Data

Tools

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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

15,338

Versions

3,244

Maintainers

403,015,044

Downloads

Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 5 months ago - 31 dependent packages - 946 thousand downloads total - 63 stars on GitHub - 1 maintainer
rmelting 1.26.0
R Interface to MELTING 5
6 versions - Latest release: 5 months ago - 13 thousand downloads total - 2 stars on GitHub - 1 maintainer
SPOTlight 1.14.0
`SPOTlight`: Spatial Transcriptomics Deconvolution
10 versions - Latest release: 4 months ago - 20.1 thousand downloads total - 199 stars on GitHub - 1 maintainer
TrIdent 1.2.0
TrIdent - Transduction Identification
2 versions - Latest release: 4 months ago - 3.06 thousand downloads total - 2 stars on GitHub - 1 maintainer
spoon 1.6.0
Address the Mean-variance Relationship in Spatial Transcriptomics Data
5 versions - Latest release: 4 months ago - 5.06 thousand downloads total - 0 stars on GitHub - 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: 3 months ago - 251 dependent packages - 5.19 million downloads total - 1 maintainer
DeMAND 1.40.0
DeMAND
6 versions - Latest release: 4 months ago - 18.2 thousand downloads total - 2 maintainers
Top 3.2% on bioconductor.org
DropletUtils 1.30.0
Utilities for Handling Single-Cell Droplet Data
7 versions - Latest release: 4 months ago - 14 dependent packages - 329 thousand 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: 5 months ago - 322 dependent packages - 7.02 million downloads total - 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 - 9.38 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: 5 months ago - 15 dependent packages - 513 thousand downloads total - 4 stars on GitHub - 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: 4 months ago - 342 dependent packages - 10.7 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: 5 months ago - 45 dependent packages - 5.52 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: 5 months ago - 111 dependent packages - 7.88 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 4 months ago - 69 dependent packages - 3.31 million downloads total - 72 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 5 months ago - 729 dependent packages - 12.1 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: 5 months ago - 45 dependent packages - 2.43 million downloads total - 106 stars on GitHub - 2 maintainers
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 5 months ago - 10 dependent packages - 408 thousand downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 5 months ago - 14.8 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
XVector 0.50.0
Foundation of external vector representation and manipulation in Bioconductor
6 versions - Latest release: 5 months ago - 36 dependent packages - 9.53 million downloads total - 1 maintainer
Top 4.3% on bioconductor.org
GEOmetadb 1.72.0
A compilation of metadata from NCBI GEO
7 versions - Latest release: 4 months ago - 93.8 thousand 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: 5 months ago - 129 dependent packages - 2.81 million downloads total - 1 maintainer
Top 6.5% on bioconductor.org
PADOG 1.52.0
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
6 versions - Latest release: 4 months ago - 2 dependent packages - 54.4 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: 3 months ago - 59 dependent packages - 2.44 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.5
an R package for visualization of tree and annotation data
13 versions - Latest release: 7 days ago - 28 dependent packages - 2.33 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 5 months ago - 377 dependent packages - 8.84 million downloads total - 63 stars on GitHub - 1 maintainer
DepecheR 1.26.0
Determination of essential phenotypic elements of clusters in high-dimensional entities
6 versions - Latest release: 5 months ago - 1 dependent package - 25 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 5 months ago - 333 dependent packages - 9.46 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: 5 months ago - 14 dependent packages - 419 thousand downloads total - 2 maintainers
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 5 months ago - 518 dependent packages - 11.3 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 - 4.24 million downloads total - 330 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 5 months ago - 37 dependent packages - 2.65 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: 5 months ago - 563 dependent packages - 11.8 million 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: 5 months ago - 12 dependent packages - 442 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: 5 months ago - 9 dependent packages - 339 thousand downloads total - 485 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 5 months ago - 43 dependent packages - 1.18 million downloads total - 3 maintainers
HiCExperiment 1.10.0
