add citation to publication (#71)

* add citation to publication

* formatting changes 

 Remove data-raw folder, update DESCRIPTION
 

 Update DESCRIPTION for commit 'Depends on Seqinfo instead of GenomeInfoDb' and version bump
 

 Update package-level documentation
 

 Add test_data2.R to data-raw, update DESCRIPTION
 

 Merge pull request #167 from gdrplatform/GDR-2908

Gdr 2908 

 fix: update var name (II)
 

 chore: bump version and update NEWS.md
 

 doc: reoxygenate
 

 refactor: average biological replicates
 

 version bump
 

 Merge pull request #787 from salzcamino/master

Update runEnrichR examples 

 Merge branch 'compbiomed:master' into master
 

 fixing errors
 

 Update NEWS and vignette
 

 Fix version bump: 1.29.2
 

 add new Rd
 

 deleted file 

 uodated vignette and DESCRITPION
 

 TFEA.ChIP v1.19.2: Meta-analysis, wrapper workflow, database update, and performance enhancements (#4)

* Added new functionalities, updated regulatory data, and improved performance

* version bump

* Extended TFBS, missing else & mouse translation

- Extended TFBS database with 63 new ChIP-Seq experiment added.
- Missing else condition in txt2GR corrected.
- mouse (mus musculus) gene ID translation to human Entrez Gene IDs implemented.

* Update DESCRIPTION

version bump

* namespace update

* version bump

* substitute for loops with applys, expand documentation, and other corrections

* minor bug in plot_RES solved

* R version dependency

* minor bug in plot_RES

* TF gene symbols updated

* plot_ES bug fixed

* version

* plot LOR instead of OR

* adds metadata to getCMstats function

* GSEA_run compures weighted score, output tables include metadata, plot_CM plots log(OR)

* bug at plotting log(OR) solved

* bug in GSEA_EnrichmentScore solved

* getCMstats modified to include distances

* Solved bug in GR2tfbs_db

Now ChIP-Seqs that don't have any peaks assigned to genes are eliminated from the output list.

* Update All-functions.R

* plot_CM function modified to accept new table containing log2OR and log10.adj.pval columns

* Bug in GSEA_run fixed

* database updated, includes distant TFBS, all documentation and test units updated

* update example datasets and its documentation

* example data updated

* correction in dataset documentation

* man pages updated

* version bump

* Unit test error solved. Checking if biomaRt host is available before translating mouse IDs

* bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

* bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

* bug in GR2tfbs solved (extracting ChIP-seq IDs)

* Added mouse to mouse ID translation and updated database

* bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

* bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

* update: TF ranking & faster GSEA_run

* Warning solving: extra man page removed

* bug solved in get_chip_index (encode ChIP selection)

* multiple boolean variable error solved

* multiple boolean variable error solved

* multiple boolean variable error solved

* Bug in preproccessInputData solved (DESeqResults to data.frame)

* New gene-TR database. See NEWS file

* New gene-TR database. See NEWS file

* tests updated

* bug in GeneID2entrez examples solved

* testing issue in test_contingency_matrix solved

* bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch

* bump x.y.z versions to odd y after creation of RELEASE_3_9    branch

* trimming whitespaces in gene IDs in preprocessInputData()

* trimming whitespaces in gene IDs in preprocessInputData()

* bug fix in GeneID2entrez: toupper() call moved to h2h section

* version bump

* bug fix in preprocessInputData: toupper() call added to h2h section

* error in GeneID2entrez solved

* Citation file added

* bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

* bump x.y.z version to odd y after creation of RELEASE_3_10 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

* bump x.y.z version to odd y following creation of RELEASE_3_11 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

* bump x.y.z version to odd y following creation of RELEASE_3_12 branch

* Simplified plotting functions and data objects stored

* bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

* bump x.y.z version to odd y following creation of RELEASE_3_13 branch

* bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

* bump x.y.z version to odd y following creation of RELEASE_3_14 branch

* Pass serialized S4 instances thru updateObject()

