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 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: 28 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
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: 28 days ago - 342 dependent packages - 7.22 million downloads total - 1 maintainer
GenomicPlot 1.2.0
Plot profiles of next generation sequencing data in genomic features
9 versions - Latest release: 19 days ago - 1.16 thousand downloads total - 2 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets
9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
ggkegg 1.0.13
KEGG pathway visualization by ggplot2
8 versions - Latest release: 3 months ago - 3.39 thousand downloads total - 191 stars on GitHub - 1 maintainer
spatialHeatmap 2.10.0
spatialHeatmap
8 versions - Latest release: 16 days ago - 5.78 thousand downloads total - 4 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: 23 days ago - 15 dependent packages - 382 thousand downloads total - 164 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
tximeta 1.22.1
Transcript Quantification Import with Automatic Metadata
7 versions - Latest release: 17 days ago - 3 dependent packages - 93 thousand downloads total - 64 stars on GitHub - 1 maintainer
ClassifyR 3.8.0
A framework for cross-validated classification problems, with applications to differential variab...
7 versions - Latest release: 30 days ago - 4 dependent packages - 21.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
PhyloProfile 1.18.0
PhyloProfile
7 versions - Latest release: 29 days ago - 7.09 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
SeqArray 1.44.0
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
7 versions - Latest release: 16 days ago - 11 dependent packages - 86.6 thousand downloads total - 42 stars on GitHub - 1 maintainer
COTAN 2.4.1
COexpression Tables ANalysis
6 versions - Latest release: 17 days ago - 3.11 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
6 versions - Latest release: 28 days ago - 27 dependent packages - 1.24 million downloads total - 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 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: 23 days ago - 13 dependent packages - 263 thousand downloads total - 2 maintainers
Top 0.5% on bioconductor.org
GenomicFeatures 1.56.0
Conveniently import and query gene models
6 versions - Latest release: 28 days ago - 183 dependent packages - 3.32 million downloads total - 1 maintainer
canceR 1.36.8
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
6 versions - Latest release: about 1 month ago - 19 thousand downloads total - 8 stars on GitHub - 1 maintainer
DAPAR 1.34.6
Tools for the Differential Analysis of Proteins Abundance with R
6 versions - Latest release: 3 months ago - 1 dependent package - 20.5 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.72.0
Efficient manipulation of biological strings
6 versions - Latest release: 28 days ago - 333 dependent packages - 6.29 million downloads total - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression
6 versions - Latest release: 5 months ago - 1.29 thousand downloads total - 73 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
glmGamPoi 1.16.0
Fit a Gamma-Poisson Generalized Linear Model
6 versions - Latest release: 17 days ago - 5 dependent packages - 149 thousand downloads total - 92 stars on GitHub - 1 maintainer
Prostar 1.34.6
Provides a GUI for DAPAR
6 versions - Latest release: 3 months ago - 17.8 thousand downloads total - 1 maintainer
plotgardener 1.10.0
Coordinate-Based Genomic Visualization Package for R
6 versions - Latest release: 26 days ago - 4 dependent packages - 9.68 thousand downloads total - 276 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.1
LC-MS and GC-MS Data Analysis
6 versions - Latest release: 17 days ago - 15 dependent packages - 853 thousand downloads total - 157 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
DEGreport 1.40.0
Report of DEG analysis
6 versions - Latest release: 19 days ago - 1 dependent package - 58.6 thousand downloads total - 22 stars on GitHub - 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: 15 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
Statial 1.6.0
A package to identify changes in cell state relative to spatial associations
6 versions - Latest release: 24 days ago - 1.84 thousand downloads total - 1 stars on GitHub - 1 maintainer
MSstatsShiny 1.6.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
6 versions - Latest release: 20 days ago - 2.75 thousand downloads total - 9 stars on GitHub - 1 maintainer
doubletrouble 1.4.0
Identification and classification of duplicated genes
6 versions - Latest release: 23 days ago - 1.65 thousand downloads total - 7 stars on GitHub - 1 maintainer
bugsigdbr 1.10.0
R-side access to published microbial signatures from BugSigDB
6 versions - Latest release: 30 days ago - 4.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
GenomicScores 2.16.0
Infrastructure to work with genomewide position-specific scores
6 versions - Latest release: 29 days ago - 6 dependent packages - 54.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
benchdamic 1.10.0
Benchmark of differential abundance methods on microbiome data
5 versions - Latest release: 22 days ago - 3.07 thousand downloads total - 5 stars on GitHub - 1 maintainer
BioNAR 1.4.4
Biological Network Analysis in R
5 versions - Latest release: 2 months ago - 1.98 thousand downloads total - 1 maintainer
extraChIPs 1.8.1
Additional functions for working with ChIP-Seq data
5 versions - Latest release: 22 days ago - 2 dependent packages - 2.54 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
biomaRt 2.60.0
Interface to BioMart databases (i.e. Ensembl)
5 versions - Latest release: 30 days ago - 124 dependent packages - 3.99 million downloads total - 31 stars on GitHub - 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 5.2% on bioconductor.org
rols 2.30.2
An R interface to the Ontology Lookup Service
