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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affxparser 1.76.0
Affymetrix File Parsing SDK
3 versions - Latest release: 6 days ago - 10 dependent packages - 323 thousand downloads total - 6 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: about 2 hours ago - 15 dependent packages - 382 thousand downloads total - 164 stars on GitHub - 1 maintainer
MsBackendMsp 1.8.0
Mass Spectrometry Data Backend for NIST msp Files
3 versions - Latest release: about 2 hours ago - 4.83 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.24.0
Functions to Access and Control Cytoscape
3 versions - Latest release: 4 days ago - 15 dependent packages - 75.9 thousand downloads total - 47 stars on GitHub - 1 maintainer
SQLDataFrame 1.18.0
Representation of SQL tables in DataFrame metaphor
4 versions - Latest release: 7 days ago - 4.69 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
BiocCheck 1.40.0
Bioconductor-specific package checks
4 versions - Latest release: 7 days ago - 6 dependent packages - 225 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
rGREAT 2.6.0
GREAT Analysis - Functional Enrichment on Genomic Regions
3 versions - Latest release: 7 days ago - 3 dependent packages - 47.1 thousand downloads total - 76 stars on GitHub - 1 maintainer
iCOBRA 1.32.0
Comparison and Visualization of Ranking and Assignment Methods
3 versions - Latest release: 7 days ago - 2 dependent packages - 17.5 thousand downloads total - 14 stars on GitHub - 1 maintainer
countsimQC 1.22.0
Compare Characteristic Features of Count Data Sets
3 versions - Latest release: 7 days ago - 1 dependent package - 8.89 thousand downloads total - 27 stars on GitHub - 1 maintainer
compcodeR 1.40.0
RNAseq data simulation, differential expression analysis and performance comparison of differenti...
3 versions - Latest release: 7 days ago - 21.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
transmogR 1.0.0
Modify a set of reference sequences using a set of variants
2 versions - Latest release: 5 days ago - 245 downloads total - 0 stars on GitHub - 1 maintainer
crisprVerse 1.6.0
Easily install and load the crisprVerse ecosystem for CRISPR gRNA design
3 versions - Latest release: 7 days ago - 2.4 thousand downloads total - 7 stars on GitHub - 1 maintainer
scMultiSim 1.0.0
Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell In...
1 version - Latest release: 7 days ago - 88 downloads total - 18 stars on GitHub - 1 maintainer
BiocDockerManager 1.11.0 removed
Access Bioconductor docker images
1 version - Latest release: 7 months ago - 3.43 thousand downloads total - 1 stars on GitHub - 1 maintainer
zenith 1.6.0
Gene set analysis following differential expression using linear (mixed) modeling with dream
4 versions - Latest release: about 6 hours ago - 2 dependent packages - 3.42 thousand downloads total - 0 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: about 9 hours ago - 1.84 thousand downloads total - 1 stars on GitHub - 1 maintainer
sccomp 1.8.0
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
3 versions - Latest release: 3 days ago - 2.66 thousand downloads total - 75 stars on GitHub - 1 maintainer
HIBAG 1.40.0
HLA Genotype Imputation with Attribute Bagging
5 versions - Latest release: 1 day ago - 20.1 thousand downloads total - 26 stars on GitHub - 1 maintainer
cbpManager 1.12.0
Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Canc...
