create a Python module
 

 create a Python module
 

 create a Python module
 

 Update doc-data.R 

 Update year for Baldoni et at reference.
 

 edgeR 4.1.31
- Fix a bug in glmTreat
- Update the edgeR user's guide
 

 edgeR 4.1.29
- Add an extra checking for Poisson bound in glmTreat.
- Update NEWS.Rd
 

 simpler/cleaner omp parallel for loops
 

 Add get/set_SparseArray_nthread()
 

 Use OpenMP only when available
 

 Redefine some coercions from ordinary matrix to sparseMatrix derivative

Restore some of the basic coercion methods that used to be defined in the
Matrix package but that the lazy Matrix maintainers decided to deprecate
in Matrix 1.7-0 (e.g. from matrix to dgRMatrix).

Also slightly reorganize code in src/SparseMatrix_mult.c
 

 Merge branch 'devel' of https://github.com/Muunraker/nipalsMCIA into devel
 

 Merge pull request #55 from Muunraker/main

V 1.20 merge 

 Merge branch 'devel' of https://github.com/Muunraker/nipalsMCIA into devel
 

 separating rectangles breaks the plot, so remove it (for now)
 

 added the white lines for the block weights heatmap too
 

 better data manipulation for ggplot
 

 removed all mentions of specific vignette numbers
 

 "GS Score" is redundant
 

 Fixed package anchors in man page.
 

 NEWS is not text.
 

 Updated NEWS file and maintainer :'
 

 Updated NEWS file and package maintainer :'
 

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

 edgeR 4.1.28
- New argument `robust` in diffSpliceDGE()
- Restructure the diffSpliceDGE() function
 

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

 Preparing new BioC RELEASE_3_20

By merging branch 'master' into 'bioc_devel'
 

 Adapt result table format from long to wide for FDR subset results (#70)

* Adapt to wide format of results table for results on gene subsets

* adpat plot examples to new result table format for FDR subsets

* update documentation 

 Merge branch 'master' of github.com:gagneurlab/FRASER
 

 Merge pull request #68 from c-mertes/fix_tests

Fix tests 

 fix warnings
 

 Merge branch 'c-mertes:master' into master
 

 Fixed drop parameter in generic "[" function and other small bug fixes (#62)

Fixes in this commit:

* Set default for `drop` to `FALSE` in `[` generic function and ignore this argument
* Extended testing to test for the `drop` argument.
* fix GitHub Action again
* update and align FRASER documentation
* Update RoxyGen documentation to 7.3.1
* Add ORCID ids to DESCRIPTION
* fixed BugReports in DESCRIPTION
* remove CCX11 flags from Makevars

---------

Co-authored-by: Christian Mertes <mertes@in.tum.de>
Co-authored-by: Drew Behrens <drewjbeh@gmail.com>
 

 Merge branch 'c-mertes:master' into master
 

 added compiled vignette
 

 small vignette update
 

 Update FRASER.Rnw 

 Update README.md 

 bug fix
 

 improved colors for volcano plot
 

 add coloring by aberrant status from subsets to plot functions
 

 update version number
 

 fix bug in aberrant function for all=TRUE
 

 update readme with FRASER 2.0 preprint
 

 correct gene level aberrant coloring for plots
 

 fix merging with external cts for single sample
 

 Merge pull request #53 from vyepez88/patch-1

Update README.md 

 readme update
 

 add FRASER 2.0 to readme
 

 fix fdr on subset for theta
 

 simplify result retrieval for FDR on subset
 

 added new plot functions to vignette
 

 fix gene pval in FDR on subset for psi3/5
 

 small bugfix
 

 fix small bug in extracting junction idx of genes in subsets
 

 add colnames to subsetted padjust for later retrieval
 

 use correct pseudocount in plot heatmap function
 

 update potential frameshift colname
 

 renamed annotated column to potentialImpact
 

 minor fix to get correct rowMeans in result table when using FDR on subset
 

 added support to get results table only for subset of genes
 

 further fix to correctly extract gene pvalues
 

 R CMD CHECK set to ignore warnings; removed zscoreCutoff and added option to specify filters to annotate only certain types of genes
 