Bioconductor class for interacting with Hi-C files in R
6 versions - Latest release: 4 months ago - 2 dependent packages - 11.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 5 months ago - 47 dependent packages - 2.36 million downloads total - 105 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 5 months ago - 33 dependent packages - 1.93 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 5 months ago - 61 dependent packages - 1.94 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: 5 months ago - 15 dependent packages - 976 thousand downloads total - 185 stars on GitHub - 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: 5 months ago - 30 dependent packages - 596 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 5 months ago - 27 dependent packages - 2.25 million 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: 2 months ago - 30 dependent packages - 1.18 million downloads total - 1 maintainer
ompBAM 1.14.0
C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files
6 versions - Latest release: 4 months ago - 1 dependent package - 9.89 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
fastseg 1.56.0
fastseg - a fast segmentation algorithm
6 versions - Latest release: 4 months ago - 1 dependent package - 153 thousand 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: 3 months ago - 181 dependent packages - 4.3 million downloads total - 4 maintainers
dcanr 1.26.0
Differential co-expression/association network analysis
6 versions - Latest release: 4 months ago - 1 dependent package - 18.6 thousand downloads total - 6 stars on GitHub - 1 maintainer
biodbChebi 1.16.0
biodbChebi, a library for connecting to the ChEBI Database
6 versions - Latest release: 4 months ago - 1 dependent package - 9.01 thousand downloads total - 2 stars on GitHub - 1 maintainer
miaDash 1.2.0
Dashboard for the interactive analysis and exploration of microbiome data
2 versions - Latest release: 4 months ago - 2.74 thousand downloads total - 1 stars on GitHub - 1 maintainer
fenr 1.8.1
Fast functional enrichment for interactive applications
14 versions - Latest release: 2 months ago - 7.19 thousand downloads total - 0 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: 5 months ago - 183 dependent packages - 4.32 million downloads total - 1 maintainer
multiGSEA 1.20.0
Combining GSEA-based pathway enrichment with multi omics data integration
7 versions - Latest release: 4 months ago - 17.6 thousand downloads total - 20 stars on GitHub - 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: 5 months ago - 740 dependent packages - 11.3 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 5 months ago - 36 dependent packages - 1.99 million downloads total - 1 maintainer
CellMixS 1.26.0
Evaluate Cellspecific Mixing
6 versions - Latest release: 4 months ago - 18.5 thousand downloads total - 7 stars on GitHub - 1 maintainer
SmartPhos 1.0.0
A phosphoproteomics data analysis package with an interactive ShinyApp
1 version - Latest release: 5 months ago - 408 downloads total - 5 stars on GitHub - 1 maintainer
spqn 1.22.0
Spatial quantile normalization
6 versions - Latest release: 4 months ago - 10.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
consensusSeekeR 1.38.0
Detection of consensus regions inside a group of experiences using genomic positions and genomic ...
6 versions - Latest release: 4 months ago - 2 dependent packages - 20.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
omicsGMF 1.0.0
Dimensionality reduction of (single-cell) omics data in R using omicsGMF
1 version - Latest release: 5 months ago - 1.02 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.38.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
8 versions - Latest release: 4 months ago - 7 dependent packages - 580 thousand downloads total - 339 stars on GitHub - 2 maintainers
idr2d 1.24.0
Irreproducible Discovery Rate for Genomic Interactions Data
7 versions - Latest release: 4 months ago - 12.6 thousand downloads total - 1 maintainer
mspms 1.2.0
Tools for the analysis of MSP-MS data
2 versions - Latest release: 4 months ago - 3.55 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.1
Single-Cell Analysis Toolkit for Gene Expression Data in R
10 versions - Latest release: 3 days ago - 96 dependent packages - 1.08 million downloads total - 1 maintainer
scider 1.8.0
Spatial cell-type inter-correlation by density in R
5 versions - Latest release: 4 months ago - 6.81 thousand downloads total - 7 stars on GitHub - 1 maintainer
biodbNci 1.13.0
biodbNci, a library for connecting to biodbNci, a library for connecting to the National Cancer I...
6 versions - Latest release: 4 months ago - 7.14 thousand 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 - 3.52 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays
7 versions - Latest release: 5 months ago - 632 dependent packages - 7.78 million downloads total - 1 maintainer
Top 8.4% on bioconductor.org
gaga 2.56.0
