Data

Tools

Indexes

Applications

Experiments

Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org

2,564

Packages

15,290

Versions

3,231

Maintainers

399,054,485

Downloads

Top 1.7% on bioconductor.org
ggtree 4.0.4
an R package for visualization of tree and annotation data
12 versions - Latest release: about 2 months ago - 28 dependent packages - 2.26 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.78.0
Software infrastructure for efficient representation of full genomes and their SNPs
8 versions - Latest release: 4 months ago - 129 dependent packages - 2.79 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.46.2
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
21 versions - Latest release: 3 months ago - 342 dependent packages - 10.6 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 4 months ago - 14 dependent packages - 417 thousand downloads total - 2 maintainers
pmp 1.22.1
Peak Matrix Processing and signal batch correction for metabolomics datasets
7 versions - Latest release: 4 months ago - 2 dependent packages - 16.9 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 4 months ago - 518 dependent packages - 11.2 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 4 months ago - 33 dependent packages - 1.92 million downloads total - 1 maintainer
fedup 1.18.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
6 versions - Latest release: 4 months ago - 8.77 thousand downloads total - 7 stars on GitHub - 1 maintainer
lineagespot 1.14.0
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
6 versions - Latest release: 3 months ago - 7.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 4 months ago - 61 dependent packages - 1.93 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.8.0
LC-MS and GC-MS Data Analysis
13 versions - Latest release: 4 months ago - 15 dependent packages - 973 thousand downloads total - 185 stars on GitHub - 1 maintainer
MetaboAnnotation 1.14.0
Utilities for Annotation of Metabolomics Data
9 versions - Latest release: 4 months ago - 20.1 thousand downloads total - 17 stars on GitHub - 1 maintainer
tpSVG 1.6.0
Thin plate models to detect spatially variable genes
5 versions - Latest release: 4 months ago - 4.86 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.1
flowCore: Basic structures for flow cytometry data
9 versions - Latest release: about 2 months ago - 51 dependent packages - 4.95 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.92.0
genefilter: methods for filtering genes from high-throughput experiments
6 versions - Latest release: 4 months ago - 66 dependent packages - 4.16 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 4 months ago - 377 dependent packages - 8.74 million downloads total - 63 stars on GitHub - 1 maintainer
DiscoRhythm 1.26.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
6 versions - Latest release: 4 months ago - 13.9 thousand downloads total - 13 stars on GitHub - 1 maintainer
prebs 1.50.0
Probe region expression estimation for RNA-seq data for improved microarray comparability
6 versions - Latest release: 3 months ago - 28 thousand downloads total - 1 maintainer
BAGS 2.50.0
A Bayesian Approach for Geneset Selection
6 versions - Latest release: 4 months ago - 28.7 thousand downloads total - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.70.1
R interface to genome annotation files and the UCSC genome browser
7 versions - Latest release: 2 months ago - 251 dependent packages - 5.14 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 4 months ago - 322 dependent packages - 6.96 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.48.0
Foundation of vector-like and list-like containers in Bioconductor
9 versions - Latest release: 4 months ago - 740 dependent packages - 11.2 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.4
Visualization of Functional Enrichment Result
20 versions - Latest release: 3 months ago - 15 dependent packages - 2.23 million downloads total - 1 maintainer
timeOmics 1.22.0
Time-Course Multi-Omics data integration
6 versions - Latest release: 4 months ago - 1 dependent package - 12.4 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 4 months ago - 49 dependent packages - 1.39 million downloads total - 1 maintainer
Top 2.8% on bioconductor.org
RUVSeq 1.44.0
Remove Unwanted Variation from RNA-Seq Data
6 versions - Latest release: 4 months ago - 7 dependent packages - 201 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
scmap 1.32.0
A tool for unsupervised projection of single cell RNA-seq data
6 versions - Latest release: 4 months ago - 49.3 thousand downloads total - 86 stars on GitHub - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 4 months ago - 14.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
adSplit 1.80.0
Annotation-Driven Clustering
6 versions - Latest release: 4 months ago - 49.2 thousand downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.18.4
A universal enrichment tool for interpreting omics data
19 versions - Latest release: 2 months ago - 59 dependent packages - 2.4 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 4 months ago - 44 dependent packages - 1.97 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.76.0
Sequence logos for DNA sequence alignments
6 versions - Latest release: 4 months ago - 15 dependent packages - 508 thousand downloads total - 4 stars on GitHub - 1 maintainer
rWikiPathways 1.30.0