* Version 2.1.1 upgrade

* Corrected version number

* Corrected version number

* patched error on BioC builder

* Version bump

* updated vignette

* updated vignette

* upgraded version

* new changes

* updated vignette and db

* changed vignette and fxs

* changed NEWS

* Delete vignettes/.Rhistory

---------

Co-authored-by: Laura Puente-Santamaria <lpsantamaria@iib.uam.es>
Co-authored-by: LauraPS1 <lpsantamaria@iib.upm.es>
Co-authored-by: luis <lpeso@iib.uam.es>
Co-authored-by: vobencha <valerie.obenchain@roswellpark.org>
Co-authored-by: vobencha <vobencha@gmail.com>
Co-authored-by: Nitesh Turaga <nitesh.turaga@gmail.com>
Co-authored-by: Hervé Pagès <hpages.on.github@gmail.com> 

 changed NEWS
 

 updated vignette and db
 

 upgraded version
 

 updated vignette
 

 Version bump
 

 patched error on BioC builder
 

 Corrected version number
 

 Version 2.1.1 upgrade
 

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 

 Simplified plotting functions and data objects stored
 

 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 

 error in GeneID2entrez solved
 

 version bump
 

 trimming whitespaces in gene IDs in preprocessInputData()
 

 trimming whitespaces in gene IDs in preprocessInputData()
 

 bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch
 

 bug in GeneID2entrez examples solved
 

 New gene-TR database. See NEWS file
 

 Bug in preproccessInputData solved (DESeqResults to data.frame)
 

 multiple boolean variable error solved
 

 bug solved in get_chip_index (encode ChIP selection)
 

 Fixed conflicts in version change
 

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 

 Added mouse to mouse ID translation and updated database
 

 bug in GR2tfbs solved (extracting ChIP-seq IDs)
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
 

 version bump
 

 correction in dataset documentation
 

 update example datasets and its documentation
 

 Bug in GSEA_run fixed
 

 Update All-functions.R 

 getCMstats modified to include distances
 

 bug at plotting log(OR) solved
 

 adds metadata to getCMstats function
 

 version
 

 TF gene symbols updated
 

 R version dependency
 

 substitute for loops with applys, expand documentation, and other corrections
 

 Merge branch 'master' of https://github.com/LauraPS1/TFEA.ChIP
 

 Update DESCRIPTION

version bump 

 version bump 

 resolve
 

 fixing infRepsImporter for oarfish & piscem
 

 improvements to allow outline plots
 

 update import used to run the function create_TxDb
 

 increase version number
 

 Merge remote-tracking branch 'upstream/devel'
 

 Merge pull request #12 from KlausVigo/devel

Devel 

 Update DESCRIPTION 

 added a function to swap the minor edges of an evonet object
 

 merge
 

 Remove BisqueRNA.
 

 add sticker for mastR
 

 Added workflow image into README.
 

 Update package: with mutiple code re-written
 

 version bump 063025
 

 Bumped version to trigger rebuild.
 

 pinned versions done
 

 bug fix
 

 Updated script that processes gnomAD data
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Merge branch 'updated_method' into develop
 

 updated each bgeecall functions imports with only the external packages and functions needed. Notably to avoid intersect function being taken from Biostring instead of IRanges
 

 Updated Rd files and added missing ones
 

 Merge branch 'updated_method' of github.com:BgeeDB/BgeeCall into updated_method
 

 added exception handling when intergenic don't receive reads
 

 Removed unused comment
 

 Corrected use of correct class attributes (attribute read_size_kmer_threshold is in class myKallisto;etadata and not myAbundanceMetadata)
 

 updated read_size_kmer_threshold with the correct class AbundanceMetadata instead of myKallistoMetadata
 

 Added code to retrieve random libraries from SRA for new Species
 

 Corrected ensembl metazoa ftp link
 

 Added generation of reference intergenic regions by removing outliers found with transcriptomic evidence
 

 Updated kallisto to use small index depending on the threshold set in the KallistoMetadata instead of a hardcoded 50
 

 Corrected format error in merging libraries
 

 Added generation of initial intergenic regions
 

 Added weighted pValue merging option for both the mean and median method
 

 Added outliers removal to intergenic abundances using Tukey's method (interquantile range)
 

 corrected error collect_padjValues not found
 

 removed the taking of the minimum pValue for merging approches
 

 modified read size threshold for small kmer use
 

 updated functions headers
 

 Added new pvalue caclulation method
 

 Add Mastodon 

 bump version
 

 Merge branch 'BIOC_master'
 

 bump version
 

 rename intergenic directory
 

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
 

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 

 Add badges 

 Merge branch 'RELEASE_3_13'
 

 bump version
 

 Merge remote-tracking branch 'upstream/devel'
 

 added processing comment to listcolumns
 

 Add Seqinfo to imports in DESCRIPTION
 

 renameSeqlevels is now exported by GenomeInfoDb package
 

 Added curl download
 

 BiFET 1.29.1

Update serialized GRanges instances. Needed because of Seqinfo move
from GenomeInfoDb package to new Seqinfo package.
 

 deltaCaptureC 1.23.1

Update serialized GRanges/RangedSummarizedExperiment instances. Needed
because of Seqinfo move from GenomeInfoDb package to new Seqinfo package.
 