3 versions - Latest release: 2 days ago - 3.21 thousand downloads total - 6 stars on GitHub - 1 maintainer
AlpsNMR 4.6.0
Automated spectraL Processing System for NMR
3 versions - Latest release: 1 day ago - 4.79 thousand downloads total - 13 stars on GitHub - 1 maintainer
QFeatures 1.14.0
Quantitative features for mass spectrometry data
3 versions - Latest release: about 18 hours ago - 6 dependent packages - 35.5 thousand downloads total - 20 stars on GitHub - 1 maintainer
ceRNAnetsim 1.16.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
4 versions - Latest release: about 19 hours ago - 4.14 thousand downloads total - 4 stars on GitHub - 1 maintainer
smoothclust 0.99.8
smoothclust
1 version - Latest release: 7 days ago - 162 downloads total - 0 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
QDNAseq 1.40.0
Quantitative DNA Sequencing for Chromosomal Aberrations
3 versions - Latest release: 7 days ago - 4 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
SeqVarTools 1.42.0
Tools for variant data
3 versions - Latest release: about 20 hours ago - 1 dependent package - 58.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
ngsReports 2.6.0
Load FastqQC reports and other NGS related files
3 versions - Latest release: 7 days ago - 7.68 thousand downloads total - 20 stars on GitHub - 1 maintainer
SparseSignatures 2.14.0
SparseSignatures
3 versions - Latest release: 2 days ago - 7.65 thousand downloads total - 10 stars on GitHub - 1 maintainer
CTexploreR 1.0.0
Explores Cancer Testis Genes
1 version - Latest release: 7 days ago - 256 downloads total - 0 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
dada2 1.32.0
Accurate, high-resolution sample inference from amplicon sequencing data
3 versions - Latest release: about 20 hours ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
sparseMatrixStats 1.16.0
Summary Statistics for Rows and Columns of Sparse Matrices
3 versions - Latest release: 7 days ago - 7 dependent packages - 792 thousand downloads total - 53 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: 7 days ago - 55 dependent packages - 834 thousand downloads total - 66 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays
3 versions - Latest release: 7 days ago - 31 dependent packages - 787 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.44.0
Differential gene expression analysis based on the negative binomial distribution
4 versions - Latest release: 7 days ago - 135 dependent packages - 2.76 million downloads total - 327 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.30.0
Fast Gene Set Enrichment Analysis
3 versions - Latest release: 3 days ago - 37 dependent packages - 1.16 million downloads total - 344 stars on GitHub - 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: 7 days ago - 37 dependent packages - 1.06 million downloads total - 33 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: 7 days ago - 118 dependent packages - 3.98 million downloads total - 30 stars on GitHub - 1 maintainer
RESOLVE 1.6.0
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
3 versions - Latest release: 2 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
msqrob2 1.12.0
Robust statistical inference for quantitative LC-MS proteomics
3 versions - Latest release: 2 days ago - 5.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.12.0
Microbiome analysis
3 versions - Latest release: 6 days ago - 5 dependent packages - 48.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: about 23 hours ago - 3.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
IsoBayes 1.2.0
IsoBayes: Single Isoform protein inference Method via Bayesian Analyses
3 versions - Latest release: about 23 hours ago - 747 downloads total - 5 stars on GitHub - 1 maintainer
psichomics 1.30.0
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
4 versions - Latest release: 1 day ago - 14.4 thousand downloads total - 33 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
karyoploteR 1.30.0
Plot customizable linear genomes displaying arbitrary data
3 versions - Latest release: 4 days ago - 7 dependent packages - 85.3 thousand downloads total - 285 stars on GitHub - 1 maintainer
cTRAP 1.22.0
Identification of candidate causal perturbations from differential gene expression data
4 versions - Latest release: 1 day ago - 6.62 thousand downloads total - 5 stars on GitHub - 1 maintainer
gypsum 1.0.0
Interface to the gypsum REST API
1 version - Latest release: 7 days ago - 1.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas
3 versions - Latest release: 1 day ago - 941 downloads total - 75 stars on GitHub - 1 maintainer
lefser 1.14.0
R implementation of the LEfSE method for microbiome biomarker discovery
4 versions - Latest release: 6 days ago - 16.8 thousand downloads total - 31 stars on GitHub - 1 maintainer
Banksy 1.0.0
Spatial transcriptomic clustering
1 version - Latest release: 7 days ago - 327 downloads total - 42 stars on GitHub - 1 maintainer
variancePartition 1.34.0
Quantify and interpret drivers of variation in multilevel gene expression experiments
5 versions - Latest release: 1 day ago - 4 dependent packages - 57.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
GenomicDataCommons 1.28.0
NIH / NCI Genomic Data Commons Access
3 versions - Latest release: 7 days ago - 2 dependent packages - 92.3 thousand downloads total - 82 stars on GitHub - 1 maintainer
iSEEhub 1.6.0
iSEE for the Bioconductor ExperimentHub
3 versions - Latest release: 1 day ago - 2.28 thousand downloads total - 4 stars on GitHub - 1 maintainer
evaluomeR 1.20.0
Evaluation of Bioinformatics Metrics
3 versions - Latest release: 1 day ago - 5.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
fastreeR 1.8.0
Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
3 versions - Latest release: 1 day ago - 2.61 thousand downloads total - 1 stars on GitHub - 1 maintainer
VERSO 1.14.0
Viral Evolution ReconStructiOn (VERSO)
3 versions - Latest release: 1 day ago - 3.43 thousand downloads total - 6 stars on GitHub - 1 maintainer
matter 2.6.0
Scientific computing for out-of-memory signals and images
4 versions - Latest release: 6 days ago - 2 dependent packages - 18.8 thousand downloads total - 52 stars on GitHub - 1 maintainer
CRISPRball 1.0.0
Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filte...
