Bioconductor Packages

Public

The complete Bioconductor software ecosystem for bioinformatics in R. Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Founded in 2001, it has grown to ~3,700 packages spanning every major area of computational biology: - Gene expression analysis (DESeq2, edgeR, limma) - Single-cell analysis (SingleCellExperiment, scran, scater) - Proteomics and mass spectrometry (MSstats, OpenMS, mzR) - Flow cytometry (flowCore, flowClust) - Genomic annotation (GenomicFeatures, AnnotationDbi, biomaRt) - Sequence analysis (Biostrings, GenomicAlignments, Rsamtools) - Epigenomics (methylKit, ChIPseeker, bsseq) - Visualization (Gviz, ggbio, ComplexHeatmap) This portfolio maps each package to its upstream GitHub repository where available, falling back to the official Bioconductor mirror (github.com/bioc/*) otherwise — giving a more complete view of the authors, contributors, and development communities behind the Bioconductor ecosystem.

Created 4/16/2026 - Last updated 7/12/2026

3.7K

Projects

111.1K commits

4.8K

Recognition

4.8K citing papers · 9 canonical works

Reach

5.4K external users · 0 downloads

293

Repositories at risk

8% of 3.7K evaluated · 3.4K healthy

3.7K

Without canonical credit

of 3.7K · 0% have detected canonical

3.9K unwrapped

Metadata coverage

repo → publication funnel

Projects in this portfolio3,710100%

with any publication linkage1233%

with canonical paper detected70%

distinct canonical works90%

canonical

mentions

193

paper

Of 3,710 projects in this portfolio, 3,587 (97%) have no detected publication linkage of any kind. These gaps are part of the story — software metadata in the wild is often missing.

Top recognized work

see all →

Most-cited publications representing software in this portfolio — the academic credit going to these projects. Items marked "detection gap" are likely portfolio software whose canonical link our pipeline failed to record.

1.
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
3,495 citations · 10.1093/bioinformatics/btm254
2.
Visualizing Genomic Data Using Gviz and Bioconductor
1,003 citations · 10.1007/978-1-4939-3578-9_16
3.
universalmotif: An R package for biological motifanalysis
37 citations · 10.21105/joss.07012
4.
TRIP - T cell receptor/immunoglobulin profiler
16 citations · 10.1186/s12859-020-03669-1
5.
Curated single cell multimodal landmark datasets for R/Bioconductor
7 citations · 10.1371/journal.pcbi.1011324
6.
SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
1 citations · 10.21105/joss.08070
7.
SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
0 citations · 10.5281/zenodo.15461604
8.
CBN2Path
0 citations · 10.5281/zenodo.16791479
9.
universalmotif: An R package for biological motif analysis
0 citations · 10.5281/zenodo.13341141

External foundational dependencies

Upstream tools the portfolio depends on whose home repos are not in this portfolio. The citation counts here belong to the cited work — they show what these projects are built on, not what this portfolio is cited for.

1.
limma powers differential expression analyses for RNA-sequencing and microarray studies
41,776 citations · used by 1 repo · 10.1093/nar/gkv007
2.
KEGG: Kyoto Encyclopedia of Genes and Genomes
38,563 citations · used by 1 repo · 10.1093/nar/28.1.27
3.
DADA2: High-resolution sample inference from Illumina amplicon data
35,072 citations · used by 1 repo · 10.1038/nmeth.3869
4.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
22,760 citations · used by 2 repos · 10.1186/gb-2009-10-3-r25
5.
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
14,245 citations · used by 1 repo · 10.1093/bioinformatics/btv351
6.
Building Predictive Models in <i>R</i> Using the <b>caret</b> Package
8,956 citations · used by 1 repo · 10.18637/jss.v028.i05
7.
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
6,300 citations · used by 1 repo · 10.1038/nature10983
8.
Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes
4,811 citations · used by 1 repo · 10.1200/jco.2008.18.1370
9.
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
3,437 citations · used by 1 repo · 10.1186/s40168-018-0605-2
10.
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
3,368 citations · used by 1 repo · 10.1038/ismej.2017.119

People & places

Bridge contributors

191

people contribute to 2+ projects in this portfolio · 12% of all contributors

Top citing institutions

Harvard University(US)745
Centre National de la Recherche Scientifique(FR)654
Karolinska Institutet(SE)605
Chinese Academy of Sciences(CN)482
University of Cambridge(GB)434

Explore Full Interactive Graph

Impact

4.8K

Total Citations

4.8K

Citing Papers

254

Linked Publications

4.7K

Software Dependents

135.0K

Citing Authors

13.4K

Citing Institutions

Biochemistry, Genetics...

Top Citing Field

	Portfolio	Citing
Domains	4	4
Fields	15	26
Subfields	53	235
Topics	133	2663

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Dependencies

36.1K

Total Dependencies

Ecosystems

324

Research SW Links

Hidden Found

Ecosystem	Packages
cran	32360
actions	2322
pypi	746
conda	397

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Community

303 items at risk — review sustainability

2.7K

Total People

Retention Rate

35%

Intl. Collaboration

10 pubs · 293 repos

At Risk

	Pubs	Repos
Core	66	...
Active	97	1540
Bus Factor	-	1

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MCP Ecosystem

3920 entities have no MCP wrapper — potential funding gaps

3.9K

Unwrapped Entities

3.9K

Portfolio Entities

Wrapping Servers

100%

Gap Rate

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