 remove installs from vignette for biocCheck
 

 small fix in vignette
 

 fix vignette
 

 improved selection of splice metrics to run
 

 Merge branch 'master' of git.bioconductor.org:packages/FRASER
 

 Merge branch 'fraser2' of github.com:c-mertes/FRASER into intron_jaccard
 

 Add update=FALSE to install 

 fix install of dependencies for github actions
 

 add manhattan plot function and update documentation
 

 force fds chr style to external counts
 

 Merge branch 'plot_coverage' into intron_jaccard
 

 adapt test case to compare to correct result when allowing short mismatches in nonsplit anchor
 

 add updated man/plotFunctions.Rd
 

 Merge branch 'plot_coverage' into intron_jaccard
 

 slightly improved intron_retention detection
 

 fix typo
 

 minor fix
 

 minor improvements
 

 fix examples
 

 fix missing spliceSiteID bug part2
 

 fix bug in spliceSiteID mapping and intron retention annotation
 

 minor changes
 

 small bug fix
 

 updated c++ code
 

 Merge branch 'master' into intron_jaccard
 

 minor bugfix
 

 fix bioccheck
 

 cleanup for bioccheck
 

 included splice type annotation
 

 calculation of gene pvals for all annotated genes
 

 update documentation & tests
 

 edgeR 4.1.27
- CITATION papers now in reverse chronological order
- Add cameraPR() example to camera.DGEGLM.Rd
- Edit punctuation in references in camera.DGEGLM.Rd
 

 Forgot st_write_parquet warning
 

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

 Renamed EBImage class to ExtImage
 

 Revert to sfarrow since it can be a pain in the ass to install the GDAL parquet driver on some systems
 

 Merge conflict
 

 add recent pushed

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

# Conflicts:
#	R/read.R
 

 Imports related to Seurat conversion
 

 Updated readXenium to read XOA v2 preview and removed unnecessary arguments
 

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

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

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

 sf arith is slow, using sfheader
 

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

 back up recent changes for `coerce`
 

 keep changes `coerce.R`
 

 updates on coerce
 

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

 "Updating local devel from remote"
 

 Updated documentation after installing new version of SFE
 

 Updated functionalities to plot images. Closing #26, #19, and #20
 

 Import functions that got moved to SFE
 

 Option to show axes in light and dark theme, closing #28
 

 attempt to comply with gcc13
 

 update README
 

 v2.5.22 fix y-flipped images on non-macOS
 

 add rasterImages+rasterParams to plot_image()
 

 Temporarily host data on Box
 

 Update to BioFormats 7.3.0
 

 Update to BioFormats 7.1.0
 

 update imports
 

 Update to BioFormats 7.0.0
 

 Version Bump for Bioconductor 3.18 (#65)

* bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

* bump x.y.z version to odd y following creation of RELEASE_3_17 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

* Bump version and NEWS file

---------

Co-authored-by: J Wokaty <jwokaty@users.noreply.github.com>
Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu> 

 Update gha and update documentation (#63)

* adapt github actions to use new BIOC versions and use always variables

* document arg and fix import warnings

---------

Co-authored-by: Christian Mertes <mertes@in.tum.de> 

 Merge branch 'plot_fdr_results' into master 

 Update inputCheckerFunctions.R 

 color aberrant status based on FDR subset results
 

 Merge pull request #55 from gagneurlab/plot_function_update

Plot function update 

 minor fix
 

 test new argument in plotting tests
 

 add test for new plot function
 

 add ggrepel package to imports
 

 explain columns for results function in detail (#52)  Closes #35 

* explain columns for results function in detail

fixes #35

* updating doc for p and z score computation

* fix result column order

* Added results documnetation to vignette

* Removed code links

* Update OUTRIDER.Rnw

* log2 formatting

* removed underscores

Co-authored-by: Felix Brechtmann <37140213+brechtmann@users.noreply.github.com> 

 Update to BioFormats 6.14.0
 

 conflict fix
 

 conflict fix
 

 conflict resolved
 

 fix(diann-converter): Allow for quantification column to be determined by client (#92)