1 version - Latest release: 7 days ago - 276 downloads total - 5 stars on GitHub - 1 maintainer
metabinR 1.6.0
Abundance and Compositional Based Binning of Metagenomes
3 versions - Latest release: 2 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
SIMLR 1.30.0
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
3 versions - Latest release: 2 days ago - 1 dependent package - 24.5 thousand downloads total - 106 stars on GitHub - 1 maintainer
OncoScore 1.32.0
A tool to identify potentially oncogenic genes
3 versions - Latest release: 2 days ago - 11 thousand downloads total - 5 stars on GitHub - 1 maintainer
drawProteins 1.24.0
Package to Draw Protein Schematics from Uniprot API output
4 versions - Latest release: 2 days ago - 1 dependent package - 14.8 thousand downloads total - 33 stars on GitHub - 1 maintainer
LACE 2.8.0
Longitudinal Analysis of Cancer Evolution (LACE)
4 versions - Latest release: 2 days ago - 4.91 thousand downloads total - 13 stars on GitHub - 1 maintainer
breakpointR 1.22.0
Find breakpoints in Strand-seq data
3 versions - Latest release: 2 days ago - 7.39 thousand downloads total - 8 stars on GitHub - 1 maintainer
Rarr 1.4.0
Read Zarr Files in R
3 versions - Latest release: 2 days ago - 2.25 thousand downloads total - 24 stars on GitHub - 1 maintainer
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements
3 versions - Latest release: 2 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
oligoClasses 1.66.0
Classes for high-throughput arrays supported by oligo and crlmm
3 versions - Latest release: 2 days ago - 12 dependent packages - 354 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.56.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
3 versions - Latest release: 2 days ago - 10 dependent packages - 335 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
EnhancedVolcano 1.22.0
Publication-ready volcano plots with enhanced colouring and labeling
3 versions - Latest release: 2 days ago - 264 thousand downloads total - 380 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.80.0
utilities for ROC, with microarray focus
3 versions - Latest release: 2 days ago - 6 dependent packages - 246 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data
4 versions - Latest release: 2 days ago - 14 dependent packages - 311 thousand downloads total - 2 maintainers
Top 1.8% on bioconductor.org
seqLogo 1.70.0
Sequence logos for DNA sequence alignments
3 versions - Latest release: 2 days ago - 13 dependent packages - 344 thousand downloads total - 4 stars on GitHub - 1 maintainer
CBNplot 1.4.0
plot bayesian network inferred from gene expression data based on enrichment analysis results
4 versions - Latest release: 2 days ago - 2.56 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
debrowser 1.32.0
Interactive Differential Expresion Analysis Browser
5 versions - Latest release: 2 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
gcatest 2.4.0
Genotype Conditional Association TEST
3 versions - Latest release: 2 days ago - 10.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
lfa 2.4.0
Logistic Factor Analysis for Categorical Data
3 versions - Latest release: 3 days ago - 1 dependent package - 39.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
ATACseqTFEA 1.6.0
Transcription Factor Enrichment Analysis for ATAC-seq
3 versions - Latest release: 3 days ago - 1.98 thousand downloads total - 0 stars on GitHub - 1 maintainer
plotgardener 1.10.0
Coordinate-Based Genomic Visualization Package for R
6 versions - Latest release: 3 days ago - 3 dependent packages - 9.55 thousand downloads total - 276 stars on GitHub - 1 maintainer
fobitools 1.12.0
Tools for Manipulating the FOBI Ontology
3 versions - Latest release: 3 days ago - 2.91 thousand downloads total - 1 stars on GitHub - 1 maintainer
dreamlet 1.2.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...
