Michael Love

33 Bioconductor packages On Bioconductor since Apr 2013 (13 years) · last active 6 months ago

Bioconductor Packages

33 packages

Package	Title	Category	Version
CTCF Bioc	Genomic coordinates of CTCF binding sites, with orientation	annotation	0.99.14
DESeq2 Bioc	Differential gene expression analysis based on the negative binomial distribution	software	1.52.0
ExploreModelMatrix Bioc	Graphical Exploration of Design Matrices	software	1.24.0
GenomicFiles Bioc	Distributed computing by file or by range	software	1.48.0
airpart Bioc	Differential cell-type-specific allelic imbalance	software	1.20.0
airway Bioc	RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014	experiment	1.32.0
apeglm Bioc	Approximate posterior estimation for GLM coefficients	software	1.34.0
biocmask Bioc removed	Data masks for SummarizedExperiment enabling dplyr-like manipulation		0.99.19
denyranges Bioc removed	Genomic coordinates of problematic genomic regions		0.99.1
easylift Bioc	An R package to perform genomic liftover	software	1.10.0
eds Bioc	eds: Low-level reader for Alevin EDS format	software	1.14.0
excluderanges Bioc	Genomic coordinates of problematic genomic regions	annotation	0.99.11
fishpond Bioc	Fishpond: downstream methods and tools for expression data	software	2.18.0
fission Bioc	RangedSummarizedExperiment for time course RNA-Seq of fission yeast in response to stress, by Leong et al., Nat Commun 2014.	experiment	1.32.0
fluentGenomics Bioc	A plyranges and tximeta workflow	workflows	1.24.0
glmGamPoi Bioc	Fit a Gamma-Poisson Generalized Linear Model	software	1.24.0
macrophage Bioc	Human macrophage immune response	experiment	1.28.0
nullranges Bioc	Generation of null ranges via bootstrapping or covariate matching	software	1.18.0
nullrangesData Bioc	ExperimentHub datasets for the nullranges package	experiment	1.18.0
oct4 Bioc	Conditional knockdown of OCT4 in mouse ESCs	experiment	1.28.0
plotgardener Bioc	Coordinate-Based Genomic Visualization Package for R	software	1.18.0
plyranges Bioc	A fluent interface for manipulating GenomicRanges	software	1.32.0
plyxp Bioc	Data masks for SummarizedExperiment enabling dplyr-like manipulation	software	1.6.1
rigvf Bioc	R interface to the IGVF Catalog	software	1.4.2
rnaseqDTU Bioc	RNA-seq workflow for differential transcript usage following Salmon quantification	workflows	1.32.0
rnaseqGene Bioc	RNA-seq workflow: gene-level exploratory analysis and differential expression	workflows	1.36.0
savingBiocObjects Bioc removed	Saving Bioconductor Objects for Sharing		0.99.1
spatialDmelxsim Bioc	Spatial allelic expression counts for fly cross embryo	experiment	1.18.0
splicelogic Bioc	splicelogic: differential transcripts to splice events	software	1.0.1
tidyomics Bioc	Easily install and load the tidyomics ecosystem	software	1.8.0
tximeta Bioc	Transcript Quantification Import with Automatic Metadata	software	1.30.0
tximport Bioc	Import and summarize transcript-level estimates for transcript- and gene-level analysis	software	1.40.0
tximportData Bioc	tximportData	experiment	1.40.0

Package repositories

Repositories of packages Michael Love maintains where an AI coding tool was found. Other people commit to these repositories too, so each line describes the repository, not Michael Love's own work.

nullranges/nullranges ↗(organization: nullranges)
Packages: nullranges
- Claude Codefirst seen 2026-08-06
  Commits: at least 1 crediting it in the message
thelovelab/tximeta ↗(organization: thelovelab)
Packages: tximeta
- Claude Codefirst seen 2026-05-22
  Named in .gitignore: CLAUDE.md
  Commits: at least 1 crediting it in the message

Finding nothing does not mean no tool was used. How this is detected.