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

15,363

Versions

3,245

Maintainers

405,628,574

Downloads

Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 6 months ago - 44 dependent packages - 2.01 million downloads total - 1 maintainer
CompoundDb 1.14.2
Creating and Using (Chemical) Compound Annotation Databases
8 versions - Latest release: 2 months ago - 3 dependent packages - 31.9 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
DRIMSeq 1.38.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
6 versions - Latest release: 5 months ago - 1 dependent package - 67.2 thousand downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.1
flowCore: Basic structures for flow cytometry data
9 versions - Latest release: 3 months ago - 51 dependent packages - 4.96 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: 6 months ago - 632 dependent packages - 7.87 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: 6 months ago - 729 dependent packages - 12.2 million downloads total - 1 maintainer
BOBaFIT 1.14.0
Refitting diploid region profiles using a clustering procedure
6 versions - Latest release: 5 months ago - 8.93 thousand downloads total - 0 stars on GitHub - 1 maintainer
padma 1.20.0
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
8 versions - Latest release: 5 months ago - 11 thousand downloads total - 3 stars on GitHub - 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: 6 months ago - 12 dependent packages - 446 thousand downloads total - 1 maintainer
DelayedRandomArray 1.18.0
Delayed Arrays of Random Values
6 versions - Latest release: 5 months ago - 1 dependent package - 10.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 6 months ago - 48 dependent packages - 4.8 million downloads total - 1 maintainer
Top 6.0% on bioconductor.org
pathifier 1.48.0
Quantify deregulation of pathways in cancer
6 versions - Latest release: 5 months ago - 48.5 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 6 months ago - 36 dependent packages - 2 million 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: 4 months ago - 251 dependent packages - 5.26 million downloads total - 1 maintainer
shiny.gosling 1.6.0
A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization for R and Shiny
6 versions - Latest release: 2 months ago - 1 dependent package - 5.05 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.5
Visualization of Functional Enrichment Result
21 versions - Latest release: about 1 month ago - 15 dependent packages - 2.33 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 6 months ago - 333 dependent packages - 9.57 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 6 months ago - 93 dependent packages - 2.1 million downloads total - 1 maintainer
Sconify 1.30.0
A toolkit for performing KNN-based statistics for flow and mass cytometry data
7 versions - Latest release: 5 months ago - 14.8 thousand 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: 29 days ago - 28 dependent packages - 2.39 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: 6 months ago - 322 dependent packages - 7.08 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: 5 months ago - 146 dependent packages - 4.31 million downloads total - 330 stars on GitHub - 1 maintainer
MsBackendRawFileReader 1.16.0
Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
6 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 6 months ago - 15.3 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 6 months ago - 74 dependent packages - 2.27 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.36.1
A unified framework for working transparently with on-disk and in-memory array-like datasets
9 versions - Latest release: 14 days ago - 111 dependent packages - 8 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 6 months ago - 49 dependent packages - 1.42 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: 3 months ago - 30 dependent packages - 1.19 million downloads total - 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: 25 days ago - 96 dependent packages - 1.1 million downloads total - 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: 6 months ago - 10 dependent packages - 410 thousand downloads total - 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: 6 months ago - 183 dependent packages - 4.37 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data
8 versions - Latest release: 6 months ago - 201 dependent packages - 2.09 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: 4 months ago - 181 dependent packages - 4.35 million downloads total - 4 maintainers
pwalign 1.6.0
Perform pairwise sequence alignments
4 versions - Latest release: 5 months ago - 9 dependent packages - 270 thousand 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: 6 months ago - 14 dependent packages - 424 thousand downloads total - 2 maintainers
Top 9.7% on bioconductor.org
DEGraph 1.62.0