 

 refactor(converter): Migrate core MSstats converter functions into MSstatsConvert (#91)

* refactor(converter): Migrate core MSstats converter classes into MSstatsConvert

* Add annotation files to MSstatsConvert package for pd, os, diau 

 fix(skyline): Modified error message for Skyline outlining that MSstats only analyzes MS1 or MS2 but not both (#89)

* fix(workflows): Modify workflows to perform dry run build upon PRs on devel branch

* docs(pr-template): Modified PR template wording

* fix(skyline): Modified error message for Skyline outlining that MSstats only analyzes MS1 or MS2 but not both 

 refactor(proteome-discoverer): Add validation for input columns (#87)

* refactor(proteome-discoverer): Add validation for input columns

* Allow PD to MSstatsTMT converter to handle both old and new column names for # Proteins and # Protein Groups 

 feat(metamorpheus): Create converter from Metamorpheus to core MSstats (#85)

 

 docs(warnings): Remove warnings related to documentation (#86)

 

 feat(metamorpheus-converter): Add clean functionality of metamorpheus converter (#83)

* feat(metamorpheus-converter): Add clean functionality of metamorpheus converter

* Modified metamorpheus annotation filename and removed techRep column from annotation file

* Modify RDS filename to MSstatsMetamorpheusFilesObject for unit testing

* create processed_data folder for testing 

 docs(pr-template): Add a pull request template (#84)

 

 feat(metamorpheus): Set up MSstatsMetamorpheusFiles class for metamorpheus (#81)

* feat(metamorpheus): Set up MSstatsMetamorpheusFiles class for metamorpheus converter

* update input data file to be from metamorpheus vignette

* Modify input metamorpheus file to have more proteins and bioreplicates 

 status 500 fix
 

 fix layout
 

 fixes
 

 plotly for design sample
 

 Apply patch to fix compilation issue on ARM submitted by @kalibera
 

 version bump
 

 swapped converter imports to msstatsconvert
 

 Updated NEWS file, added a missing export
 

 Optimization in R code after discussion in https://github.com/rcastelo/GSVA/issues/71
 

 Bugfix on a rare combination of GSVA parameters
 

 version bump 1.15.13
 

 Update manual pages (#537)

 

 Rename estimateDivergence to addDivergence (#531)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 BioFileCache as imported package: vignette building failing
 

 minor bug corrections 3
 

 to version 0.99.6 minor bugs
 

 Add design matrix F1000Res publication to CITATION file
 

 Update of help pages; version number bumped to 1.35.5
 

 adapted intro of vignettes
 

 Update NEWS and version bump
 

 qPLEXanalyzer-package 

 Bioconductor_April_release_final_commit
 

 1.11.110 : billing19 internalization, `Protein group IDs` colclass, obsolete functions
 

 v0.99.23
 

 v0.99.22
 

 sanity check
 

 Bioconductor April release commit
 

 Included RnBeads.hg38 as dependency
 

 return zero rowed data.tables for empty outputs
 

 version bump
 

 update base vignette
 

 remove fixtures introduced due to error in org.Hs.eg.db
 

 bump
 

 Merge pull request #58 from RGLab/warning-fcs3.2

    give warning instead of the exception on FCS3.2 

 v2.5.20 update trans2d() and warp2_trans()
 

 version bump
 

 chore: version bump
 

 fix: change dependency qlcMatrix
 

 v2.5.19
 

 Clarified maintainer instructions for handling new submissions.
 