3 versions - Latest release: 3 days ago - 1.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
TAPseq 1.16.0
Targeted scRNA-seq primer design for TAP-seq
4 versions - Latest release: 3 days ago - 4.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
GBScleanR 1.8.0
Error correction tool for noisy genotyping by sequencing (GBS) data
3 versions - Latest release: 6 days ago - 2.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
SimBu 1.6.0
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
4 versions - Latest release: 6 days ago - 1.83 thousand downloads total - 12 stars on GitHub - 1 maintainer
miloR 2.0.0
Differential neighbourhood abundance testing on a graph
3 versions - Latest release: 6 days ago - 10.4 thousand downloads total - 306 stars on GitHub - 1 maintainer
UCell 2.8.0
Rank-based signature enrichment analysis for single-cell data
5 versions - Latest release: 3 days ago - 1 dependent package - 29.3 thousand downloads total - 111 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
PCAtools 2.16.0
PCAtools: Everything Principal Components Analysis
3 versions - Latest release: 3 days ago - 2 dependent packages - 67.6 thousand downloads total - 315 stars on GitHub - 1 maintainer
RAREsim 1.8.0
Simulation of Rare Variant Genetic Data
3 versions - Latest release: 3 days ago - 1.67 thousand downloads total - 4 stars on GitHub - 1 maintainer
HicAggR 1.0.0
Set of 3D genomic interaction analysis tools
1 version - Latest release: 7 days ago - 0 stars on GitHub - 1 maintainer
TnT 1.26.0
Interactive Visualization for Genomic Features
3 versions - Latest release: 3 days ago - 7.94 thousand downloads total - 14 stars on GitHub - 1 maintainer
enhancerHomologSearch 1.10.0
Identification of putative mammalian orthologs to given enhancer
5 versions - Latest release: 3 days ago - 2.56 thousand downloads total - 0 stars on GitHub - 1 maintainer
GenomicInteractionNodes 1.8.0
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
3 versions - Latest release: 3 days ago - 1.78 thousand downloads total - 0 stars on GitHub - 1 maintainer
scRNAseqApp 1.4.0
A single-cell RNAseq Shiny app-package
4 versions - Latest release: 6 days ago - 1.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
hicVennDiagram 1.2.0
Venn Diagram for genomic interaction data
4 versions - Latest release: 3 days ago - 742 downloads total - 0 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
SpatialExperiment 1.14.0
S4 Class for Spatially Resolved -omics Data
3 versions - Latest release: 3 days ago - 27 dependent packages - 57.5 thousand downloads total - 45 stars on GitHub - 1 maintainer
Top 8.2% on bioconductor.org
zellkonverter 1.14.0
Conversion Between scRNA-seq Objects
4 versions - Latest release: 3 days ago - 6 dependent packages - 43.4 thousand downloads total - 132 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
ANCOMBC 2.6.0
Microbiome differential abudance and correlation analyses with bias correction
3 versions - Latest release: 3 days ago - 2 dependent packages - 50.4 thousand downloads total - 89 stars on GitHub - 1 maintainer
AlphaMissenseR 1.0.0
Accessing AlphaMissense Data Resources in R
1 version - Latest release: 7 days ago - 187 downloads total - 4 stars on GitHub - 1 maintainer
DELocal 1.4.0
Identifies differentially expressed genes with respect to other local genes
4 versions - Latest release: 4 days ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
GenomAutomorphism 1.6.0
Compute the automorphisms between DNA's Abelian group representations
3 versions - Latest release: 4 days ago - 1.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
proteasy 1.6.0
Protease Mapping
3 versions - Latest release: 4 days ago - 1.07 thousand downloads total - 2 stars on GitHub - 1 maintainer
epialleleR 1.12.0
Fast, Epiallele-Aware Methylation Caller and Reporter
3 versions - Latest release: 4 days ago - 2.98 thousand downloads total - 3 stars on GitHub - 1 maintainer
TargetSearch 2.6.0
A package for the analysis of GC-MS metabolite profiling data
4 versions - Latest release: 5 days ago - 30.7 thousand downloads total - 4 stars on GitHub - 1 maintainer