove the testing for generics.
Still you canno't have two functions named identicaly for two different objects that doesn't inherit from each other.
When there is inheritance it's fine, you only have to declare one setGeneric for the superclass and no generic for the inherited one.
So I now BSRsignature inherits from BSRInference and so you can reuse getGenes and stuffs( because BSRsignature was just adding pathways slot and removing inf.param and LRinter that can be kept to me point of vue.
So that was working well until I found problems with BSRsignatureComp and BSRinferenceComwhich both use getPval method...and other stuffs...
The if FALSE of the doc is the main work to be done
Also add unit testing.
Finally I need to change the functions pointed out by reviewer infParam, colA, colB etc...
 

 We remove all the static images in the vignette.
Now every chunk is run for good in the Main Vignette.
This is runing almost during 2 minutes.
We use data subset and correct some mistakes that make the vignette runs for ages.
(when symbol.col was set, part of code in dataprepare)
We integrate SpatialExperiment. We can deal with that. Interoperability is better.
We can also deal with SummarizedExperiment to extract counts.
Counts pass to dataprepare can be from different classes. See dataprepare.

We have to do the differential-Vignette now.

Try to add signatures in the generic function.
Also symplify without testing for one example, it seems to work.

Reviews are here : https://github.com/Bioconductor/Contributions/issues/3554
What I have done is listed here :
https://docs.google.com/document/d/1HJiLlaTSmPpWt8oMdCc7ksM757VQ-fX8jIAm4jscMN4/edit?usp=sharing

Also we have done :

- Avoid overly verbose package startup messages in .onAttach.
- We add the infrasctucuture for Test.
- Avoid writing files for the user by default (filename argument in
learnParameters,BSRDataModel-method). This is set to NULL
- If finally removed the old way to print the figures in svg / pdf / png. Now you call the functions and user will handle the ouput.
That was a bad behavior we didn't correct.
- We remove png and dev.off calls .
- Rappdirs for package related directory was changed.
- Use of BioBase::testConnection was changed to curl::has_internet()
- One worker was set for the vignette.

Note : I d like to correct the way learnparameters print the pdf in order to include in the output in the vignette.

There is plenty of little things easier to do...

The big next step is to test the doc again (remove FALSE) without taking ages...
 

 change to curl::has_internet the old function and change rappdirs to tools::user_dir
 

 Update R file
 

 Update .Rmd files
 

 fix_bug_20241129
 

 update examples/tests
 

 change examples to speed up package building
 

 bug fix; render correct pbMDS() legend titles
 

 TF influence function (#120)

* added loadMAVISp function

* added function documentation and return

* added dataTRRUST data file

* changes for correct documentation

* removed print statement

* removed extra space

* improved documentation

* specified imports

* added suprresion of vroom warnings when loading data

* suppressed name repair information

* added function for tf consequence

* added man file for loadMAVISp

* updated namespace

* removed trailing spaces

* updated TRRUST column names

* updated imports in description file

* improved data control, removed internal function

* changed code structure

* added condition to choose rasp consensus if no rosetta

* improved documentation for dataMAVISp

* added use of PRA output

* removed potential use of tf expression data

* minor changes to code structure

* removed empty space

* added support for ensemble mode

* improved documentation

* improved regex for column identification

* fixed misspelling of RaSP

* minor changes

* ensemble mode to support different simulations

* added default simulation for ensemble mode

* correction of map function for simple mode

* removed line used in testing

* bump to z version number

* added user specification for stability classification

* added default for stabClassMAVISp

* improved documentation for type of ensemble

* Improved error message for mode

* removed extra check of user input

* improved documentation

* added mavisp example data

* added test file for TFinfluence

* changed variable name

* added small mavisp database

* added test for loadMAVISp

* updated path to mavisp database

* updated vignette with TFinfluence and loadMAVISp

* added small description of TFinfluence

* updated data file to have same object name as in the docs

* reoxygenization of package

* moved csv database to extdata

* added req to DESCRIPTION

* parametrized location of test data

* fixed tests to make them run successfully

* changed examples to be working

* added dataset_info.csv which is essential to parse the database

* version bump following new BioC release

* updated NEWS file

* changed test so that it is more effective

* improved tests for loadMAVISP function

* edits to vignette

* further fixes on vignette

---------

Co-authored-by: Matteo Tiberti <[email protected]> 

 updated news file
 

 Merge pull request #122 from ELELAB/fix121_3.19_release

Fixes version numbering due to Bioconductor 3.19 release 

 Further reduce test time and fix actions (#21)

* Update build-test-deploy.yml

Use R version 4.5

* Update Actions to use Bioc devel

* Fix matrix config

* Reduce test runtime for features

* Run Actions with R 4.4

* Bump cache version

* Install pandoc in actions script 

 20241128_fixbugs
 

 v1.2.0
 

 V1.2.0
 

 V1.2.0
 

 V1.2.0
 

 V1.2.0
 

 V1.2.0
 

 modify
 

 V-1.0.0
 

 V-1.0.0
 

 remove
 

 Add files via upload 

 Delete R/doEnrich.R 

 Add files via upload 

 Fixed code to throw errors when spatial coordinates are missing.
 

 Updated README.md 

 Added tests.
 

 Updated package to untrack system files.
 

