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 4.7% on bioconductor.org
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data
3 versions - Latest release: 5 months ago - 77.8 thousand downloads total - 502 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: 3 days ago - 2 dependent packages - 727 thousand downloads total - 446 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
maftools 2.20.0 💰
Summarize, Analyze and Visualize MAF Files
3 versions - Latest release: 9 days ago - 8 dependent packages - 224 thousand downloads total - 417 stars on GitHub - 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: 4 days ago - 264 thousand downloads total - 380 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.30.0
Fast Gene Set Enrichment Analysis
3 versions - Latest release: 5 days ago - 37 dependent packages - 1.16 million downloads total - 344 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: 9 days ago - 135 dependent packages - 2.76 million downloads total - 327 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
PCAtools 2.16.0
PCAtools: Everything Principal Components Analysis
3 versions - Latest release: 5 days ago - 2 dependent packages - 67.6 thousand downloads total - 315 stars on GitHub - 1 maintainer
miloR 2.0.0
Differential neighbourhood abundance testing on a graph
3 versions - Latest release: 8 days ago - 10.6 thousand downloads total - 306 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: 6 days ago - 7 dependent packages - 85.3 thousand downloads total - 285 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
Top 2.7% on bioconductor.org
TCGAbiolinks 2.32.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
4 versions - Latest release: about 9 hours ago - 6 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
Top 8.4% on bioconductor.org
MOFA2 1.14.0
Multi-Omics Factor Analysis v2
4 versions - Latest release: 2 days ago - 22.5 thousand downloads total - 271 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
microbiome 1.24.0
Microbiome Analytics
2 versions - Latest release: 6 months ago - 1 dependent package - 113 thousand downloads total - 270 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
slingshot 2.12.0
Tools for ordering single-cell sequencing
3 versions - Latest release: 1 day ago - 4 dependent packages - 89.5 thousand downloads total - 225 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
tradeSeq 1.18.0
trajectory-based differential expression analysis for sequencing data
3 versions - Latest release: 7 days ago - 27.2 thousand downloads total - 221 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
iSEE 2.16.0
Interactive SummarizedExperiment Explorer
3 versions - Latest release: 8 days ago - 7 dependent packages - 33.6 thousand downloads total - 218 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
MAST 1.28.0
Model-based Analysis of Single Cell Transcriptomics
2 versions - Latest release: 6 months ago - 6 dependent packages - 158 thousand downloads total - 212 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
splatter 1.26.0
Simple Simulation of Single-cell RNA Sequencing Data
2 versions - Latest release: 6 months ago - 5 dependent packages - 41.9 thousand downloads total - 205 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
GenVisR 1.36.0
Genomic Visualizations in R
3 versions - Latest release: 1 day ago - 50.3 thousand downloads total - 194 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 8.3% on bioconductor.org
EnrichedHeatmap 1.34.0
Making Enriched Heatmaps
3 versions - Latest release: 9 days ago - 5 dependent packages - 44.4 thousand downloads total - 183 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
methylKit 1.28.0
DNA methylation analysis from high-throughput bisulfite sequencing results
2 versions - Latest release: 6 months ago - 3 dependent packages - 91.1 thousand downloads total - 182 stars on GitHub - 2 maintainers
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
microbiomeMarker 1.10.0
microbiome biomarker analysis toolkit
4 versions - Latest release: 1 day ago - 13.5 thousand downloads total - 160 stars on GitHub - 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
Top 9.4% on bioconductor.org
MicrobiotaProcess 1.14.1
A comprehensive R package for managing and analyzing microbiome and other ecological data within ...
3 versions - Latest release: 29 days ago - 19.1 thousand downloads total - 156 stars on GitHub - 1 maintainer
decoupleR 2.8.0
decoupleR: Ensemble of computational methods to infer biological activities from omics data
2 versions - Latest release: 6 months ago - 3 dependent packages - 23.6 thousand downloads total - 154 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
SingleR 2.4.1
Reference-Based Single-Cell RNA-Seq Annotation
3 versions - Latest release: 3 months ago - 3 dependent packages - 190 thousand downloads total - 154 stars on GitHub - 1 maintainer
Top 9.7% on bioconductor.org
muscat 1.16.0
Multi-sample multi-group scRNA-seq data analysis tools
2 versions - Latest release: 6 months ago - 1 dependent package - 18.8 thousand downloads total - 148 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
ballgown 2.36.0
Flexible, isoform-level differential expression analysis
3 versions - Latest release: 1 day ago - 3 dependent packages - 148 thousand downloads total - 141 stars on GitHub - 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
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
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
decontam 1.22.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
2 versions - Latest release: 6 months ago - 1 dependent package - 56.6 thousand downloads total - 131 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
2 versions - Latest release: 6 months ago - 13 dependent packages - 354 thousand downloads total - 130 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
plyranges 1.24.0
A fluent interface for manipulating GenomicRanges
3 versions - Latest release: about 11 hours ago - 19 dependent packages - 74.9 thousand downloads total - 127 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
scDblFinder 1.16.0
scDblFinder
2 versions - Latest release: 7 months ago - 1 dependent package - 54.4 thousand downloads total - 126 stars on GitHub - 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
Top 1.9% on bioconductor.org
MSnbase 2.30.1
Base Functions and Classes for Mass Spectrometry and Proteomics
4 versions - Latest release: 9 days ago - 30 dependent packages - 394 thousand downloads total - 119 stars on GitHub - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data
