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

bioconductor.org packages

Top 0.6% on bioconductor.org
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments
8 versions - Latest release: 3 months ago - 132 dependent packages - 4.84 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: 2 months ago - 146 dependent packages - 4.12 million downloads total - 330 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 3 months ago - 31 dependent packages - 932 thousand downloads total - 64 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: 3 months ago - 45 dependent packages - 2.34 million downloads total - 106 stars on GitHub - 2 maintainers
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 3 months ago - 49 dependent packages - 1.36 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: about 1 month ago - 101 dependent packages - 3.43 million downloads total - 1 maintainer
surfaltr 1.16.0
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
6 versions - Latest release: 2 months ago - 8.15 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 3 months ago - 44 dependent packages - 1.95 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 3 months ago - 93 dependent packages - 2.04 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: 3 months ago - 61 dependent packages - 1.9 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: 3 months ago - 729 dependent packages - 11.8 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.0
Variance stabilization and calibration for microarray data
6 versions - Latest release: 3 months ago - 30 dependent packages - 1.15 million 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: 3 months ago - 96 dependent packages - 1.03 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: 19 days ago - 181 dependent packages - 4.2 million downloads total - 4 maintainers
Top 1.5% on bioconductor.org
xcms 4.8.0
LC-MS and GC-MS Data Analysis
13 versions - Latest release: 3 months ago - 15 dependent packages - 963 thousand downloads total - 185 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 3 months ago - 48 dependent packages - 4.68 million downloads total - 1 maintainer
AlphaBeta 1.24.0
Computational inference of epimutation rates and spectra from high-throughput DNA methylation dat...
6 versions - Latest release: 2 months ago - 15 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: 3 months ago - 15 dependent packages - 499 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 3 months ago - 43 dependent packages - 1.15 million downloads total - 3 maintainers
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 3 months ago - 47 dependent packages - 2.31 million downloads total - 103 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: 3 months ago - 27 dependent packages - 2.15 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: 3 months ago - 111 dependent packages - 7.64 million downloads total - 1 maintainer
Top 3.6% on bioconductor.org
NOISeq 2.54.0
Exploratory analysis and differential expression for RNA-seq data
6 versions - Latest release: 2 months ago - 5 dependent packages - 133 thousand downloads total - 1 maintainer
Linnorm 2.34.0
Linear model and normality based normalization and transformation method (Linnorm)
6 versions - Latest release: 2 months ago - 1 dependent package - 34.6 thousand 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: 3 months ago - 54 dependent packages - 1.68 million downloads total - 1 maintainer
concordexR 1.10.0
Identify Spatial Homogeneous Regions with concordex
6 versions - Latest release: 2 months ago - 6.63 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 3 months ago - 36 dependent packages - 1.96 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 3 months ago - 74 dependent packages - 2.23 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 3 months ago - 37 dependent packages - 2.6 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: 3 months ago - 33 dependent packages - 1.89 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: 3 months ago - 201 dependent packages - 1.96 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: 8 days ago - 38 dependent packages - 2.19 million downloads total - 345 stars on GitHub - 1 maintainer
Coralysis 1.0.0
Coralysis sensitive identification of imbalanced cell types and states in single-cell data via mu...
