Ecosyste.ms: Packages

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

bioconductor.org packages

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Top 3.8% on bioconductor.org
BiocStyle 2.32.0
Standard styles for vignettes and other Bioconductor documents
3 versions - Latest release: 9 days ago - 1,223 dependent packages - 736 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.42.0
Foundation of vector-like and list-like containers in Bioconductor
5 versions - Latest release: 8 days ago - 706 dependent packages - 7.4 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.50.0
S4 generic functions used in Bioconductor
3 versions - Latest release: 8 days ago - 701 dependent packages - 8.14 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.34.0
SummarizedExperiment container
3 versions - Latest release: 8 days ago - 590 dependent packages - 4.93 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
GenomicRanges 1.56.0
Representation and manipulation of genomic intervals
4 versions - Latest release: 8 days ago - 577 dependent packages - 6.3 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.38.0
Foundation of integer range manipulation in Bioconductor
3 versions - Latest release: 8 days ago - 545 dependent packages - 7.99 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.64.0
Biobase: Base functions for Bioconductor
3 versions - Latest release: 8 days ago - 509 dependent packages - 7.87 million downloads total - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.38.0
Bioconductor facilities for parallel evaluation
3 versions - Latest release: 9 days ago - 356 dependent packages - 5.51 million downloads total - 63 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.40.0
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
10 versions - Latest release: 8 days ago - 327 dependent packages - 7.14 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.72.0
Efficient manipulation of biological strings
6 versions - Latest release: 8 days ago - 324 dependent packages - 6.24 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
4 versions - Latest release: 8 days ago - 315 dependent packages - 5.07 million downloads total - 1 maintainer
Top 0.3% on bioconductor.org
AnnotationDbi 1.66.0
Manipulation of SQLite-based annotations in Bioconductor
3 versions - Latest release: 8 days ago - 247 dependent packages - 6 million downloads total - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.64.0
R interface to genome annotation files and the UCSC genome browser
3 versions - Latest release: 8 days ago - 239 dependent packages - 3.84 million downloads total - 1 maintainer
Top 0.4% on bioconductor.org
Rsamtools 2.20.0
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
3 versions - Latest release: 8 days ago - 208 dependent packages - 3.89 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.26.0
S4 Classes for Single Cell Data
3 versions - Latest release: 8 days ago - 186 dependent packages - 1.06 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.56.0
Conveniently import and query gene models
6 versions - Latest release: 8 days ago - 175 dependent packages - 3.3 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: 8 days ago - 171 dependent packages - 3.01 million downloads total - 4 maintainers
Top 0.5% on bioconductor.org
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution
4 versions - Latest release: 9 days ago - 135 dependent packages - 2.76 million downloads total - 327 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.40.0
Representation and manipulation of short genomic alignments
5 versions - Latest release: 8 days ago - 128 dependent packages - 3.54 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.72.0
Software infrastructure for efficient representation of full genomes and their SNPs
5 versions - Latest release: 8 days ago - 125 dependent packages - 1.99 million downloads total - 1 maintainer
Top 2.6% on bioconductor.org
biomaRt 2.60.0
Interface to BioMart databases (i.e. Ensembl)
5 versions - Latest release: 9 days ago - 118 dependent packages - 3.98 million downloads total - 30 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.30.0
A unified framework for working transparently with on-disk and in-memory array-like datasets
3 versions - Latest release: 8 days ago - 107 dependent packages - 4.95 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.82.0
graph: A package to handle graph data structures
3 versions - Latest release: 8 days ago - 100 dependent packages - 2.55 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.50.0
Annotation of Genetic Variants
4 versions - Latest release: 8 days ago - 89 dependent packages - 1.54 million downloads total - 1 maintainer
Top 4.8% on bioconductor.org
BiocFileCache 2.10.2
Manage Files Across Sessions
