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: 7 days ago - 171 dependent packages - 3.01 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: 7 days ago - 327 dependent packages - 7.14 million downloads total - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets
8 versions - Latest release: 28 days ago - 2.02 thousand downloads total - 12 stars on GitHub - 1 maintainer
GenomicPlot 1.0.8
Plot profiles of next generation sequencing data in genomic features
8 versions - Latest release: 18 days ago - 914 downloads total - 2 stars on GitHub - 1 maintainer
PhyloProfile 1.18.0
PhyloProfile
7 versions - Latest release: 8 days ago - 7.09 thousand downloads total - 29 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: 8 days ago - 4 dependent packages - 21.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
spatialHeatmap 2.8.5
spatialHeatmap
7 versions - Latest release: about 2 months ago - 5.37 thousand downloads total - 4 stars on GitHub - 1 maintainer
ggkegg 1.0.13
KEGG pathway visualization by ggplot2
7 versions - Latest release: 2 months ago - 2.12 thousand downloads total - 190 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
plotgardener 1.10.0
Coordinate-Based Genomic Visualization Package for R
6 versions - Latest release: 5 days ago - 3 dependent packages - 9.55 thousand downloads total - 276 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: 2 days ago - 1.84 thousand downloads total - 1 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: 1 day ago - 13 dependent packages - 263 thousand downloads total - 2 maintainers
doubletrouble 1.4.0
Identification and classification of duplicated genes
6 versions - Latest release: 2 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: 9 days ago - 4.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.56.0
Conveniently import and query gene models
6 versions - Latest release: 7 days ago - 175 dependent packages - 3.3 million downloads total - 1 maintainer
Top 5.8% on bioconductor.org
GenomicScores 2.16.0
Infrastructure to work with genomewide position-specific scores
6 versions - Latest release: 8 days ago - 6 dependent packages - 54.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
SeqArray 1.42.4
Data Management of Large-Scale Whole-Genome Sequence Variant Calls
6 versions - Latest release: about 1 month ago - 11 dependent packages - 85.4 thousand downloads total - 42 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.72.0
Efficient manipulation of biological strings
6 versions - Latest release: 7 days ago - 324 dependent packages - 6.24 million downloads total - 1 maintainer
Top 9.2% on bioconductor.org
debrowser 1.32.0
Interactive Differential Expresion Analysis Browser
5 versions - Latest release: 5 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression
5 versions - Latest release: 4 months ago - 830 downloads total - 69 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
tximeta 1.20.3
Transcript Quantification Import with Automatic Metadata
5 versions - Latest release: 3 months ago - 3 dependent packages - 90.9 thousand downloads total - 63 stars on GitHub - 1 maintainer
rawrr 1.12.0
Direct Access to Orbitrap Data and Beyond
5 versions - Latest release: 8 days ago - 1 dependent package - 9.26 thousand downloads total - 50 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
DEGreport 1.38.5
Report of DEG analysis
5 versions - Latest release: 4 months ago - 1 dependent package - 58 thousand downloads total - 21 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: 7 days ago - 128 dependent packages - 3.54 million downloads total - 1 maintainer
Top 7.0% on bioconductor.org
Rhdf5lib 1.26.0
hdf5 library as an R package
5 versions - Latest release: 1 day ago - 3 dependent packages - 1.85 million downloads total - 6 stars on GitHub - 1 maintainer
MSstatsShiny 1.4.3
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
5 versions - Latest release: 2 months ago - 2.43 thousand downloads total - 9 stars on GitHub - 1 maintainer
extraChIPs 1.8.1
Additional functions for working with ChIP-Seq data
5 versions - Latest release: 1 day ago - 2.42 thousand downloads total - 7 stars on GitHub - 1 maintainer
HIBAG 1.40.0
HLA Genotype Imputation with Attribute Bagging
5 versions - Latest release: 3 days ago - 20.1 thousand downloads total - 26 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: 9 days ago - 118 dependent packages - 3.98 million downloads total - 30 stars on GitHub - 1 maintainer
MoleculeExperiment 1.4.0
Prioritising a molecule-level storage of Spatial Transcriptomics Data
5 versions - Latest release: 6 days ago - 1.44 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
glmGamPoi 1.14.3
Fit a Gamma-Poisson Generalized Linear Model
5 versions - Latest release: 2 months ago - 5 dependent packages - 138 thousand downloads total - 84 stars on GitHub - 1 maintainer
benchdamic 1.10.0
Benchmark of differential abundance methods on microbiome data
5 versions - Latest release: 1 day ago - 3.07 thousand downloads total - 5 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: about 22 hours ago - 1.91 thousand downloads total - 0 stars on GitHub - 1 maintainer
enhancerHomologSearch 1.10.0
Identification of putative mammalian orthologs to given enhancer
5 versions - Latest release: 5 days ago - 2.56 thousand downloads total - 0 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: 7 days ago - 706 dependent packages - 7.4 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: 7 days ago - 125 dependent packages - 1.99 million downloads total - 1 maintainer
tidybulk 1.16.0
Brings transcriptomics to the tidyverse
5 versions - Latest release: 1 day ago - 9.77 thousand downloads total - 159 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.2.0
LC-MS and GC-MS Data Analysis
