The Bioconductor research frontier.
We mirror every Bioconductor release and devel cycle on ndexr. This page reads our own database to summarise what's landing right now — the people, the subjects, and the packages — so a working biostatistician can see the field at a glance.
What we mirror
bioc-3.23 software packages — the core Bioconductor stack.
Genome / TxDb / OrgDb / pd.* annotation packages.
Reference datasets shipped as packages.
Workflow vignettes and Bioconductor books.
Both the
3.22 release
and
3.23 devel
trees are mirrored in full at
s3://ndexr/bioc/<release>/<repo>/src/contrib/
. Browse live state at
repo.ndexr.io
.
What's landing right now
99 brand-new software packages in bioc-3.23 vs bioc-3.22 release
Themes tagged from each package's primary
biocViews
. This is the most direct readout of where the field is investing right now — single-cell still dominates, but spatial omics and proteomics are catching up fast.
scTypeEval, scConform, BatChef, CellMentor, RankMap, jvecfor, hammers, Seqtometry, StatescopeR — annotation, batch correction, conformal inference, fast kNN.
APAlyzer, LRDE (long-read DE), splicelogic, lncRna, postNet, RNAshapeQC, VISTA — long-read aware methods are the obvious shift.
Aerith (SILAC visualisation), proBatch, PTMods, leapR, plaid, glycoTraitR, tidyexposomics, toppgene.
betterChromVAR, decemedip, RBedMethyl (ONT), HiCool, damidBind, epiSeeker, epiRomics.
MetaboAnnotatoR, metabom8, MetaProViz, lcmsPlot, sfi, ExpoRiskR — all-ion and exposome-aware.
ClonalSim, LACHESIS (whole-genome tumour evolution), MutSeqR, parati, SEMPLR, wavFeatExt.
fastRanges, ZarrArray, BiocBuildReporter, BiocMaintainerApp, Rega (EGA), imageFeatureTCGA.
Battlefield, SpatialArtifacts, HiSpaR, HistoImagePlot — niche / margin selection and artifact QC.
benchdamic, MeLSI, SpiecEasi, CrcBiomeScreen — DA benchmarking and metric learning.
fRagmentomics, PlinkMatrix, queeems, shiny.gosling.
staRgate (auto-gating), CompensAID (spillover), MDSvis.
BiocPkgDash, ImageArray, SMTrackR, tidyprint, R453Plus1Toolbox.
Twelve researchers, the Bioconductor surface
Author counts come from a parse of the
authors
field across all bioc software packages we mirror. The set below is picked to span the field rather than rank it — the same twelve names cover core data structures, single-cell, bulk RNA-seq, mass spectrometry, microbiome, enrichment, and visualization.
DropletUtils, scran, beachmat, the alabaster framework (alabaster.base/.sce/.matrix/...) — the workhorse for scRNA-seq preprocessing and the file-shape for Bioconductor objects.
tximport / tximeta with Michael Love; iCOBRA, compcodeR, countsimQC, ExploreModelMatrix, alevinQC, treeclimbR — the QC and benchmarking layer for RNA-seq pipelines.
DESeq2, fishpond / swish, tximport, tximeta, plyranges, plotgardener, nullranges — the canonical DE stack and the genomic-ranges grammar that surrounds it.
DESeq2, EBImage (microscopy), vsn (variance stabilisation), affy/tilingArray. Co-author of the canonical Bioconductor textbook.
Biostrings, BSgenome, GenomicRanges, IRanges, AnnotationDbi, beachmat — most of Bioconductor's foundation classes pass through his hands.
AnVIL family, cellxgenedp, AlphaMissenseR, BiocParallel back-ends, DirichletMultinomial. Long-time Bioc project lead.
Spectra and the MsBackend* family (Sql, Msp, MetaboLights), MetaboAnnotation / MetaboCoreUtils, ensembldb, CompoundDb — modular MS data access.
MSnbase, QFeatures, MsExperiment, PSMatch, ProtGenerics, hpar, qcmetrics — the open proteomics stack.
SingleCellExperiment (the class everyone uses), RUVSeq, scone, zinbwave, mbkmeans, awst, EDASeq.
GeneTonic, ideal, pcaExplorer, mosdef, quantiseqr — Shiny-shaped exploration on top of DESeq2.
clusterProfiler, enrichplot, DOSE, GOSemSim, ChIPseeker, ggtree / ggtreeDendro / ggtreeSpace, ggsc, ggmsa — almost every paper's enrichment panel comes from these.
MultiAssayExperiment, cBioPortalData, the AnVIL family (AnVIL, AnVILGCP, AnVILAz, AnVILBase, AnVILPublish), BiocCheck, BiocBaseUtils.
If you're starting fresh on a subject
Anchor packages per subject area — the ones a paper or pipeline almost always passes through. All present in our mirror.
SingleCellExperiment · scran · scater · DropletUtils · scDblFinder · batchelor · MultiAssayExperiment.
DESeq2 · edgeR · limma · tximport / tximeta · fgsea · clusterProfiler.
SpatialExperiment · STexampleData · STdeconvolve · BayesSpace.
MSnbase · QFeatures · Spectra · MsBackendSql · MsBackendMetaboLights · PSMatch.
xcms · MetaboAnnotation · MetaboCoreUtils · CompoundDb · MsFeatures.
mia · TreeSummarizedExperiment · curatedMetagenomicData · microbiome · benchdamic.
minfi · methylKit · ChIPseeker · DiffBind · chromVAR.
VariantAnnotation · maftools · VariantTools · MutationalPatterns.
MultiAssayExperiment · cBioPortalData · MOFA2 · mixOmics.
Where it lives in our mirror
Every package above is in our bucket — both the 3.22 release and the 3.23 devel cycle:
s3://ndexr/bioc/3.22/bioc/src/contrib/<package>_<ver>.tar.gz
s3://ndexr/bioc/3.23/bioc/src/contrib/<package>_<ver>.tar.gz
s3://ndexr/bioc/3.23/data/annotation/src/contrib/<package>_<ver>.tar.gz
s3://ndexr/bioc/3.23/data/experiment/src/contrib/<package>_<ver>.tar.gz
s3://ndexr/bioc/3.23/workflows/src/contrib/<package>_<ver>.tar.gz
Live coverage at
repo.ndexr.io
. Page numbers are regenerated from
r_pkg_state
— the same table this site reads from for
stats.ndexr.io
and
repo.ndexr.io
.