4 versions - Latest release: 15 days ago - 88 dependent packages - 1.85 million downloads total - 11 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
ComplexHeatmap 2.18.0
Make Complex Heatmaps
2 versions - Latest release: 7 months ago - 87 dependent packages - 1.02 million downloads total - 21 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
AnnotationHub 3.10.1
Client to access AnnotationHub resources
3 versions - Latest release: 15 days ago - 87 dependent packages - 966 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: 8 days ago - 86 dependent packages - 616 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.82.0
Methods for Affymetrix Oligonucleotide Arrays
3 versions - Latest release: 8 days ago - 74 dependent packages - 1.85 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.86.0
genefilter: methods for filtering genes from high-throughput experiments
3 versions - Latest release: 8 days ago - 65 dependent packages - 3.3 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.48.0
R Interface to HDF5
4 versions - Latest release: 8 days ago - 63 dependent packages - 2.08 million downloads total - 59 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.48.0
Provides plotting capabilities for R graph objects
3 versions - Latest release: 8 days ago - 60 dependent packages - 1.51 million downloads total - 1 maintainer
Top 2.5% on bioconductor.org
MultiAssayExperiment 1.30.1
Software for the integration of multi-omics experiments in Bioconductor
3 versions - Latest release: 1 day ago - 57 dependent packages - 245 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
ExperimentHub 2.10.0
Client to access ExperimentHub resources
2 versions - Latest release: 6 months ago - 56 dependent packages - 427 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
Gviz 1.48.0
Plotting data and annotation information along genomic coordinates
4 versions - Latest release: 9 days ago - 55 dependent packages - 834 thousand downloads total - 66 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scran 1.30.2
Methods for Single-Cell RNA-Seq Data Analysis
4 versions - Latest release: 4 months ago - 53 dependent packages - 391 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.32.0
HDF5 backend for DelayedArray objects
4 versions - Latest release: 8 days ago - 53 dependent packages - 978 thousand downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data
4 versions - Latest release: 8 days ago - 53 dependent packages - 1.39 million downloads total - 1 maintainer
Top 3.9% on bioconductor.org
preprocessCore 1.66.0
A collection of pre-processing functions
3 versions - Latest release: 2 days ago - 50 dependent packages - 2.16 million downloads total - 14 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.66.0
Gene set enrichment data structures and methods
3 versions - Latest release: 8 days ago - 49 dependent packages - 973 thousand downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.16.0
flowCore: Basic structures for flow cytometry data
5 versions - Latest release: 8 days ago - 49 dependent packages - 4.77 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.82.0
Annotation for microarrays
3 versions - Latest release: 8 days ago - 48 dependent packages - 3.59 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)
3 versions - Latest release: 8 days ago - 47 dependent packages - 1.86 million downloads total - 82 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.78.0
impute: Imputation for microarray data
3 versions - Latest release: 8 days ago - 44 dependent packages - 1.47 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.36.0
Q-value estimation for false discovery rate control
3 versions - Latest release: 8 days ago - 44 dependent packages - 1.53 million downloads total - 106 stars on GitHub - 2 maintainers
Top 4.6% on bioconductor.org
DelayedMatrixStats 1.26.0
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
3 versions - Latest release: 9 days ago - 43 dependent packages - 1.1 million downloads total - 15 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.52.0
Surrogate Variable Analysis
3 versions - Latest release: 8 days ago - 41 dependent packages - 800 thousand downloads total - 3 maintainers
Top 1.0% on bioconductor.org
MatrixGenerics 1.16.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
3 versions - Latest release: 8 days ago - 39 dependent packages - 2.95 million downloads total - 1 maintainer
Top 3.3% on bioconductor.org
ensembldb 2.28.0
Utilities to create and use Ensembl-based annotation databases
3 versions - Latest release: 9 days ago - 37 dependent packages - 1.06 million downloads total - 33 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.30.0
Fast Gene Set Enrichment Analysis