5 versions - Latest release: 7 days ago - 15 dependent packages - 851 thousand downloads total - 157 stars on GitHub - 1 maintainer
COTAN 2.2.4
COexpression Tables ANalysis
5 versions - Latest release: about 1 month ago - 2.68 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: 7 days ago - 49 dependent packages - 4.77 million downloads total - 1 maintainer
SPOTlight 1.8.0
`SPOTlight`: Spatial Transcriptomics Deconvolution
5 versions - Latest release: 6 days ago - 6.1 thousand downloads total - 139 stars on GitHub - 1 maintainer
DAPAR 1.34.6
Tools for the Differential Analysis of Proteins Abundance with R
5 versions - Latest release: 3 months ago - 1 dependent package - 19.9 thousand downloads total - 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
canceR 1.36.8
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
5 versions - Latest release: 20 days ago - 18.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
UCell 2.8.0
Rank-based signature enrichment analysis for single-cell data
5 versions - Latest release: 5 days ago - 1 dependent package - 29.3 thousand downloads total - 111 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: 7 days ago - 25 dependent packages - 1.23 million downloads total - 1 maintainer
SPIAT 1.6.0
Spatial Image Analysis of Tissues
5 versions - Latest release: 9 days ago - 2.95 thousand downloads total - 16 stars on GitHub - 1 maintainer
variancePartition 1.34.0
Quantify and interpret drivers of variation in multilevel gene expression experiments
5 versions - Latest release: 4 days ago - 4 dependent packages - 57.1 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.5% on bioconductor.org
celda 1.20.0
CEllular Latent Dirichlet Allocation
5 versions - Latest release: 1 day ago - 2 dependent packages - 32.5 thousand downloads total - 133 stars on GitHub - 1 maintainer
BioNERO 1.12.0
Biological Network Reconstruction Omnibus
5 versions - Latest release: 2 days ago - 1 dependent package - 8.17 thousand downloads total - 17 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data
5 versions - Latest release: 3 months ago - 1.91 thousand downloads total - 8 stars on GitHub - 1 maintainer
Prostar 1.34.6
Provides a GUI for DAPAR
5 versions - Latest release: 3 months ago - 17.4 thousand downloads total - 1 maintainer
TAPseq 1.16.0
Targeted scRNA-seq primer design for TAP-seq
4 versions - Latest release: 5 days ago - 4.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
fenr 1.0.5
Fast functional enrichment for interactive applications
4 versions - Latest release: 2 months ago - 733 downloads total - 0 stars on GitHub - 1 maintainer
gDNAx 1.2.0
Diagnostics for assessing genomic DNA contamination in RNA-seq data
4 versions - Latest release: about 15 hours ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
glmSparseNet 1.22.0
Network Centrality Metrics for Elastic-Net Regularized Models
4 versions - Latest release: 9 days ago - 8.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
metapod 1.12.0
Meta-Analyses on P-Values of Differential Analyses
4 versions - Latest release: about 17 hours ago - 4 dependent packages - 204 thousand downloads total - 1 maintainer
rrvgo 1.14.2
Reduce + Visualize GO
4 versions - Latest release: 30 days ago - 17 thousand downloads total - 20 stars on GitHub - 1 maintainer
cogeqc 1.8.0
Systematic quality checks on comparative genomics analyses
4 versions - Latest release: 2 days ago - 2.43 thousand downloads total - 8 stars on GitHub - 1 maintainer
nnSVG 1.6.4
Scalable identification of spatially variable genes in spatially-resolved transcriptomics data
4 versions - Latest release: 22 days ago - 2.67 thousand downloads total - 10 stars on GitHub - 1 maintainer
DELocal 1.4.0
Identifies differentially expressed genes with respect to other local genes
4 versions - Latest release: 6 days ago - 1.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
ggspavis 1.9.10
Visualization functions for spatial transcriptomics data
4 versions - Latest release: 9 days ago - 4.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
MSstats 4.12.0
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experi...
4 versions - Latest release: 1 day ago - 8 dependent packages - 64.1 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
dittoSeq 1.14.3
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
4 versions - Latest release: 21 days ago - 4 dependent packages - 46.2 thousand downloads total - 1 maintainer
SparseArray 1.2.4
Efficient in-memory representation of multidimensional sparse arrays
4 versions - Latest release: 3 months ago - 5 dependent packages - 495 thousand downloads total - 1 maintainer
MEIGOR 1.36.2
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
4 versions - Latest release: 20 days ago - 2 dependent packages - 16.4 thousand downloads total - 1 maintainer
sSNAPPY 1.8.0
Single Sample directioNAl Pathway Perturbation analYsis
4 versions - Latest release: 8 days ago - 2.66 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.0.0
Methylation array and sequencing spatial analysis methods
4 versions - Latest release: about 19 hours ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
CATALYST 1.28.0
Cytometry dATa anALYSis Tools
4 versions - Latest release: 6 days ago - 4 dependent packages - 46.6 thousand downloads total - 61 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
csaw 1.38.0
ChIP-Seq Analysis with Windows
4 versions - Latest release: 1 day ago - 8 dependent packages - 72.1 thousand downloads total - 1 maintainer
animalcules 1.18.3
Interactive microbiome analysis toolkit
4 versions - Latest release: 3 months ago - 8.28 thousand downloads total - 51 stars on GitHub - 1 maintainer
scFeatures 1.4.0
scFeatures: Multi-view representations of single-cell and spatial data for disease outcome predic...