 Added helper function for creating takane-related metadata.

Strictly speaking, this doesn't really belong here as gypsum doesn't
deal with the actual content of the files. However, there's no better
place to put it right now, so we'll just stick it in here and do some
voodoo to avoid roping in excessive dependencies.
 

 Added helper function for creating takane-related metadata.

Strictly speaking, this doesn't really belong here as gypsum doesn't
deal with the actual content of the files. However, there's no better
place to put it right now, so we'll just stick it in here and do some
voodoo to avoid roping in excessive dependencies.
 

 fix: fixed small error in degrees of freedom
 

 bump version
 

 handle NCBI style of seqlevels
 

 bug fix: condition length > 1
 

 Replace old prefix for new test repository
 

 Add missing export to readGMT()
 

 fix minor documentation typo in ?readGMT
 

 fix .3
 

 fix
 

 Import pairwiseAlignment only from pwalign instead of everything
 

 adjusted pipeline
 

 update naming
 

 remove file added by mistake 

 minor optimzations to runtime and memory usage'
 

 Remove files following merge sort to reduce disk usage 

 add note to documentation
 

 rename to ShoalFinder, adds EstimateShoal function
 

 removes a 1: usage in evoweaver predictor
 

 Update rpkgchecks.yml 

 Update rpkgchecks.yml (#16)

 

 update news and description
 

 new functions, dependency updates
 

 Updates naming, removes a potentially problematic example
 

 version bump 1.27.2
 

 Legend improvements
 

 fix of README.md
 

 version bump 1.21.10
 

 version bump 1.21.9
 

 update version
 

 update typo in xenium make data files
 

 store files in subdirectories
 

 select correct replicate
 

 Fixed warning in C code triggered by -Wformat-security
 

 update NEWS files
 

 use exportClass tags
 

 update NEWS file
 

 version bump 1.39.35
 

 clean up code after removal of redundant check
 

 Merge pull request #57 from StijnVandenbulcke/master

Updating News and Description files 

 Update NEWS.md 

 Merge pull request #56 from StijnVandenbulcke/master

Fixed Issues 

 Update msqrob.R

Fixed bug related to ordering of levels when using ridge regression 

 Increased default timeout
 

 fix link to BLOSUM62
 

 doc: reran roxygen2::roxygenize()
 

 doc: bump version 0.99.34
 

 doc: add install notes for installing missing pkgs
 

 Fix of help page for msaConservationScore() to account for move of matrices to the 'pwalign' package
 

 Merge remote-tracking branch 'refs/remotes/origin/master'
 

 Fix of typo in vignette source
 

 bump version to 1.11.7
 

 Small tweak to NAMESPACE

Import selectively from Biostrings to avoid the following load-time
warning:
  replacing previous import ‘Biostrings::pairwiseAlignment’
  by ‘pwalign::pairwiseAlignment’ when loading ‘iPAC’
 

 compareStrings() has moved from Biostrings to pwalign
 

 stringDist() and the BLOSUM matrices have moved from Biostrings to pwalign
 

 pairwiseAlignment() has moved from Biostrings to pwalign

- Make necessary adjustments to DESCRIPTION and imports to account for
  pairwiseAlignment() being now in pwalign instead of Biostrings.

- Also remove Tutorial.R, Tutorial.html, and Tutorial.md from the
  vignettes/ folder. Only Tutorial.Rmd belongs to git. The other files
  get automatically generated and added to the resulting package source
  tarball by 'R CMD build', and so should not be added to git.
 

 This is completely updated version of the package that addresses all the changes. Detail responses are below.
COMMENT:
The vignette contains the following line:
Introduction to the KMCUT package
*  but the name of the package is kmcut (all lower-case). R in general, and package names in particular, are case-sensitive.

RESPONSE:
The package name was changed to lower-case letters.