3 versions - Latest release: 6 days ago - 37 dependent packages - 1.16 million downloads total - 344 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.62.0
FASTQ input and manipulation
3 versions - Latest release: 8 days ago - 36 dependent packages - 1.63 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.60.0
Resampling-based multiple hypothesis testing
3 versions - Latest release: 8 days ago - 36 dependent packages - 2 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
XVector 0.44.0
Foundation of external vector representation and manipulation in Bioconductor
3 versions - Latest release: 8 days ago - 35 dependent packages - 5.98 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
KEGGREST 1.44.0
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)
3 versions - Latest release: 8 days ago - 34 dependent packages - 2.38 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.80.0
An interface to the BOOST graph library
3 versions - Latest release: 8 days ago - 33 dependent packages - 1.47 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays
3 versions - Latest release: 9 days ago - 31 dependent packages - 787 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.30.1
Base Functions and Classes for Mass Spectrometry and Proteomics
4 versions - Latest release: 10 days ago - 30 dependent packages - 394 thousand downloads total - 119 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
DNAcopy 1.76.0
DNA Copy Number Data Analysis
2 versions - Latest release: 7 months ago - 29 dependent packages - 592 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.72.0
Variance stabilization and calibration for microarray data
3 versions - Latest release: 8 days ago - 29 dependent packages - 890 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.12.0
Single-Cell RNA-Seq Analysis Utilities
2 versions - Latest release: 7 months ago - 29 dependent packages - 533 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
BiocSingular 1.20.0
Singular Value Decomposition for Bioconductor Packages
3 versions - Latest release: 9 days ago - 27 dependent packages - 691 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
zlibbioc 1.50.0
An R packaged zlib-1.2.5
4 versions - Latest release: 8 days ago - 27 dependent packages - 6.42 million downloads total - 1 maintainer
Top 6.1% on bioconductor.org
SpatialExperiment 1.14.0
S4 Class for Spatially Resolved -omics Data
3 versions - Latest release: 5 days ago - 27 dependent packages - 57.5 thousand downloads total - 45 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
basilisk 1.16.0
Freezing Python Dependencies Inside Bioconductor Packages
5 versions - Latest release: 1 day ago - 26 dependent packages - 143 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
5 versions - Latest release: 8 days ago - 25 dependent packages - 1.23 million downloads total - 1 maintainer
Top 2.3% on bioconductor.org
topGO 2.54.0
Enrichment Analysis for Gene Ontology
2 versions - Latest release: 6 months ago - 25 dependent packages - 458 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 3.12.0
an R package for visualization of tree and annotation data
4 versions - Latest release: 8 days ago - 25 dependent packages - 1.14 million downloads total - 1 maintainer
Top 2.2% on bioconductor.org
ggbio 1.50.0
Visualization tools for genomic data
3 versions - Latest release: 6 months ago - 24 dependent packages - 439 thousand downloads total - 109 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.68.0
Tools for manipulating GO and microarrays
2 versions - Latest release: 7 months ago - 23 dependent packages - 501 thousand downloads total - 1 maintainer
Top 2.5% on bioconductor.org
mzR 2.38.0
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
3 versions - Latest release: 9 days ago - 23 dependent packages - 954 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.46.0
Handling and analysis of high-throughput microbiome census data
2 versions - Latest release: 7 months ago - 21 dependent packages - 687 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.80.0
Exploratory analysis for two-color spotted microarray data
2 versions - Latest release: 7 months ago - 21 dependent packages - 547 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
InteractionSet 1.32.0
Base Classes for Storing Genomic Interaction Data
3 versions - Latest release: 1 day ago - 20 dependent packages - 109 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
plyranges 1.24.0
A fluent interface for manipulating GenomicRanges
3 versions - Latest release: about 19 hours ago - 19 dependent packages - 74.9 thousand downloads total - 127 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.36.0
Generic infrastructure for Bioconductor mass spectrometry packages
3 versions - Latest release: 2 days ago - 19 dependent packages - 979 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.14.1
