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Help Wanted

This page lists packages in various stages that may need assistance to stay in Bioconductor. Either the package is voluntarily given up and requesting a new maintainer or the package is marked for deprecation.

Table of Contents

• Voluntarily Listed
• Deprecated Packages
• Packages With Large Files

Voluntarily Listed

This section lists Bioconductor packages whose maintainer no longer wishes to maintain their package or need assistance. The package may not currently be failing, but the maintainer wishes either a new maintainer transfer or assistance with maintaining the code base as time or expertise has changed. An interested party should contact bioc-devel@r-project.org with the currently listed maintainer in the table also cc'd to get access to a package. If a maintainer is interested in listing their package, please either submit a pull request to this page or make a request at bioc-devel@r-project.org.

Deprecated Packages

This section lists Bioconductor packages marked with PackageStatus: Deprecated in the release and development versions of Bioconductor. These packages either have requested deprecation or the packages are failing and the maintainers have been unresponsive. If you are intersted in saving a deprecated package, please send an email to bioc-devel@r-project.org. It should be noted we try and reach out to maintainers before deprecating a package with automatic build failure messages as well as private emails. If anyone knows a maintainer is still active and interested in keeping their package in Bioconductor, please encourage them to reach out at bioc-devel@r-proejct.org as soon as possible.

RELEASE

Software Packages

• BiGGR
• CINdex
• CellScore
• DEP
• Harshlight
• LinTInd
• MADSEQ
• PhenStat
• ReactomeGraph4R
• Repitools
• Rfastp
• SARC
• Streamer
• TitanCNA
• TransView
• XNAString
• bgx
• biodbHmdb
• biodbNcbi
• biodbNci
• biodbUniprot
• ccmap
• cisPath
• gpuMagic
• hiAnnotator
• hiReadsProcessor
• hypeR
• interactiveDisplay
• interactiveDisplayBase
• lapmix
• lute
• netZooR
• oppti
• qckitfastq
• rGADEM
• rRDP
• seqArchR
• seqArchRplus
• seqTools
• traviz

Experiment Packages

• AneuFinderData
• RGMQLlib
• chromstaRData
• curatedCRCData
• rRDPData

Annotation Packages

• BSgenome.Hsapiens.UCSC.hg17
• BSgenome.Hsapiens.UCSC.hg17.masked

Workflow Packages

• spicyWorkflow

DEVEL

Software Packages

• hmdbQuery

Experiment Packages

No deprecated packages.

Annotation Packages

• BSgenome.Hsapiens.UCSC.hg17
• BSgenome.Hsapiens.UCSC.hg17.masked

Workflow Packages

No deprecated packages.

Packages with Large Files

This section lists Bioconductor packages that contain large files directly distributed in the code base. Bioconductor is exploring alternative hosting solutions for packages that are more cost-effective and efficient. This prevents packages from having files over 100 MB directly in the package. The files may still be distributed via external sites such as Zenodo or Dryad, and then either hosted in ExperimentHub or AnnotationHub, or provided with a caching mechanism using BiocFileCache. Data can no longer be hosted directly in the package, and Bioconductor does not support git-lfs or hosting on private locations like GitHub or Dropbox; it must be a secure location.

These packages have been warned about the large files in their source code and have yet to reach out for action. If the data remains past the next release, the package will be deprecated. We encourage if you utilize one of these packages to help us locate the maintainer to find alternative solutions or if the maintainer is unreachable to request a transfer of maintainership at bioc-devel@r-project.org