1 version - Latest release: 3 months ago - 1.58 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.18.4
A universal enrichment tool for interpreting omics data
19 versions - Latest release: about 1 month ago - 59 dependent packages - 2.33 million downloads total - 1 maintainer
HiCaptuRe 1.0.0
HiCaptuRe: Manipulating and integrating Capture Hi-C data
1 version - Latest release: 3 months ago - 761 downloads total - 1 maintainer
SuperCellCyto 1.0.0
SuperCell For Cytometry Data
1 version - Latest release: 3 months ago - 678 downloads total - 13 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: 3 months ago - 12 dependent packages - 434 thousand downloads total - 1 maintainer
multiGSEA 1.20.0
Combining GSEA-based pathway enrichment with multi omics data integration
7 versions - Latest release: about 2 months ago - 16.6 thousand downloads total - 20 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: 3 months ago - 183 dependent packages - 4.23 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 3 months ago - 377 dependent packages - 8.57 million downloads total - 63 stars on GitHub - 1 maintainer
RedisParam 1.12.1
Provide a 'redis' back-end for BiocParallel
7 versions - Latest release: 4 days ago - 6.35 thousand downloads total - 1 maintainer
autonomics 1.18.0
Unified Statistical Modeling of Omics Data
9 versions - Latest release: 2 months ago - 9.57 thousand downloads total - 3 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: 3 months ago - 632 dependent packages - 7.54 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: 3 months ago - 66 dependent packages - 4.12 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: 3 months ago - 10 dependent packages - 403 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 3 months ago - 333 dependent packages - 9.21 million downloads total - 1 maintainer
GenomicTuples 1.44.0
Representation and Manipulation of Genomic Tuples
6 versions - Latest release: 3 months ago - 21.9 thousand downloads total - 5 stars on GitHub - 1 maintainer
combi 1.22.0
Compositional omics model based visual integration
6 versions - Latest release: about 2 months ago - 10.3 thousand downloads total - 0 stars on GitHub - 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: 3 months ago - 45 dependent packages - 5.3 million downloads total - 1 maintainer
SPONGE 1.32.0
Sparse Partial Correlations On Gene Expression
7 versions - Latest release: 2 months ago - 2 dependent packages - 14.8 thousand 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: 3 months ago - 30 dependent packages - 577 thousand downloads total - 123 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 3 months ago - 322 dependent packages - 6.85 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: 22 days ago - 251 dependent packages - 5.06 million downloads total - 1 maintainer
Top 9.6% on bioconductor.org
NCIgraph 1.58.0
Pathways from the NCI Pathways Database
6 versions - Latest release: 2 months ago - 1 dependent package - 33.1 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: about 1 month ago - 484 thousand downloads total - 384 stars on GitHub - 1 maintainer
gg4way 1.8.0
4way Plots of Differential Expression
8 versions - Latest release: 3 months ago - 5.79 thousand downloads total - 0 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: about 1 month ago - 604 dependent packages - 9.12 million downloads total - 1 maintainer
DNEA 1.0.0
Differential Network Enrichment Analysis for Biological Data
1 version - Latest release: 3 months ago - 1.44 thousand downloads total - 3 stars on GitHub - 1 maintainer
AWFisher 1.24.0
An R package for fast computing for adaptively weighted fisher's method
6 versions - Latest release: 2 months ago - 13.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.6.0
Interactive visualization and manipulation of nested networks
7 versions - Latest release: 2 months ago - 4 dependent packages - 62.8 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
parody 1.68.0
Parametric And Resistant Outlier DYtection
7 versions - Latest release: 2 months ago - 1 dependent package - 49.1 thousand downloads total - 1 maintainer
hdxmsqc 1.6.0
An R package for quality Control for hydrogen deuterium exchange mass spectrometry experiments
5 versions - Latest release: 2 months ago - 3.54 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpaceTrooper 1.0.1
SpaceTrooper performs Quality Control analysis of Image-Based spatial
2 versions - Latest release: 2 days ago - 1.22 thousand downloads total - 8 stars on GitHub - 1 maintainer
rnaseqcomp 1.40.0
Benchmarks for RNA-seq Quantification Pipelines
6 versions - Latest release: about 1 month ago - 1 dependent package - 19.6 thousand downloads total - 8 stars on GitHub - 1 maintainer
PDATK 1.18.0
Pancreatic Ductal Adenocarcinoma Tool-Kit
7 versions - Latest release: 2 months ago - 9.6 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaDICT 1.0.0
Microbiome data integration method via shared dictionary learning
1 version - Latest release: 3 months ago - 612 downloads total - 2 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 3 months ago - 14 dependent packages - 412 thousand downloads total - 2 maintainers