5 versions - Latest release: 3 months ago - 3 dependent packages - 57.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 28 days ago - 322 dependent packages - 5.09 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: 28 days ago - 129 dependent packages - 2 million downloads total - 1 maintainer
enhancerHomologSearch 1.10.0
Identification of putative mammalian orthologs to given enhancer
5 versions - Latest release: 26 days ago - 2.56 thousand downloads total - 0 stars on GitHub - 1 maintainer
rfaRm 1.14.2
An R interface to the Rfam database
5 versions - Latest release: 3 months ago - 4.46 thousand downloads total - 2 maintainers
UCell 2.8.0
Rank-based signature enrichment analysis for single-cell data
5 versions - Latest release: 26 days ago - 1 dependent package - 29.3 thousand downloads total - 111 stars on GitHub - 1 maintainer
rrvgo 1.16.0
Reduce + Visualize GO
5 versions - Latest release: 21 days ago - 17.7 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
Rhdf5lib 1.26.0
hdf5 library as an R package
5 versions - Latest release: 23 days ago - 3 dependent packages - 1.85 million downloads total - 6 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: 28 days ago - 132 dependent packages - 3.57 million downloads total - 1 maintainer
BSgenomeForge 1.2.3
Forge BSgenome data packages
5 versions - Latest release: about 1 month ago - 1 dependent package - 8.28 thousand downloads total - 1 maintainer
tidybulk 1.16.0
Brings transcriptomics to the tidyverse
5 versions - Latest release: 23 days ago - 1 dependent package - 9.88 thousand downloads total - 159 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
BiocFileCache 2.10.2
Manage Files Across Sessions
5 versions - Latest release: about 1 month ago - 97 dependent packages - 1.89 million downloads total - 11 stars on GitHub - 1 maintainer
AnVIL 1.14.2
Bioconductor on the AnVIL compute environment
5 versions - Latest release: 3 months ago - 4 dependent packages - 32.3 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: 28 days ago - 51 dependent packages - 4.77 million downloads total - 1 maintainer
nnSVG 1.6.4
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
5 versions - Latest release: about 1 month ago - 2 dependent packages - 3.17 thousand downloads total - 10 stars on GitHub - 1 maintainer
variancePartition 1.34.0
Quantify and interpret drivers of variation in multilevel gene expression experiments
5 versions - Latest release: 25 days ago - 4 dependent packages - 57.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
exomePeak2 1.14.3
Peak Calling and differential analysis for MeRIP-Seq
5 versions - Latest release: 5 months ago - 8.19 thousand downloads total - 23 stars on GitHub - 1 maintainer
rawrr 1.12.0
Direct Access to Orbitrap Data and Beyond
5 versions - Latest release: 29 days ago - 1 dependent package - 9.26 thousand downloads total - 50 stars on GitHub - 1 maintainer
Top 8.2% on bioconductor.org
dittoSeq 1.14.3
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
5 versions - Latest release: about 1 month ago - 6 dependent packages - 49.4 thousand downloads total - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus
5 versions - Latest release: 23 days ago - 1 dependent package - 8.17 thousand downloads total - 17 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: 22 days ago - 27 dependent packages - 143 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 7.5% on bioconductor.org
celda 1.20.0
CEllular Latent Dirichlet Allocation
5 versions - Latest release: 23 days ago - 2 dependent packages - 32.5 thousand downloads total - 133 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
debrowser 1.32.0
Interactive Differential Expresion Analysis Browser
5 versions - Latest release: 26 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
MSstatsPTM 2.4.4
Statistical Characterization of Post-translational Modifications
5 versions - Latest release: 3 months ago - 2 dependent packages - 7.43 thousand downloads total - 6 stars on GitHub - 1 maintainer
ORFik 1.22.2
Open Reading Frames in Genomics
5 versions - Latest release: 3 months ago - 2 dependent packages - 16.3 thousand downloads total - 32 stars on GitHub - 1 maintainer
MEIGOR 1.36.2
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
5 versions - Latest release: about 1 month ago - 2 dependent packages - 16.9 thousand downloads total - 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: 28 days ago - 740 dependent packages - 7.45 million downloads total - 1 maintainer
SparseArray 1.2.4
High-performance sparse data representation and manipulation in R
5 versions - Latest release: 3 months ago - 5 dependent packages - 570 thousand downloads total - 1 maintainer
SPIAT 1.6.0
Spatial Image Analysis of Tissues
5 versions - Latest release: 30 days ago - 2.95 thousand downloads total - 16 stars on GitHub - 1 maintainer
RNAdecay 1.22.2
Maximum Likelihood Decay Modeling of RNA Degradation Data
5 versions - Latest release: 3 months ago - 5.73 thousand downloads total - 1 maintainer
matter 2.6.1
Scientific computing for out-of-memory signals and images
5 versions - Latest release: 19 days ago - 2 dependent packages - 19 thousand downloads total - 52 stars on GitHub - 1 maintainer
MSstatsLiP 1.10.0
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
5 versions - Latest release: 17 days ago - 2.64 thousand downloads total - 3 stars on GitHub - 1 maintainer
MoleculeExperiment 1.4.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data
5 versions - Latest release: 27 days ago - 1.44 thousand downloads total - 10 stars on GitHub - 1 maintainer
bioCancer 1.32.0
Interactive Multi-Omics Cancers Data Visualization and Analysis
5 versions - Latest release: 17 days ago - 12.4 thousand downloads total - 19 stars on GitHub - 1 maintainer
HIBAG 1.40.0
HLA Genotype Imputation with Attribute Bagging
5 versions - Latest release: 24 days ago - 20.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
SVMDO 1.4.0
Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by D...