 GeuvadisTranscriptExpr 1.37.1

Update serialized GRanges instances. Needed because of Seqinfo move
from GenomeInfoDb package to new Seqinfo package.
 

 LOLA 1.39.1

Update serialized GRanges/CompressedGRangesList instances. Needed
because of Seqinfo move from GenomeInfoDb package to new Seqinfo package.
 

 mitoClone2 1.15.1

Update serialized GRanges instances. Needed because of Seqinfo move
from GenomeInfoDb package to new Seqinfo package.
 

 Solved legacy matadata labels issue (#120)

* Solved legacy matadata labels issue

It was causing reported missing COEX even if present

* Fixed minor bug in getter

* Solved a minor documentation issue 

 rifi 1.13.1

Update serialized RangedSummarizedExperiment instances. Needed because of
Seqinfo move from GenomeInfoDb package to new Seqinfo package.
 

 Changed to git ignore rather than svn
 

 TFEA.ChIP 1.29.1

Update serialized GRanges instances. Needed because of Seqinfo move
from GenomeInfoDb package to new Seqinfo package.
 

 Merge branch 'devel' of github.com:fmicompbio/eisaR into devel
 

 Merge branch 'master' into devel
 

 Bump up version
 

 Refine settings in shiny (PON, icons)
 

 Update descriptions of default parameters in mutFilterCan
 

 vignette editted. samtools version to auto
 

 rebuld manual
 

 add GenomeInfoDb for seqlevelsStyle
 

 add empty line in NEWS
 

 update version number in NEWS
 

 Merge branch 'devel' of https://github.com/shuye2009/GenomicPlot into devel
 

 import seqlevelsStyle from GenomoeinfoDb
 

 add scale bar.
 

 Attempt to solve https://github.com/LieberInstitute/DeconvoBuddies/actions/runs/15907951917/job/44867749445#step:15:48 with DelayedMatrixStats. Based on https://www.bioconductor.org/packages/release/bioc/vignettes/DelayedMatrixStats/inst/doc/DelayedMatrixStatsOverview.html#supported-methods, this should do it.
 

 Attempt to resolve error detected by GHA at https://github.com/LieberInstitute/DeconvoBuddies/actions/runs/15906471653/job/44862609498#step:15:43
 

 Bug fixes: updated version, resolved minor issues
 

 We made get_mean_ratio() more flexible so it can work well with sparse matrices.

Details:

```R
library("Matrix")
m <- Matrix(c(0, 0, 2:0), 3, 5)
m[1,1] <- 2
m[3, 4] <- 3

base::rowMeans(m) ## Doesn't work as it doesn't support sparse matrices
stopifnot(identical(
    base::rowMeans(as.matrix(m)),
    MatrixGenerics::rowMeans(m)
))

matrixStats::rowMedians(m) ## Doesn't work as it doesn't support sparse matrices
Matrix::rowMedians(m) ## Doesn't exist
stopifnot(identical(
    matrixStats::rowMedians(as.matrix(m)),
    MatrixGenerics::rowMedians(m)
))

## MatrixGenerics works well with regular matrix objects
m2 <- as.matrix(m)
MatrixGenerics::rowMedians(m2)
MatrixGenerics::rowMeans(m2)
```

Co-authored-by: Cynthia SC <bioinformatic2019@gmail.com>
 

 Update README.md 

 Update script to include nodes table for get pathways (#45)

 

 Update MatrixQCvis.Rmd
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 trigger push
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 Update check-bioc.yml
 

 merge master
 

 Added summary track to url copy
 

 Added table and GO analysis to DEG module, uses plotly gl and soon ready for 2d DTEG
 

 Testing webgl plot for megabrowser
 

 New megafst format support included
 

 Improved DEG model
 

 Fixed bug for URL linker
 

 Added UMAP support in metadata tab
 

 Added checkbox to url updater for collapsed_introns
 

 Fixed sequence copy and added checkbox for collapse introns
 

 Fixed collapse intron bug
 

 Browser settings panel is now hidden by default
 

 Removed bs code of browser
 

 Added animation style and improved tutorial
 

 Improved codon plot
 

 More modern view on browser selection panel
 

 Solved test failures (#119)

There were differences in the results depending on the usage
of `torch` or lack there-of.