COMMENT:
*  Man pages have very long titles, each of them made of several sentences that repeat exactly the content of the Description section. Good man page titles should be short (a few words only).

RESPONSE:
Titles of man pages were shortened.

COMMENT:
*  You seem to misunderstand the purpose of importing other packages in your package. The examples in most man pages start with many library() calls e.g. in kmoptpermcut:
library(survival)
library(stringr)
library(data.table)
library(tools)
library(pracma)
library(foreach)
library(doParallel)
library(parallel)
library(kmcut)
*  Please note that packages that are imported are automatically available to the code inside your package so there's no need to put the extra burden to manually load each of them on the user. For loading the kmcut package itself, a widely accepted convention is to not pollute the examples in the man pages of a given package (say foo) with explicit calls to library(foo). The reason for this convention is that it is considered reasonable to assume that the package is already loaded when the user is looking at its man pages.

RESPONSE:
All library() calls in examples were removed.

COMMENT:
*  Please minimize the dependencies of your package and only import what you actually need to import. For example, the package does not seem to use anything from the stringr package so that dependency is not needed. Please re-evaluate all the other dependencies and make sure to drop those that you don't need.

RESPONSE:
The dependencies on  and other unnecessary packages were removed.

COMMENT:
*  Also please re-evaluate the need for all the library() calls at the beginning of the vignette (although keeping library(kmcut) is fine there and is actually needed).

RESPONSE:
All library() calls at the beginning of the vignette were removed, except for library(kmcut)

 COMMENT:
*  Bioconductor recommend against the use of flatcase style for your function names (e.g. kmoptpermcut, transposetable, kmqcut, kmucut, etc...), as it makes the names hard to read and/or remember. Please use snake_case or camelCase instead.

RESPONSE:
All function names were changed to include underscores (as in  snake_case )

COMMENT:
*  About the file with gene expression-like features. The vignette says: "The first column must contain sample identifiers and and the first row must contain gene identifiers." Isn't it the otherway around?

RESPONSE:
You are correct. This error was fixed.

COMMENT:
*  The kmoptpermcut() function is extremely slow, to a point that seems to make it almost unsuitable for real-world data. For example, calling it on the example_genes_295.txt file provided in the package takes 89 sec on my laptop when n_iter is set to 1000. However, the file only contains 2 rows (i.e. 2 genes) and the man page for kmoptpermcut() recommends to set n_iter to 10,000. This means that using the recommended n_iter on a file with 100 genes will take more than 10 hours!

RESPONSE:
Unfortunately, km_opt_pcut() cannot be made much faster. It estimates the unknown sampling distribution of the test statistics by applying the permutation test, which is very slow. It is recommended that kmoptpermcut be run on at least 16 CPUs (this can be achieved on a low/midrange desktop or high-end laptop). This function is meant to be applied to a relatively small subset of candidate genes identified by the km_opt_scut function. The recommendation regarding application of km_opt_pcut() to a relatively small subset of genes identified by km_opt_scut() was added to the vignette. The size of the package's built-in example dataset was reduced to better reflect the number of samples in a real life dataset.

COMMENT:
*  How useful is the kmoptpermcut() function when called with wpdf=FALSE? In this case, the function will display a series of plot, one after the other, the next one replacing the previous one at a possibly fast pace, with barely enough time for the user to look at them!

RESPONSE:
When  km_opt_pcut()  is used with wpdf=FALSE from RStudio or R GUI, after the execution is over, the user can go back and forth through the plots by clicking  left  and  right  arrows. The main reason why this option was added is to provide a functionality to embed the graphs during the vignette compilation.

COMMENT:
*  If the goal is to make it as simple as possible for clinical oncologists or other scientists without strong programming skills to use the package, then some improvements on how errors are handled would be welcome. For example, I doubt that the targeted audience will be able to make sense of an error message like this one:
> kmoptscut(fname="survival_data_295.txt", sfname="example_genes_295b.txt")
Error in order(sdat$sample_id) : argument 1 is not a vector

RESPONSE:
The check of file existence and other argument checks were added to all functions.

