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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peakPantheR 1.16.1
Peak Picking and Annotation of High Resolution Experiments
4 versions - Latest release: 3 months ago - 5.72 thousand downloads total - 12 stars on GitHub - 1 maintainer
switchde 1.28.0
Switch-like differential expression across single-cell trajectories
3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 19 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data
6 versions - Latest release: 3 months ago - 2.37 thousand downloads total - 8 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: 23 days ago - 30 dependent packages - 397 thousand downloads total - 120 stars on GitHub - 1 maintainer
SCnorm 1.24.0
Normalization of single cell RNA-seq data
3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 45 stars on GitHub - 1 maintainer
ExperimentHubData 1.28.0
Add resources to ExperimentHub
3 versions - Latest release: 6 months ago - 3 dependent packages - 27.5 thousand downloads total - 1 maintainer
TPP2D 1.18.0
Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
3 versions - Latest release: 6 months ago - 5.21 thousand downloads total - 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: 21 days ago - 342 dependent packages - 7.22 million downloads total - 1 maintainer
ReUseData 1.2.2
Reusable and reproducible Data Management
5 versions - Latest release: 5 months ago - 1.11 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)
3 versions - Latest release: 21 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 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: 21 days ago - 212 dependent packages - 3.91 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.24.0
Visualization of Functional Enrichment Result
3 versions - Latest release: 21 days ago - 15 dependent packages - 1.18 million downloads total - 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: 21 days ago - 96 dependent packages - 622 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.72.0
Efficient manipulation of biological strings
6 versions - Latest release: 21 days ago - 333 dependent packages - 6.29 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.34.0
SummarizedExperiment container
3 versions - Latest release: 21 days ago - 632 dependent packages - 4.97 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: 21 days ago - 183 dependent packages - 3.32 million downloads total - 1 maintainer
BioCor 1.26.0
Functional similarities
3 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.16.0
flowCore: Basic structures for flow cytometry data
5 versions - Latest release: 21 days ago - 51 dependent packages - 4.77 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.1
LC-MS and GC-MS Data Analysis
6 versions - Latest release: 10 days ago - 15 dependent packages - 853 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.36.0
Q-value estimation for false discovery rate control
3 versions - Latest release: 21 days ago - 45 dependent packages - 1.54 million downloads total - 106 stars on GitHub - 2 maintainers
Top 0.1% on bioconductor.org
S4Vectors 0.42.0
Foundation of vector-like and list-like containers in Bioconductor
5 versions - Latest release: 21 days ago - 740 dependent packages - 7.45 million downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
6 versions - Latest release: 21 days ago - 27 dependent packages - 1.24 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: 21 days ago - 33 dependent packages - 1.48 million 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: 21 days ago - 59 dependent packages - 1.4 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
zlibbioc 1.50.0
An R packaged zlib-1.2.5
4 versions - Latest release: 21 days ago - 29 dependent packages - 6.47 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: 21 days ago - 604 dependent packages - 6.34 million 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: 21 days ago - 28 dependent packages - 1.15 million downloads total - 1 maintainer
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: 21 days ago - 45 dependent packages - 2.99 million 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: 21 days ago - 30 dependent packages - 894 thousand 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: 21 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 21 days ago - 322 dependent packages - 5.09 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: 21 days ago - 563 dependent packages - 8.04 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.32.0
HDF5 backend for DelayedArray objects
4 versions - Latest release: 21 days ago - 54 dependent packages - 990 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.30.1
A unified framework for working transparently with on-disk and in-memory array-like datasets
4 versions - Latest release: 10 days ago - 111 dependent packages - 5 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: 21 days ago - 35 dependent packages - 2.41 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.62.0
FASTQ input and manipulation
3 versions - Latest release: 21 days ago - 36 dependent packages - 1.63 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.40.0
Representation and manipulation of short genomic alignments
5 versions - Latest release: 21 days ago - 132 dependent packages - 3.57 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: 21 days ago - 129 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: 21 days ago - 36 dependent packages - 6.03 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.48.0
Provides plotting capabilities for R graph objects
3 versions - Latest release: 21 days ago - 61 dependent packages - 1.52 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: 21 days ago - 201 dependent packages - 1.07 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: 21 days ago - 251 dependent packages - 3.87 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.60.0
Resampling-based multiple hypothesis testing