RSVSim 1.50.0
RSVSim: an R/Bioconductor package for the simulation of structural variations
6 versions - Latest release: 2 months ago - 29.6 thousand downloads total - 1 maintainer
ASURAT 1.14.0
Functional annotation-driven unsupervised clustering for single-cell data
6 versions - Latest release: 2 months ago - 8.36 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: 2 months ago - 23.7 thousand downloads total - 3 maintainers
GeneGA 1.60.0
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
6 versions - Latest release: 2 months ago - 21.5 thousand downloads total - 1 maintainer
scLANE 1.0.0
Model Gene Expression Dynamics with Spline-Based NB GLMs, GEEs, & GLMMs
1 version - Latest release: 3 months ago - 481 downloads total - 1 maintainer
protGear 1.14.0
Protein Micro Array Data Management and Interactive Visualization
6 versions - Latest release: 2 months ago - 9.33 thousand downloads total - 1 stars on GitHub - 1 maintainer
stPipe 1.0.1
Upstream pre-processing for Sequencing-Based Spatial Transcriptomics
2 versions - Latest release: about 1 month ago - 887 downloads total - 4 stars on GitHub - 1 maintainer
cbaf 1.32.0
Automated functions for comparing various omic data from cbioportal.org
7 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
Ibex 1.0.0
Methods for BCR single-cell embedding
2 versions - Latest release: about 2 months ago - 345 downloads total - 25 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
CSAR 1.62.0
Statistical tools for the analysis of ChIP-seq data
6 versions - Latest release: 2 months ago - 47.3 thousand 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: about 1 month ago - 342 dependent packages - 10.5 million downloads total - 1 maintainer
censcyt 1.18.0
Differential abundance analysis with a right censored covariate in high-dimensional cytometry
6 versions - Latest release: about 2 months ago - 8.56 thousand downloads total - 0 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: 8 days ago - 51 dependent packages - 4.94 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: 3 months ago - 740 dependent packages - 11 million downloads total - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 3 months ago - 6 dependent packages - 311 thousand downloads total - 1 maintainer
markeR 1.0.0
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
1 version - Latest release: 3 months ago - 624 downloads total - 7 stars on GitHub - 1 maintainer
methylInheritance 1.34.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...
7 versions - Latest release: about 2 months ago - 1 dependent package - 16.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files
6 versions - Latest release: 3 months ago - 9 dependent packages - 328 thousand downloads total - 481 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: about 1 month ago - 69 dependent packages - 3.2 million downloads total - 69 stars on GitHub - 1 maintainer
UNDO 1.52.0
Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions
6 versions - Latest release: about 2 months ago - 22.6 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
cqn 1.56.0
Conditional quantile normalization
6 versions - Latest release: 2 months ago - 4 dependent packages - 72.6 thousand downloads total - 1 maintainer
casper 2.44.0
Characterization of Alternative Splicing based on Paired-End Reads
6 versions - Latest release: 2 months ago - 29.9 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 3 months ago - 518 dependent packages - 11 million downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 12 stars on GitHub - 1 maintainer
Seqinfo 1.0.0
A simple S4 class for storing basic information about a collection of genomic sequences
1 version - Latest release: 3 months ago - 351 thousand downloads total - 1 maintainer
UniProt.ws 2.50.0
R Interface to UniProt Web Services
6 versions - Latest release: 3 months ago - 6 dependent packages - 79.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
tkWidgets 1.88.0
R based tk widgets
6 versions - Latest release: about 2 months ago - 7 dependent packages - 273 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: 3 months ago - 129 dependent packages - 2.74 million downloads total - 1 maintainer
mutscan 1.0.0
Preprocessing and Analysis of Deep Mutational Scanning Data
1 version - Latest release: 3 months ago - 695 downloads total - 14 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: 3 months ago - 36 dependent packages - 9.24 million downloads total - 1 maintainer
PhenoGeneRanker 1.18.0
PhenoGeneRanker: A gene and phenotype prioritization tool
6 versions - Latest release: 2 months ago - 7.24 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.4
an R package for visualization of tree and annotation data
12 versions - Latest release: 9 days ago - 28 dependent packages - 2.17 million downloads total - 1 maintainer
mogsa 1.44.0
Multiple omics data integrative clustering and gene set analysis
6 versions - Latest release: 2 months ago - 29.8 thousand downloads total - 1 maintainer