rWikiPathways - R client library for the WikiPathways API
6 versions - Latest release: 3 months ago - 5 dependent packages - 77.6 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
GenomicRanges 1.62.1
Representation and manipulation of genomic intervals
10 versions - Latest release: 3 months ago - 604 dependent packages - 9.29 million downloads total - 1 maintainer
biocmake 1.2.0
CMake for Bioconductor
3 versions - Latest release: 3 months ago - 13.9 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays
7 versions - Latest release: 4 months ago - 632 dependent packages - 7.69 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.50.2
Differential gene expression analysis based on the negative binomial distribution
11 versions - Latest release: 4 months ago - 146 dependent packages - 4.2 million downloads total - 330 stars on GitHub - 1 maintainer
Top 3.7% on bioconductor.org
safe 3.50.0
Significance Analysis of Function and Expression
6 versions - Latest release: 4 months ago - 2 dependent packages - 110 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
EnhancedVolcano 1.28.2
Publication-ready volcano plots with enhanced colouring and labeling
7 versions - Latest release: 3 months ago - 499 thousand downloads total - 384 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 4 months ago - 48 dependent packages - 4.73 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 4 months ago - 729 dependent packages - 12 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R
8 versions - Latest release: 4 months ago - 54 dependent packages - 1.73 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 3 months ago - 69 dependent packages - 3.27 million downloads total - 72 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 4 months ago - 74 dependent packages - 2.25 million downloads total - 1 maintainer
Rcollectl 1.10.0
Help use collectl with R in Linux, to measure resource consumption in R processes
6 versions - Latest release: 3 months ago - 4.51 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.38.2
Import and summarize transcript-level estimates for transcript- and gene-level analysis
8 versions - Latest release: 29 days ago - 13 dependent packages - 555 thousand downloads total - 141 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 4 months ago - 43 dependent packages - 1.17 million downloads total - 3 maintainers
trio 3.48.0
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
6 versions - Latest release: 3 months ago - 32.7 thousand downloads total - 1 maintainer
COMPASS 1.48.0
Combinatorial Polyfunctionality Analysis of Single Cells
6 versions - Latest release: 4 months ago - 29.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
beachmat 2.26.0
Compiling Bioconductor to Handle Each Matrix Type
7 versions - Latest release: 3 months ago - 15 dependent packages - 1.78 million downloads total - 5 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 4 months ago - 36 dependent packages - 1.98 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 3 months ago - 101 dependent packages - 3.48 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.44.0
Foundation of integer range manipulation in Bioconductor
8 versions - Latest release: 4 months ago - 563 dependent packages - 11.7 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R
26 versions - Latest release: 2 months ago - 181 dependent packages - 4.27 million downloads total - 4 maintainers
Top 0.9% on bioconductor.org
XVector 0.50.0
Foundation of external vector representation and manipulation in Bioconductor
6 versions - Latest release: 4 months ago - 36 dependent packages - 9.43 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 4 months ago - 45 dependent packages - 2.39 million downloads total - 106 stars on GitHub - 2 maintainers
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 4 months ago - 37 dependent packages - 2.63 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments
8 versions - Latest release: 4 months ago - 132 dependent packages - 4.92 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
MatrixGenerics 1.22.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
7 versions - Latest release: 4 months ago - 45 dependent packages - 5.44 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 4 months ago - 27 dependent packages - 2.21 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: about 2 months ago - 38 dependent packages - 2.27 million downloads total - 345 stars on GitHub - 1 maintainer
clustifyr 1.22.0
Classifier for Single-cell RNA-seq Using Cell Clusters
8 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 123 stars on GitHub - 1 maintainer
DelayedDataFrame 1.26.0
Delayed operation on DataFrame using standard DataFrame metaphor
6 versions - Latest release: 4 months ago - 1 dependent package - 12.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
CIMICE 1.18.0
CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
6 versions - Latest release: 3 months ago - 8.64 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 4 months ago - 333 dependent packages - 9.37 million downloads total - 1 maintainer
Top 5.4% on bioconductor.org
QDNAseq 1.46.0
Quantitative DNA Sequencing for Chromosomal Aberrations
6 versions - Latest release: 3 months ago - 4 dependent packages - 78.2 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
iBBiG 1.54.0
Iterative Binary Biclustering of Genesets