4 versions - Latest release: about 21 hours ago - 1.45 thousand downloads total - 10 stars on GitHub - 1 maintainer
MungeSumstats 1.12.0
Standardise summary statistics from GWAS
4 versions - Latest release: 8 days ago - 23 thousand downloads total - 64 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
batchelor 1.20.0
Single-Cell Batch Correction Methods
4 versions - Latest release: about 24 hours ago - 5 dependent packages - 244 thousand downloads total - 1 maintainer
SimBu 1.6.0
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
4 versions - Latest release: 8 days ago - 1.83 thousand downloads total - 12 stars on GitHub - 1 maintainer
MSstatsPTM 2.4.4
Statistical Characterization of Post-translational Modifications
4 versions - Latest release: 3 months ago - 2 dependent packages - 6.92 thousand downloads total - 6 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: 2 days ago - 2 dependent packages - 3.42 thousand downloads total - 0 stars on GitHub - 1 maintainer
scRNAseqApp 1.4.0
A single-cell RNAseq Shiny app-package
4 versions - Latest release: 9 days ago - 1.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
bioCancer 1.30.8
Interactive Multi-Omics Cancers Data Visualization and Analysis
4 versions - Latest release: about 2 months ago - 12 thousand downloads total - 19 stars on GitHub - 1 maintainer
drawProteins 1.24.0
Package to Draw Protein Schematics from Uniprot API output
4 versions - Latest release: 4 days ago - 1 dependent package - 14.8 thousand downloads total - 33 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
basilisk.utils 1.16.0
Basilisk Installation Utilities
4 versions - Latest release: 1 day ago - 2 dependent packages - 125 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
4 versions - Latest release: 7 days ago - 315 dependent packages - 5.07 million downloads total - 1 maintainer
mastR 1.4.0
Markers Automated Screening Tool in R
4 versions - Latest release: 1 day ago - 1.96 thousand downloads total - 4 stars on GitHub - 1 maintainer
RNAdecay 1.22.2
Maximum Likelihood Decay Modeling of RNA Degradation Data
4 versions - Latest release: 3 months ago - 5.32 thousand downloads total - 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: 9 days ago - 135 dependent packages - 2.76 million downloads total - 327 stars on GitHub - 1 maintainer
fgga 1.12.0
Hierarchical ensemble method based on factor graph
4 versions - Latest release: 1 day ago - 3.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.3% on bioconductor.org
RedeR 3.0.0
Interactive visualization and manipulation of nested networks
4 versions - Latest release: 1 day ago - 4 dependent packages - 48.3 thousand downloads total - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation
4 versions - Latest release: 1 day ago - 1.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 3 days ago - 3.07 thousand downloads total - 3 stars on GitHub - 1 maintainer
BSgenomeForge 1.2.3
Forge BSgenome data packages
4 versions - Latest release: 21 days ago - 1 dependent package - 7.7 thousand downloads total - 1 maintainer
PureCN 2.10.0
Copy number calling and SNV classification using targeted short read sequencing
4 versions - Latest release: about 22 hours ago - 25.8 thousand downloads total - 120 stars on GitHub - 1 maintainer
ceRNAnetsim 1.16.0
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
4 versions - Latest release: 3 days ago - 4.14 thousand downloads total - 4 stars on GitHub - 1 maintainer
AnVIL 1.14.2
Bioconductor on the AnVIL compute environment
4 versions - Latest release: 3 months ago - 4 dependent packages - 31.2 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
zellkonverter 1.14.0
Conversion Between scRNA-seq Objects
4 versions - Latest release: 5 days ago - 6 dependent packages - 43.4 thousand downloads total - 132 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: 1 day ago - 1 dependent package - 83.2 thousand downloads total - 1 maintainer
EWCE 1.12.0
Expression Weighted Celltype Enrichment
4 versions - Latest release: 9 days ago - 8.86 thousand downloads total - 51 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
TargetSearch 2.6.0
A package for the analysis of GC-MS metabolite profiling data
4 versions - Latest release: 7 days ago - 30.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.48.0
R Interface to HDF5
4 versions - Latest release: 7 days ago - 63 dependent packages - 2.08 million downloads total - 59 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
rols 2.30.2
An R interface to the Ontology Lookup Service
4 versions - Latest release: 3 months ago - 3 dependent packages - 56.4 thousand downloads total - 11 stars on GitHub - 1 maintainer