Two-sample tests on a graph
6 versions - Latest release: 5 months ago - 1 dependent package - 34.5 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: 4 months ago - 101 dependent packages - 3.56 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: 6 months ago - 33 dependent packages - 1.95 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: 4 months ago - 342 dependent packages - 10.8 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: 6 months ago - 563 dependent packages - 11.9 million 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: 4 months ago - 515 thousand downloads total - 384 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 6 months ago - 45 dependent packages - 2.46 million downloads total - 106 stars on GitHub - 2 maintainers
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: 6 months ago - 129 dependent packages - 2.84 million downloads total - 1 maintainer
geyser 1.2.0
Gene Expression displaYer of SummarizedExperiment in R
2 versions - Latest release: 5 months ago - 3.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R
8 versions - Latest release: 6 months ago - 54 dependent packages - 1.8 million 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: 4 months ago - 59 dependent packages - 2.49 million downloads total - 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: 6 months ago - 36 dependent packages - 9.64 million downloads total - 1 maintainer
Top 8.0% on bioconductor.org
pathRender 1.78.0
Render molecular pathways
6 versions - Latest release: 5 months ago - 40.1 thousand downloads total - 1 maintainer
cTRAP 1.28.0
Identification of candidate causal perturbations from differential gene expression data
7 versions - Latest release: 5 months ago - 14.9 thousand downloads total - 5 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: 6 months ago - 61 dependent packages - 1.95 million downloads total - 1 maintainer
Top 4.5% on bioconductor.org
derfinder 1.44.0
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via ...
6 versions - Latest release: 5 months ago - 6 dependent packages - 104 thousand downloads total - 44 stars on GitHub - 1 maintainer
attract 1.62.0
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor La...
6 versions - Latest release: 5 months ago - 42.4 thousand downloads total - 1 maintainer
XeniumIO 1.2.0
Import and represent Xenium data from the 10X Xenium Analyzer
2 versions - Latest release: 5 months ago - 3.23 thousand downloads total - 0 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: 6 months ago - 66 dependent packages - 4.2 million downloads total - 1 maintainer
Top 2.4% on bioconductor.org
EBImage 4.52.0
Image processing and analysis toolbox for R
6 versions - Latest release: 5 months ago - 18 dependent packages - 662 thousand downloads total - 75 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
Mulcom 1.60.0
Calculates Mulcom test
6 versions - Latest release: 5 months ago - 41.8 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: 6 months ago - 47 dependent packages - 2.39 million downloads total - 110 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments
8 versions - Latest release: 6 months ago - 132 dependent packages - 5.03 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 6 months ago - 518 dependent packages - 11.4 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: 4 months ago - 604 dependent packages - 9.47 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 6 months ago - 37 dependent packages - 2.67 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 6 months ago - 377 dependent packages - 8.94 million downloads total - 63 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.48.1
Foundation of vector-like and list-like containers in Bioconductor
10 versions - Latest release: 10 days ago - 740 dependent packages - 11.4 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 - 3.36 million downloads total - 72 stars on GitHub - 1 maintainer
Uniquorn 2.30.0
Identification of cancer cell lines based on their weighted mutational/ variational fingerprint
6 versions - Latest release: 5 months ago - 18.4 thousand downloads total - 1 maintainer
ZygosityPredictor 1.10.0
Package for prediction of zygosity for variants/genes in NGS data
6 versions - Latest release: 5 months ago - 6.88 thousand downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 6 months ago - 27 dependent packages - 2.29 million downloads total - 1 maintainer
Top 6.7% on bioconductor.org
BiocVersion 3.22.0
Set the appropriate version of Bioconductor packages
7 versions - Latest release: 5 months ago - 1 dependent package - 10.4 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 6 months ago - 31 dependent packages - 955 thousand downloads total - 63 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: 6 months ago - 6 dependent packages - 324 thousand downloads total - 1 maintainer
maskBAD 1.54.0