GaGa hierarchical model for high-throughput data analysis
6 versions - Latest release: 5 months ago - 1 dependent package - 42 thousand downloads total - 1 maintainer
vtpnet 0.50.0
variant-transcription factor-phenotype networks
6 versions - Latest release: 4 months ago - 25.9 thousand downloads total - 1 maintainer
RedisParam 1.12.1
Provide a 'redis' back-end for BiocParallel
7 versions - Latest release: 2 months ago - 7.16 thousand downloads total - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 5 months ago - 6 dependent packages - 321 thousand downloads total - 1 maintainer
SimBu 1.12.0
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
7 versions - Latest release: 4 months ago - 9.12 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: 2 months ago - 38 dependent packages - 2.31 million downloads total - 345 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.6.2
Interactive visualization and manipulation of nested networks
8 versions - Latest release: about 1 month ago - 4 dependent packages - 64.7 thousand downloads total - 1 maintainer
SigsPack 1.24.0
Mutational Signature Estimation for Single Samples
6 versions - Latest release: 4 months ago - 11.3 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: 2 months ago - 51 dependent packages - 4.96 million downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SCAN.UPC 2.52.0
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
6 versions - Latest release: 4 months ago - 45.1 thousand downloads total - 1 maintainer
consensusDE 1.28.0
RNA-seq analysis using multiple algorithms
6 versions - Latest release: 4 months ago - 14 thousand downloads total - 1 maintainer
riboSeqR 1.44.0
Analysis of sequencing data from ribosome profiling experiments
6 versions - Latest release: 4 months ago - 27.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.5
Visualization of Functional Enrichment Result
21 versions - Latest release: 21 days ago - 15 dependent packages - 2.28 million downloads total - 1 maintainer
SpaceMarkers 2.0.0
Spatial Interaction Markers
4 versions - Latest release: 4 months ago - 5.15 thousand downloads total - 5 stars on GitHub - 1 maintainer
omicplotR 1.30.0
Visual Exploration of Omic Datasets Using a Shiny App
6 versions - Latest release: 4 months ago - 15.4 thousand downloads total - 1 maintainer
Top 5.5% on bioconductor.org
iSEE 2.22.0
Interactive SummarizedExperiment Explorer
6 versions - Latest release: 4 months ago - 8 dependent packages - 64.1 thousand downloads total - 228 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: 5 months ago - 49 dependent packages - 1.4 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: 5 months ago - 132 dependent packages - 4.96 million downloads total - 1 maintainer
evaluomeR 1.26.0
Evaluation of Bioinformatics Metrics
7 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
DiffBind 3.20.0
Differential Binding Analysis of ChIP-Seq Peak Data
6 versions - Latest release: 4 months ago - 2 dependent packages - 305 thousand downloads total - 1 maintainer
rcellminer 2.32.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
7 versions - Latest release: 5 months ago - 24.9 thousand downloads total - 3 maintainers
TransView 1.54.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
8 versions - Latest release: about 1 month ago - 28.9 thousand downloads total - 1 maintainer
twoddpcr 1.34.0
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
6 versions - Latest release: 4 months ago - 16.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
flowCyBar 1.46.0
Analyze flow cytometric data using gate information
6 versions - Latest release: 4 months ago - 22.9 thousand downloads total - 1 maintainer
doubletrouble 1.10.0
Identification and classification of duplicated genes
13 versions - Latest release: 4 months ago - 8.55 thousand downloads total - 31 stars on GitHub - 1 maintainer
RiboCrypt 1.16.0
Interactive visualization in genomics
7 versions - Latest release: 4 months ago - 8.48 thousand downloads total - 5 stars on GitHub - 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: 5 months ago - 66 dependent packages - 4.17 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 5 months ago - 44 dependent packages - 1.99 million downloads total - 1 maintainer
affyContam 1.68.0
structured corruption of affymetrix cel file data
6 versions - Latest release: 4 months ago - 1 dependent package - 48.8 thousand downloads total - 1 maintainer
CiteFuse 1.22.0
CiteFuse: multi-modal analysis of CITE-seq data
6 versions - Latest release: 4 months ago - 1 dependent package - 14 thousand downloads total - 25 stars on GitHub - 1 maintainer
RareVariantVis 2.38.0
A suite for analysis of rare genomic variants in whole genome sequencing data
6 versions - Latest release: 4 months ago - 20.4 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
MeasurementError.cor 1.82.0
Measurement Error model estimate for correlation coefficient
6 versions - Latest release: 4 months ago - 34.7 thousand downloads total - 1 maintainer