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October 25, 2023

Bioconductors:

We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books.

There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows, 1 new book, and many updates and improvements to existing packages.

Bioconductor 3.18 is compatible with R 4.3, and is supported on Linux, 64-bit Windows, Intel 64-bit macOS 11 (Big Sur) or higher and macOS arm64. This release will also include updated Bioconductor Docker containers.

Thank you to everyone for your contribution to Bioconductor

Visit Bioconductor BiocViews for details and downloads.

Contents

Getting Started with Bioconductor 3.18

To update to or install Bioconductor 3.18:

  1. Install R 4.3. Bioconductor 3.18 has been designed expressly for this version of R.

  2. Follow the instructions at Installing Bioconductor.

New Software Packages

There are 69 new software packages in this release of Bioconductor.

New Data Experiment Packages

There are 10 new data experiment packages in this release of Bioconductor.

New Annotation Packages

There are 8 new annotation packages.

New Workflow Packages

There are no new workflow packages in this release of Bioconductor.

New Online Books

There is one new online book.

NEWS from existing Software Packages

NEWS from existing Data Experiment Packages

NEWS from existing Workflows

Deprecated and Defunct Packages

Thirty three software packages were removed from this release (after being deprecated in Bioc 3.17): alpine, ArrayExpressHTS, ASpediaFI, BiocDockerManager, ChIC, chromswitch, copynumber, CopywriteR, dasper, epihet, GAPGOM, GeneAccord, genotypeeval, maanova, metavizr, MethCP, MIGSA, MIMOSA, NanoStringQCPro, NBSplice, netboxr, NxtIRFcore, ODER, pkgDepTools, PrecisionTrialDrawer, proBatch, proFIA, pulsedSilac, savR, sigPathway, STAN, TarSeqQC, tscR

Please note: gcatest and lfa, previously announced as deprecated in 3.17, has been updated and remain in Bioconductor.

Forty nine software packages are deprecated in this release and will be removed in Bioc 3.19: baySeq, BGmix, bigPint, biodbMirbase, BioMM, biomvRCNS, Clonality, CSSP, deco, DeepBlueR, DMRforPairs, exomeCopy, fcoex, gaggle, GCSscore, genbankr, GISPA, GOsummaries, GRridge, HPAStainR, imageHTS, LineagePulse, logitT, LowMACA, LPEadj, macat, mAPKL, mbOmic, MEIGOR, Metab, MSstatsSampleSize, multiSight, netbiov, OmicsLonDA, PFP, plethy, pwrEWAS, qrqc, Ringo, RNAdecay, SCATE, SEPIRA, seqbias, seqCNA, SISPA, snapCGH, sscore, Travel, trena

Two experimental data packages were removed from this release (after being deprecated in BioC 3.17): alpineData, plasFIA

Ten experimental data packages are deprecated in this release and will be removed in Bioc 3.19: ccTutorial, ChIC.data, DLBCL, mAPKLData, MAQCsubsetILM, MIGSAdata, pwrEWAS.data, SCATEData, seqCNA.annot, stjudem

One annotation packages was removed from this release (after being deprecated in Bioc 3.17). MafH5.gnomAD.v3.1.1.GRCh38

No annotation packages were deprecated in this release and will be removed in Bioc 3.19.

No workflow packages were removed from this release (after being deprecated in Bioc 3.17).

No workflow packages were deprecated in this release and will be removed in 3.19.

No books were removed from this release (after being deprecated in Bioc 3.17).

No books were deprecated in this release and will be removed in 3.19.