COMMENT:
Documenting a function argument like this:
fname: character vector that specifies the name of the file etc...
*  without specifying that the character vector must be of length 1 suggests that the character vector could be of arbitrary length. Note that many functions in R that work on character data are vectorized and can handle a character vector of arbitrary length (e.g. tolower() or grepl()) but that doesn't seem to be the case here. Please disambiguate.

RESPONSE:
This was clarified in the updated version, all man pages now state that file name must be a character vector of length one.

COMMENT:
*  Finally note that coordinating right-censored survival data and gene expression-like features, and keeping them aligned when subsetting the data, is exactly what the SummarizedExperiment container is for. In your case, the SummarizedExperiment object would have the feature ids as rownames and the sample ids as colnames, and the right-censored survival time data would be stored in the colData component of the object. All you would need to do is implement a function that loads the input data in a SummarizedExperiment object e.g. load_kmcut_input(). The function would essentially do something like this:
load_kmcut_input <- function(epath, spath)
{
    edat <- read.delim(epath, header = TRUE, stringsAsFactors = FALSE)
    sdat <- read.delim(spath, header = TRUE, row.names = 1)
    ...
    ... some sanity checks about 'edat' and 'sdat'
    ...
    assay <- as.matrix(edat[ , -1])
    rownames(assay) <- edat[ , 1]
    coldata <- DataFrame(sdat)
    SummarizedExperiment(list(expr=assay), colData=coldata)
}
Typical use:
epath <- system.file("extdata", "example_genes_295.txt", package = "kmcut")
spath <- system.file("extdata", "survival_data_295.txt", package = "kmcut")
kmcut_se <- load_kmcut_input(epath, spath)
kmcut_se
12. Then all functions in the package would take such object as input instead of fname and sfname, making them slightly easier to use and avoiding the need to load the same data from disk again and again.
Furthermore, the user can now subset the data at will by doing things like kmcut_se["MYH2", c("SEQC_NB002", "SEQC_NB003")] with the guarantee that the right-censored survival data and the gene expression-like data remain aligned at all time, hence avoiding the need of utility functions like extractrows() or extractcolumns(). Every Bioconductor user knows how to perform such basic subsetting operation. This is the true Bioconductor way and it has proven to be a very valuable approach to software design.

RESPONSE:
All core function were changed to take a SummarizedExperiment object as input. A function that creates SummarizedExperiment objects from two input files, create_se_object(), was also added.
 </pre>
    </div>
  
    

      Package: CardinalWorkflows

      Commit: b1bfb8147012177dcb3013c82c3b6b30f63c09d7

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 23:48:45 -0400

      Commit message:


	  
		
 v1.35.5
 
    
  
    

      Package: CardinalWorkflows

      Commit: 9592e29305454c76bb2ead990cc1905fda0a1875

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2024-04-24 12:19:16 -0400

      Commit message:


	  
		
 add startup message
 
    
  
    

      Package: svaNUMT

      Commit: 03c48947a951f4e594b991eb78bdf46d09e82dcb

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

      Date: 2024-04-24 20:48:02 -0700

      Commit message:


	  
		
 pairwiseAlignment() and related have moved from Biostrings to pwalign
 
    
  
    

      Package: GenomicFeatures

      Commit: 755b3dfc8347b279be5986a14a9aed8e0b83da1f

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

      Date: 2024-04-24 20:34:48 -0700

      Commit message:


	  
		
 minor cosmetic
 
    
  
    

      Package: BSgenome

      Commit: a1925b59a6ddb038c2e0e9fb101ab1ef6506c48d

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

      Date: 2024-04-24 20:33:23 -0700

      Commit message:


	  
		
 minor cosmetic
 
    
  
  


</div>

</div>