Masking probes with binding affinity differences
6 versions - Latest release: 5 months ago - 30.2 thousand downloads total - 1 maintainer
scone 1.34.0
Single Cell Overview of Normalized Expression data
7 versions - Latest release: 5 months ago - 35.1 thousand downloads total - 52 stars on GitHub - 1 maintainer
cosmiq 1.44.0
cosmiq - COmbining Single Masses Into Quantities
6 versions - Latest release: 5 months ago - 25.5 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: 3 months ago - 38 dependent packages - 2.36 million downloads total - 345 stars on GitHub - 1 maintainer
Top 6.6% on bioconductor.org
GSEAlm 1.70.0
Linear Model Toolset for Gene Set Enrichment Analysis
6 versions - Latest release: 5 months ago - 52.3 thousand downloads total - 1 maintainer
flowMeans 1.70.0
Non-parametric Flow Cytometry Data Gating
6 versions - Latest release: 5 months ago - 2 dependent packages - 60.2 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.76.0
Sequence logos for DNA sequence alignments
6 versions - Latest release: 6 months ago - 15 dependent packages - 518 thousand downloads total - 4 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: 6 months ago - 30 dependent packages - 602 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
flagme 1.66.0
Analysis of Metabolomics GC/MS Data
6 versions - Latest release: 5 months ago - 38.4 thousand downloads total - 2 maintainers
MatrixRider 1.42.0
Obtain total affinity and occupancies for binding site matrices on a given sequence
6 versions - Latest release: 5 months ago - 20.9 thousand downloads total - 1 maintainer
Rfastp 1.20.3
An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX ...
8 versions - Latest release: about 1 month ago - 16.5 thousand downloads total - 1 maintainer
miaTime 1.0.0
Microbiome Time Series Analysis
1 version - Latest release: 6 months ago - 1.76 thousand downloads total - 1 maintainer
RCX 1.14.2
R package implementing the Cytoscape Exchange (CX) format
9 versions - Latest release: 2 days ago - 1 dependent package - 10.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
diffGeneAnalysis 1.92.0
Performs differential gene expression Analysis
6 versions - Latest release: 5 months ago - 37.8 thousand downloads total - 1 maintainer
CardinalIO 1.8.0
Read and write mass spectrometry imaging files
5 versions - Latest release: 5 months ago - 1 dependent package - 11.6 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: 6 months ago - 9 dependent packages - 343 thousand downloads total - 486 stars on GitHub - 1 maintainer
hierinf 1.28.0
Hierarchical Inference
6 versions - Latest release: 5 months ago - 11.3 thousand downloads total - 1 maintainer
PANR 1.56.0
Posterior association networks and functional modules inferred from rich phenotypes of gene pertu...
6 versions - Latest release: 5 months ago - 30.5 thousand downloads total - 1 maintainer
normalize450K 1.38.0
Preprocessing of Illumina Infinium 450K data
6 versions - Latest release: 5 months ago - 17 thousand downloads total - 1 maintainer
diffUTR 1.18.0
diffUTR: Streamlining differential exon and 3' UTR usage
6 versions - Latest release: 5 months ago - 9.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
vbmp 1.78.0
Variational Bayesian Multinomial Probit Regression
6 versions - Latest release: 5 months ago - 44.2 thousand 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: 6 months ago - 15 dependent packages - 979 thousand downloads total - 185 stars on GitHub - 1 maintainer
MetaboCoreUtils 1.18.1
Core Utils for Metabolomics Data
8 versions - Latest release: 4 months ago - 5 dependent packages - 119 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
puma 3.52.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...
6 versions - Latest release: 5 months ago - 1 dependent package - 58 thousand downloads total - 1 maintainer
Spaniel 1.24.0
Spatial Transcriptomics Analysis
6 versions - Latest release: 5 months ago - 14 thousand downloads total - 1 maintainer
Top 8.6% on bioconductor.org
AnnotationFilter 1.34.0
Facilities for Filtering Bioconductor Annotation Resources
6 versions - Latest release: 5 months ago - 19 dependent packages - 1.38 million downloads total - 5 stars on GitHub - 1 maintainer
MethylAid 1.44.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets
6 versions - Latest release: 5 months ago - 29.9 thousand downloads total - 1 maintainer
transite 1.28.0
RNA-binding protein motif analysis
8 versions - Latest release: 5 months ago - 14 thousand downloads total - 1 maintainer
panelcn.mops 1.32.0
CNV detection tool for targeted NGS panel data
6 versions - Latest release: 5 months ago - 1 dependent package - 20.7 thousand downloads total - 1 maintainer
dearseq 1.22.0
Differential Expression Analysis for RNA-seq data through a robust variance component test
6 versions - Latest release: 5 months ago - 2 dependent packages - 20.7 thousand downloads total - 6 stars on GitHub - 1 maintainer