6 versions - Latest release: 3 months ago - 1 dependent package - 36.5 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files
6 versions - Latest release: 4 months ago - 9 dependent packages - 336 thousand downloads total - 485 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 4 months ago - 6 dependent packages - 319 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
oligoClasses 1.72.0
Classes for high-throughput arrays supported by oligo and crlmm
6 versions - Latest release: 4 months ago - 12 dependent packages - 440 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.1
Variance stabilization and calibration for microarray data
7 versions - Latest release: about 1 month ago - 30 dependent packages - 1.17 million downloads total - 1 maintainer
GenomicTuples 1.44.0
Representation and Manipulation of Genomic Tuples
6 versions - Latest release: 4 months ago - 22.5 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 4 months ago - 93 dependent packages - 2.07 million downloads total - 1 maintainer
BREW3R.r 1.6.0
R package associated to BREW3R
5 versions - Latest release: 4 months ago - 5.13 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 4 months ago - 10 dependent packages - 406 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
BiocStyle 2.38.0
Standard styles for vignettes and other Bioconductor documents
7 versions - Latest release: 3 months ago - 1,298 dependent packages - 1.05 million downloads total - 14 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data
8 versions - Latest release: 4 months ago - 201 dependent packages - 2.02 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.36.0
A unified framework for working transparently with on-disk and in-memory array-like datasets
8 versions - Latest release: 4 months ago - 111 dependent packages - 7.79 million downloads total - 1 maintainer
ngsReports 2.12.1
Load FastqQC reports and other NGS related files
8 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 23 stars on GitHub - 1 maintainer
pepStat 1.44.0
Statistical analysis of peptide microarrays
6 versions - Latest release: 3 months ago - 22.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.62.0
Query the gene models of a given organism/assembly
9 versions - Latest release: 4 months ago - 183 dependent packages - 4.29 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics
8 versions - Latest release: 4 months ago - 30 dependent packages - 591 thousand downloads total - 123 stars on GitHub - 1 maintainer
rCGH 1.40.0
Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
6 versions - Latest release: 3 months ago - 1 dependent package - 27.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
illuminaio 0.52.0
Parsing Illumina Microarray Output Files
6 versions - Latest release: 3 months ago - 12 dependent packages - 594 thousand downloads total - 5 stars on GitHub - 1 maintainer
SanityR 1.0.0
R/Bioconductor interface to the Sanity model gene expression analysis
1 version - Latest release: 4 months ago - 1.15 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
monocle 2.38.0
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
7 versions - Latest release: 4 months ago - 6 dependent packages - 489 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 4 months ago - 47 dependent packages - 2.34 million downloads total - 105 stars on GitHub - 1 maintainer
CellMapper 1.36.0
Predict genes expressed selectively in specific cell types
6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
BiocHubsShiny 1.10.0
View AnnotationHub and ExperimentHub Resources Interactively
8 versions - Latest release: 4 months ago - 7.81 thousand downloads total - 0 stars on GitHub - 1 maintainer
CausalR 1.42.0
Causal network analysis methods
6 versions - Latest release: 4 months ago - 20.4 thousand downloads total - 2 maintainers
MSstatsShiny 1.12.1
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
11 versions - Latest release: 2 days ago - 9.86 thousand downloads total - 9 stars on GitHub - 1 maintainer
VplotR 1.20.0
Set of tools to make V-plots and compute footprint profiles
7 versions - Latest release: 3 months ago - 10.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
consICA 2.8.0
consensus Independent Component Analysis
6 versions - Latest release: 4 months ago - 8.87 thousand downloads total - 0 stars on GitHub - 1 maintainer
uSORT 1.36.0
uSORT: A self-refining ordering pipeline for gene selection
6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
9 versions - Latest release: 4 months ago - 96 dependent packages - 1.06 million downloads total - 1 maintainer
frenchFISH 1.22.0
Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections
6 versions - Latest release: 4 months ago - 8.95 thousand downloads total - 1 maintainer
TrajectoryGeometry 1.18.0
This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
8 versions - Latest release: 4 months ago - 7.48 thousand downloads total - 1 maintainer
progeny 1.32.0
Pathway RespOnsive GENes for activity inference from gene expression
6 versions - Latest release: 4 months ago - 2 dependent packages - 53.8 thousand downloads total - 108 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.16.0
Illumina DNA methylation array normalization and metrics
6 versions - Latest release: 4 months ago - 5 dependent packages - 182 thousand downloads total - 1 maintainer
PROPS 1.32.0
PRObabilistic Pathway Score (PROPS)
7 versions - Latest release: 4 months ago - 14.6 thousand downloads total - 1 maintainer