3 versions - Latest release: 21 days ago - 37 dependent packages - 2.02 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.78.0
impute: Imputation for microarray data
3 versions - Latest release: 21 days ago - 44 dependent packages - 1.48 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.64.0
Biobase: Base functions for Bioconductor
3 versions - Latest release: 21 days ago - 518 dependent packages - 7.92 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.66.0
Gene set enrichment data structures and methods
3 versions - Latest release: 21 days ago - 49 dependent packages - 980 thousand 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: 21 days ago - 66 dependent packages - 3.31 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: 21 days ago - 101 dependent packages - 2.57 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.50.0
Annotation of Genetic Variants
4 versions - Latest release: 21 days ago - 93 dependent packages - 1.55 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.52.0
Surrogate Variable Analysis
3 versions - Latest release: 21 days ago - 43 dependent packages - 805 thousand downloads total - 3 maintainers
standR 1.6.0
Spatial transcriptome analyses of Nanostring's DSP data in R
3 versions - Latest release: 6 months ago - 3.38 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data
4 versions - Latest release: 6 months ago - 80.3 thousand downloads total - 502 stars on GitHub - 1 maintainer
GeneGeneInteR 1.28.0
Tools for Testing Gene-Gene Interaction at the Gene Level
3 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.48.0
R Interface to HDF5
4 versions - Latest release: 21 days ago - 69 dependent packages - 2.09 million downloads total - 59 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.30.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis
3 versions - Latest release: 6 months ago - 13 dependent packages - 360 thousand downloads total - 130 stars on GitHub - 1 maintainer
RNAinteract 1.50.0
Estimate Pairwise Interactions from multidimensional features
3 versions - Latest release: 6 months ago - 23.7 thousand 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: 21 days ago - 255 dependent packages - 6.03 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.82.0
Methods for Affymetrix Oligonucleotide Arrays
3 versions - Latest release: 21 days ago - 74 dependent packages - 1.86 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.82.0
Annotation for microarrays
3 versions - Latest release: 21 days ago - 48 dependent packages - 3.61 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: 21 days ago - 729 dependent packages - 8.2 million downloads total - 1 maintainer
metabolomicsWorkbenchR 1.12.0
Metabolomics Workbench in R
3 versions - Latest release: 6 months ago - 1 dependent package - 4.37 thousand downloads total - 1 maintainer
diggit 1.34.0
Inference of Genetic Variants Driving Cellular Phenotypes
3 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
InteractiveComplexHeatmap 1.10.0
Make Interactive Complex Heatmaps
3 versions - Latest release: 6 months ago - 4 dependent packages - 15.6 thousand downloads total - 112 stars on GitHub - 1 maintainer
ToxicoGx 2.6.0
Analysis of Large-Scale Toxico-Genomic Data
3 versions - Latest release: 6 months ago - 4.15 thousand downloads total - 1 maintainer
MDTS 1.22.0
Detection of de novo deletion in targeted sequencing trios
3 versions - Latest release: 6 months ago - 7.04 thousand downloads total - 1 maintainer
iSeq 1.54.0
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
3 versions - Latest release: 6 months ago - 24.1 thousand downloads total - 1 maintainer
clustifyr 1.14.0
Classifier for Single-cell RNA-seq Using Cell Clusters
3 versions - Latest release: 7 months ago - 9.06 thousand downloads total - 101 stars on GitHub - 1 maintainer
DESpace 1.2.1
DESpace: a framework to discover spatially variable genes
4 versions - Latest release: 3 months ago - 1.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
categoryCompare 1.46.0
Meta-analysis of high-throughput experiments using feature annotations
3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
covEB 1.28.0
Empirical Bayes estimate of block diagonal covariance matrices
3 versions - Latest release: 6 months ago - 9.93 thousand downloads total - 1 maintainer
plyinteractions 1.0.0
Extending tidy verbs to genomic interactions
3 versions - Latest release: 6 months ago - 1.03 thousand downloads total - 0 stars on GitHub - 1 maintainer
UMI4Cats 1.12.0
UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data
3 versions - Latest release: 6 months ago - 3.93 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
SpeCond 1.56.0
Condition specific detection from expression data
3 versions - Latest release: 6 months ago - 32.8 thousand downloads total - 1 maintainer
MsQuality 1.2.1
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
4 versions - Latest release: 2 months ago - 1.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
PADOG 1.44.0
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
3 versions - Latest release: 6 months ago - 2 dependent packages - 39.5 thousand downloads total - 1 maintainer
CircSeqAlignTk 1.4.0
A toolkit for end-to-end analysis of RNA-seq data for circular genomes
3 versions - Latest release: 6 months ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
twilight 1.78.0
Estimation of local false discovery rate
3 versions - Latest release: 6 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
LineagePulse 1.21.0 removed
Differential expression analysis and model fitting for single-cell RNA-seq data
2 versions - Latest release: 6 months ago - 7.08 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.56.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
3 versions - Latest release: 6 months ago - 26.3 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 17 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
GDCRNATools 1.22.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...