 Update DESCRIPTION 

 message
 

 Update extract.probe.regions.Rd 

 Update calc.probe.coords.Rd 

 Update extract_probe_regions.R 

 Update DESCRIPTION 

 here
 

 Update DESCRIPTION 

 Update DESCRIPTION 

 Update check.for.cc.switch.Rd 

 Update identifying_probe_SNPs_introduction.Rmd 

 Update DESCRIPTION 

 Add files via upload 

 Update extract.probe.regions.Rd 

 Update check.for.cc.switch.Rd 

 Create CpG_SNP_intersection.Rd 

 Add files via upload 

 Update DATA_info 

 Update calc.probe.coords.Rd 

 Update flag.overlap.Rd 

 Create manifest_anno_object 

 Add files via upload 

 Update flag.overlap.Rd 

 Update SNP_bed.Rd 

 Update CpG_info.Rd 

 Create SNP_bed.Rd 

 Update calc.probe.coords.Rd 

 Update NAMESPACE 

 fix vignettes 3
 

 fix errors
 

 Fixed DESCRIPTION file
 

 chore: bump version to 2.39.1, update authors and imports
 

 Update data.table dependency
 

 Update NR in metascope_id
 

 Fix check notes
 

 Merge changes
 

 Update blast and reassignment functions (ARO code review)
 

 blast_result_metrics returns vectors
 

 fixed blast_reassignment
 

 removed old files
 

 blast reassignment error handling
 

 .data$species_threshold
 

 documentation
 

 export
 

 Fix blast_Res
 

 update blast output files
 

 Update metascope_blast.R 

 Add new directory
 

 Correct test
 

 Fix roxygen tag
 

 Use new package format
 

 update props.R
 

 one more tweak
 

 fixes for R_NO_REMAP
 

 improve speed cont
 

 fix betaTest
 

 fix single-sample problem and NA handling in detectP vers 2.11.4
 

 update NEWS
 

 Fix bedgraph error due to NA handling in meth.diff export

Fixes #331

Fix the error in `tests/testthat/test-17-bedgraph.r` due to NA handling in `meth.diff` export as log-transformed value.

* **R/bedgraph.R**
  - Disallow transformation of `meth.diff` values in `bedgraph` function for `methylDiff` objects.
  - Add a check to ensure `log.transform` is `FALSE` when `col.name` is `meth.diff`.

* **tests/testthat/test-17-bedgraph.r**
  - Update tests to ensure `log.transform` is not allowed for `meth.diff` values.
  - Add a test to check for error when `log.transform` is `TRUE` for `meth.diff`.
  - Add tests for `methylDiffDB` objects to ensure `log.transform` is not allowed for `meth.diff` values.

* **R/methylDBFunctions.R**
  - Add a check to ensure `log.transform` is `FALSE` when `col.name` is `meth.diff`.
  - Disallow transformation of `meth.diff` values in `bedgraph` function for `methylDiffDB` objects.

---

For more details, open the [Copilot Workspace session](https://copilot-workspace.githubnext.com/al2na/methylKit/issues/331?shareId=XXXX-XXXX-XXXX-XXXX). 

 1.17.1  loosolab -> bhagwataditya
 

 Bumped version to trigger rebuild for new assorthead.
 

 small tweak
 

 Register UCSC genome criGri1 (mapped to NCBI assembly C_griseus_v1.0)
 

 Rsamtools 2.23.1

zlibbioc is deprecated and no longer needed --> remove it from the
LinkingTo and Imports fields.
 

 heatmap output as ggplot object
 

 test for get_dataset_object consolidation tests
 

 bug:fix
 

 address errors
 

 Merge pull request #66 from LTLA/tatamize

Switch from the old beachmat API to the new tatami library. 

 Switch from the old beachmat API to the new tatami library.
 

 Merge pull request #19 from jackgisby/devel-dev

Changes for Bioconductor pre-review (v0.99.1) 

 Add additional changes to reduce check time, generate documentation
 

 Reduce runtime for preservation tests
 

 Reduce runtime for enrichment tests
 

 Bump version
 

 deprecated

 - unresponsive
 

 fixed a breaking bug in mitch_plots()
 

 Version bump in devel
 

 bug fix
 

 bug fix
 

 tests(dataProcessPlotsPTM): Fix unit tests in dataProcessPlotsPTM
 

 update
 

 bug fix
 

 update
 

 Add unit tests
 

 Hide bundled tools from GitHub language stats
 

 removing owlready install, adding victor tarca's work
 

 Added ontoDiff
 

 help error for custom2go
 

 Release 1.3.2
 

 Release 1.3.1
 

 Version bump devel.
 

 update GHA
 

 update sc_mutations: count UMIs
 

 NA cast checks in initializeCpp can be disabled.

This avoids an unnecessary check for NAs when the caller knows that their
matrix can't have NAs - or they don't care about casting NAs because their
downstream code doesn't properly handle NAs anyway.
 

 Correctly cast NAs from integer/logical matrices to doubles.

Otherwise, the integer/logical NAs just get treated as -2^31.
 

 Cleaned up docs about the expectations on the reference data.
 

 v1.3.1
 

 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 

 v1.1.6
 

 v1.1.5
 

 v1.1.4
 

 test corrections
 

 new tests
 

 version 1.1.3
 

 add support for linear logFC
 

 adding assorthead to avoid failures on the BBS
 

 function documentation update and input check
 

 add beachmat.hdf5 in suggests
 

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

 v1.0.1
 

 Added project site in vignettes and DESCRIPTION.
 

 Use R 4.5 and Bioc 3.21
 

 Fix conflicts in merge
 

 Bioc 3.19 and R 4.4 in check-bioc.yml
 

 Update package description
 

 Exposures -> exposure
 

 New versions of figs
 

 New metadata.csv
 

 Correct path to local files and internal location in make-data.R
 

 Update NEWS and DESCRIPTION files