Also now the first UMAP plot created during execution of the
function `cellsUniformClustering()` will use the first condition
in the `COTAN` object if available 

 Merge pull request #178 from gdrplatform/GDR-2986

Gdr 2986 

 refactor: restore lapply
 

 refactor: switch from lapply to loop
 

 refactor: fix lapply
 

 chore: bump version and update NEWS.md
 

 Version  bump
 

 Replaced link that leads to suspicious website 

 version bump
 

 Remove msigdbdf reference

The extra package is no longer necessary
 

 Update the link to the smaller rds xenium object
 

 news
 

 Add an example of geseca analysis for 10x xenium data
 

 Merge branch 'update-color-for-geseca-plots' into 'master'

Update color for geseca plots

See merge request alserglab/pr/fgsea/fgsea!2 

 Update breaks for color gradient
 

 Merge branch 'update-plots-for-seurat-5' into 'master'

Update addGesecaScores for Seurat-5

See merge request alserglab/pr/fgsea/fgsea!1 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 update volcano, genes_plot, assay_plot and vignette from puhti
 

 Merge pull request #205 from sufyansuleman/add-dbsnp-tarball-support

Added support for arbitrary Bioc SNPlocs tarballs (dbS > 156) 

 Added support for arbitrary Bioc SNPlocs tarballs (dbS > 156)
 

 Merge branch 'master' into devel
 

 Update changes on the new version
 

 Update filter report
 

 Change path to manual
 

 Add dbsnpCutoff and nonCutoff to shiny
 

 Handle special case: PON file only has a header
 

 Fix a small bug in text
 

 Merge branch 'WX'
 

 fixed vignette
 

 fix drv
 

 update Description
 

 update dependencies and changed txdbmaker in vignette
 

 fix hyper
 

 update vignette to be compatible with new intergenic
 

 Update Bluesky badge 

 rolled back R requirement from >=4.5 to >=4.2
 

 updating test data to newest object versions
 

 Bump version
 

 Remove R_front script.
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Bump version to 0.3.0 for Bioconductor devel
 

 add examples of different w_x/w_y for clusters/genes on vignette
 

 bump version number.
 

 Only return unique peaks in `segregate_seqs`
 

 Sanitise peak input names before running FIMO

Too many underscores seem to cause issues
 

 chore: bump version and update NEWS.md
 

 refactor: update logic
 

 Bump V
 

 Update R-CMD-check.yaml 

 removed version C++
 

 updated C++
 

 Bugfixes for saving VLS strings in data frames.

- Avoid overwriting the VLS flag between columns.
- Fetch the missing value placeholder from the correct handle.
- Use the correct flag in the tests.
 

 easyRNASeq 2.45.1: Replace GenomeInfoDb with Seqinfo in Imports
 

 Organism.dplyr 1.37.1: Replace GenomeInfoDb with Seqinfo in Imports
 

 v1.37.2: minor modification: SpikePos dataset now included in biosigner
 

 Merge pull request #1 from federicomarini/hotfix_obsoleteGO

Hotfix obsolete go term 

 Replacing obsolete term - GO:0006629 is the new one and should solve the build error
 

 version bump
 

 Merge branch 'RELEASE_3_21' into devel
 

 Merge pull request #786 from salzcamino/master

runScDblFinder seed 

 bumped version number
 

 removed PhyloProfileData
 

 Devel version number
 

 Use release version number
 

 readd example results
 

 Merge branch 'devel' of github.com:xyang2uchicago/BioTIP into devel
 

 Update DESCRIPTION 

 Update myplotIc.R

corrected typo in line 13 if() sentence 

 Update myplotIc.R

add the parameter p.IC to the function myplotIc.R 

 fix typo in BioTIP wrap
 

 fix typo in BioTIP wrap
 

 added temporarily removed files
 

 Merge branch 'master' into devel
 

 Merge branch 'master' of github.com:jokergoo/ComplexHeatmap
 

 Merge pull request #1154 from skelly001/develop

Fix slow distance matrix calculation 

 names<-,HeatmapAnnotation updates all necessary slots
 

 Fix slow distance matrix calculation when using correlation-based distance and NAs are present
 

 set row_reorder and column_reorder to FALSE

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ComplexHeatmap@107788 bc3139a8-67e5-0310-9ffc-ced21a209358