3 versions - Latest release: 6 months ago - 36.3 thousand downloads total - 2 maintainers
coseq 1.26.0
Co-Expression Analysis of Sequencing Data
3 versions - Latest release: 6 months ago - 14.9 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.12.0
Microbiome analysis
3 versions - Latest release: 22 days ago - 7 dependent packages - 49.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.34.0
Nucleosome positioning package for R
3 versions - Latest release: 6 months ago - 27.2 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
methylKit 1.28.0
DNA methylation analysis from high-throughput bisulfite sequencing results
3 versions - Latest release: 6 months ago - 3 dependent packages - 92.5 thousand downloads total - 182 stars on GitHub - 2 maintainers
BufferedMatrix 1.66.0
A matrix data storage object held in temporary files
3 versions - Latest release: 6 months ago - 1 dependent package - 33.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
AnVILPublish 1.12.0
Publish Packages and Other Resources to AnVIL Workspaces
3 versions - Latest release: 6 months ago - 3.94 thousand downloads total - 1 maintainer
aCGH 1.80.0
Classes and functions for Array Comparative Genomic Hybridization data
3 versions - Latest release: 6 months ago - 5 dependent packages - 62.7 thousand downloads total - 1 maintainer
Cardinal 3.4.3
A mass spectrometry imaging toolbox for statistical analysis
4 versions - Latest release: 5 months ago - 26.1 thousand downloads total - 1 maintainer
MetNet 1.20.0
Inferring metabolic networks from untargeted high-resolution mass spectrometry data
3 versions - Latest release: 6 months ago - 6.9 thousand downloads total - 1 maintainer
MsBackendMgf 1.10.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
3 versions - Latest release: 6 months ago - 3 dependent packages - 22 thousand downloads total - 4 stars on GitHub - 2 maintainers
CINdex 1.30.0
Chromosome Instability Index
3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
GBScleanR 1.8.0
Error correction tool for noisy genotyping by sequencing (GBS) data
3 versions - Latest release: 21 days ago - 2.17 thousand downloads total - 0 stars on GitHub - 1 maintainer
infinityFlow 1.12.0
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 1 maintainer
RGSEA 1.36.0
Random Gene Set Enrichment Analysis
3 versions - Latest release: 6 months ago - 17.3 thousand downloads total - 1 maintainer
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
6 versions - Latest release: 8 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
SwathXtend 2.24.0
SWATH extended library generation and statistical data analysis
3 versions - Latest release: 6 months ago - 10.6 thousand downloads total - 1 maintainer
MGFR 1.28.0
Marker Gene Finder in RNA-seq data
3 versions - Latest release: 6 months ago - 1 dependent package - 10.4 thousand downloads total - 1 maintainer
chihaya 1.2.0
Save Delayed Operations to a HDF5 File
3 versions - Latest release: 6 months ago - 1 dependent package - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
maser 1.20.0
Mapping Alternative Splicing Events to pRoteins
3 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 16 stars on GitHub - 1 maintainer