Core Utils for Mass Spectrometry Data
3 versions - Latest release: 5 months ago - 19 dependent packages - 152 thousand downloads total - 16 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
pcaMethods 1.94.0
A collection of PCA methods
2 versions - Latest release: 7 months ago - 19 dependent packages - 579 thousand downloads total - 44 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
AnnotationFilter 1.28.0
Facilities for Filtering Bioconductor Annotation Resources
3 versions - Latest release: 9 days ago - 19 dependent packages - 815 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
gdsfmt 1.40.0
R Interface to CoreArray Genomic Data Structure (GDS) Files
3 versions - Latest release: about 17 hours ago - 18 dependent packages - 211 thousand downloads total - 18 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
EBImage 4.46.0
Image processing and analysis toolbox for R
3 versions - Latest release: 9 days ago - 18 dependent packages - 500 thousand downloads total - 67 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
TFBSTools 1.42.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis
3 versions - Latest release: 2 days ago - 17 dependent packages - 288 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
MotifDb 1.46.0
An Annotated Collection of Protein-DNA Binding Sequence Motifs
3 versions - Latest release: 2 days ago - 17 dependent packages - 102 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
BiocNeighbors 1.20.2
Nearest Neighbor Detection for Bioconductor Packages
3 versions - Latest release: 4 months ago - 16 dependent packages - 616 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.24.0
Functions to Access and Control Cytoscape
3 versions - Latest release: 6 days ago - 15 dependent packages - 75.9 thousand downloads total - 47 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.24.0
Visualization of Functional Enrichment Result
3 versions - Latest release: 8 days ago - 15 dependent packages - 1.17 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.0
LC-MS and GC-MS Data Analysis
5 versions - Latest release: 8 days ago - 15 dependent packages - 851 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.14.0
Spectra Infrastructure for Mass Spectrometry Data
3 versions - Latest release: 2 days ago - 15 dependent packages - 46.7 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
snpStats 1.52.0
SnpMatrix and XSnpMatrix classes and methods
2 versions - Latest release: 6 months ago - 15 dependent packages - 395 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
bumphunter 1.44.0
Bump Hunter
2 versions - Latest release: 6 months ago - 15 dependent packages - 394 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
GSVA 1.52.1
Gene Set Variation Analysis for Microarray and RNA-Seq Data
7 versions - Latest release: 2 days ago - 15 dependent packages - 382 thousand downloads total - 164 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
beachmat 2.20.0
Compiling Bioconductor to Handle Each Matrix Type
4 versions - Latest release: 2 days ago - 14 dependent packages - 919 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data
4 versions - Latest release: 5 days ago - 14 dependent packages - 311 thousand downloads total - 2 maintainers
Top 2.1% on bioconductor.org
biovizBase 1.50.0
Basic graphic utilities for visualization of genomic data.
2 versions - Latest release: 7 months ago - 14 dependent packages - 1.04 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.70.0
Sequence logos for DNA sequence alignments
3 versions - Latest release: 5 days ago - 13 dependent packages - 344 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
Category 2.68.0
Category Analysis
2 versions - Latest release: 6 months ago - 13 dependent packages - 513 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
GOSemSim 2.28.1
GO-terms Semantic Similarity Measures
3 versions - Latest release: 4 months ago - 13 dependent packages - 1.15 million downloads total - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis
2 versions - Latest release: 6 months ago - 13 dependent packages - 354 thousand downloads total - 130 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
flowWorkspace 4.16.0
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
6 versions - Latest release: 2 days ago - 13 dependent packages - 263 thousand downloads total - 2 maintainers
Top 3.7% on bioconductor.org
bsseq 1.40.0
Analyze, manage and store bisulfite sequencing data
3 versions - Latest release: 2 days ago - 12 dependent packages - 201 thousand downloads total - 34 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
STRINGdb 2.16.0
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
4 versions - Latest release: 1 day ago - 12 dependent packages - 99.9 thousand downloads total - 1 maintainer