5 versions - Latest release: 22 days ago - 1.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scran 1.30.2
Methods for Single-Cell RNA-Seq Data Analysis
5 versions - Latest release: 4 months ago - 62 dependent packages - 399 thousand downloads total - 1 maintainer
animalcules 1.18.3
Interactive microbiome analysis toolkit
5 versions - Latest release: 3 months ago - 8.8 thousand downloads total - 50 stars on GitHub - 1 maintainer
SPOTlight 1.8.0
`SPOTlight`: Spatial Transcriptomics Deconvolution
5 versions - Latest release: 27 days ago - 6.1 thousand downloads total - 139 stars on GitHub - 1 maintainer
fenr 1.0.5
Fast functional enrichment for interactive applications
5 versions - Latest release: 3 months ago - 1.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
SiPSiC 1.2.2
Calculate Pathway Scores for Each Cell in scRNA-Seq Data
5 versions - Latest release: 3 months ago - 1.28 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
TrajectoryUtils 1.10.1
Single-Cell Trajectory Analysis Utilities
4 versions - Latest release: 3 months ago - 5 dependent packages - 65.6 thousand downloads total - 1 maintainer
ILoReg 1.12.1
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
4 versions - Latest release: 3 months ago - 3.61 thousand downloads total - 4 stars on GitHub - 1 maintainer
CNVRanger 1.18.1
Summarization and expression/phenotype association of CNV ranges
4 versions - Latest release: 2 months ago - 8.7 thousand downloads total - 4 stars on GitHub - 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
GOfuncR 1.22.2
Gene ontology enrichment using FUNC
4 versions - Latest release: 3 months ago - 20.3 thousand downloads total - 1 maintainer
spicyR 1.14.3
Spatial analysis of in situ cytometry data
4 versions - Latest release: 4 months ago - 2 dependent packages - 7.73 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
densvis 1.14.0
Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
4 versions - Latest release: 22 days ago - 1 dependent package - 83.2 thousand downloads total - 1 maintainer
TargetSearch 2.6.0
A package for the analysis of GC-MS metabolite profiling data
4 versions - Latest release: 28 days ago - 30.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
CaDrA 1.2.0
Candidate Driver Analysis
4 versions - Latest release: 18 days ago - 825 downloads total - 24 stars on GitHub - 1 maintainer
lpNet 2.34.2
Linear Programming Model for Network Inference
4 versions - Latest release: 3 months ago - 19.1 thousand downloads total - 1 maintainer
psichomics 1.30.0
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
4 versions - Latest release: 24 days ago - 14.4 thousand downloads total - 33 stars on GitHub - 1 maintainer
qcmetrics 1.42.0
A Framework for Quality Control
4 versions - Latest release: 28 days ago - 1 dependent package - 19.4 thousand downloads total - 2 stars on GitHub - 1 maintainer
LACE 2.8.0
Longitudinal Analysis of Cancer Evolution (LACE)
4 versions - Latest release: 25 days ago - 4.91 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
trackViewer 1.38.2
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop pl...
4 versions - Latest release: about 1 month ago - 3 dependent packages - 52.1 thousand downloads total - 1 maintainer
NeuCA 1.8.1
NEUral network-based single-Cell Annotation tool
4 versions - Latest release: 2 months ago - 2.02 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
BiocNeighbors 1.20.2
Nearest Neighbor Detection for Bioconductor Packages
4 versions - Latest release: 5 months ago - 18 dependent packages - 632 thousand downloads total - 1 maintainer
ccrepe 1.38.1
ccrepe_and_nc.score
4 versions - Latest release: 3 months ago - 20.6 thousand downloads total - 1 maintainer
VanillaICE 1.64.1
A Hidden Markov Model for high throughput genotyping arrays
4 versions - Latest release: about 1 month ago - 2 dependent packages - 40 thousand downloads total - 1 maintainer
R3CPET 1.34.1
3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
4 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
lefser 1.14.0
R implementation of the LEfSE method for microbiome biomarker discovery
4 versions - Latest release: 30 days ago - 1 dependent package - 16.8 thousand downloads total - 31 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
cTRAP 1.22.0
Identification of candidate causal perturbations from differential gene expression data
4 versions - Latest release: 24 days ago - 6.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
DExMA 1.10.7
Differential Expression Meta-Analysis
4 versions - Latest release: 5 months ago - 3.5 thousand downloads total - 1 maintainer