3 versions - Latest release: 21 days ago - 1 dependent package - 12.2 thousand downloads total - 118 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
SC3 1.32.0
Single-Cell Consensus Clustering
3 versions - Latest release: about 18 hours ago - 4 dependent packages - 63.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
InteractiveComplexHeatmap 1.10.0
Make Interactive Complex Heatmaps
2 versions - Latest release: 6 months ago - 1 dependent package - 14.6 thousand downloads total - 112 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 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 1.4% on bioconductor.org
qvalue 2.36.0
Q-value estimation for false discovery rate control
3 versions - Latest release: 7 days ago - 44 dependent packages - 1.53 million downloads total - 106 stars on GitHub - 2 maintainers
SIMLR 1.30.0
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
3 versions - Latest release: 4 days ago - 1 dependent package - 24.5 thousand downloads total - 106 stars on GitHub - 1 maintainer
clustifyr 1.14.0
Classifier for Single-cell RNA-seq Using Cell Clusters
2 versions - Latest release: 6 months ago - 8.57 thousand downloads total - 101 stars on GitHub - 1 maintainer
rBLAST 1.0.0
R Interface for the Basic Local Alignment Search Tool
1 version - Latest release: 9 days ago - 100 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
SNPRelate 1.36.1
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
3 versions - Latest release: 2 months ago - 11 dependent packages - 172 thousand downloads total - 96 stars on GitHub - 1 maintainer
simplifyEnrichment 1.12.0
Simplify Functional Enrichment Results
2 versions - Latest release: 6 months ago - 3 dependent packages - 21.9 thousand downloads total - 94 stars on GitHub - 1 maintainer
BayesSpace 1.12.0
Clustering and Resolution Enhancement of Spatial Transcriptomes
2 versions - Latest release: 6 months ago - 1 dependent package - 11.6 thousand downloads total - 89 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: 5 days ago - 2 dependent packages - 50.4 thousand downloads total - 89 stars on GitHub - 1 maintainer
progeny 1.24.0
Pathway RespOnsive GENes for activity inference from gene expression
2 versions - Latest release: 6 months ago - 1 dependent package - 25.3 thousand downloads total - 88 stars on GitHub - 1 maintainer
Top 7.1% on bioconductor.org
TitanCNA 1.40.0
Subclonal copy number and LOH prediction from whole genome sequencing of tumours
2 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 87 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
scmap 1.24.0
A tool for unsupervised projection of single cell RNA-seq data
2 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 86 stars on GitHub - 1 maintainer
netZooR 1.6.0
Unified methods for the inference and analysis of gene regulatory networks
2 versions - Latest release: 6 months ago - 2.05 thousand downloads total - 84 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
BASiCS 2.14.0
Bayesian Analysis of Single-Cell Sequencing data
2 versions - Latest release: 6 months ago - 2 dependent packages - 16.7 thousand downloads total - 83 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
ggtreeExtra 1.12.0
An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"
2 versions - Latest release: 6 months ago - 3 dependent packages - 33.5 thousand downloads total - 83 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: 7 days ago - 47 dependent packages - 1.86 million downloads total - 82 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: 9 days ago - 2 dependent packages - 92.3 thousand downloads total - 82 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: 9 days ago - 3 dependent packages - 47.1 thousand downloads total - 76 stars on GitHub - 1 maintainer
cmapR 1.14.0
CMap Tools in R
2 versions - Latest release: 6 months ago - 20.4 thousand downloads total - 76 stars on GitHub - 1 maintainer
GeneTonic 2.8.0
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional ...
3 versions - Latest release: 8 days ago - 10 thousand downloads total - 75 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: 5 days ago - 2.66 thousand downloads total - 75 stars on GitHub - 1 maintainer
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas
3 versions - Latest release: 3 days ago - 941 downloads total - 75 stars on GitHub - 1 maintainer
schex 1.16.1
Hexbin plots for single cell omics data
3 versions - Latest release: 3 months ago - 3 dependent packages - 13.3 thousand downloads total - 71 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 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 3.3% on bioconductor.org
destiny 3.18.0
Creates diffusion maps
3 versions - Latest release: 9 days ago - 4 dependent packages - 132 thousand downloads total - 67 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
hypeR 2.2.0
An R Package For Geneset Enrichment Workflows
3 versions - Latest release: about 7 hours ago - 8.49 thousand downloads total - 65 stars on GitHub - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network
2 versions - Latest release: 1 day ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
scPipe 2.2.0
Pipeline for single cell multi-omic data pre-processing
2 versions - Latest release: 6 months ago - 14.7 thousand downloads total - 64 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 7.7% on bioconductor.org
Nebulosa 1.12.1
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
3 versions - Latest release: about 1 month ago - 34.7 thousand downloads total - 63 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
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 3.0% on bioconductor.org
metagenomeSeq 1.46.0
Statistical analysis for sparse high-throughput sequencing
3 versions - Latest release: 1 day ago - 10 dependent packages - 148 thousand downloads total - 62 stars on GitHub - 1 maintainer
scMerge 1.18.0
scMerge: Merging multiple batches of scRNA-seq data
2 versions - Latest release: 6 months ago - 2 dependent packages - 22.5 thousand downloads total - 62 stars on GitHub - 1 maintainer
projectR 1.18.0
Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering
2 versions - Latest release: 7 months ago - 1 dependent package - 6.89 thousand downloads total - 62 stars on GitHub - 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
Voyager 1.4.0
From geospatial to spatial omics
2 versions - Latest release: 6 months ago - 2.65 thousand downloads total - 60 stars on GitHub - 1 maintainer
Top 9.2% on bioconductor.org
debrowser 1.32.0
Interactive Differential Expresion Analysis Browser
5 versions - Latest release: 4 days ago - 29.4 thousand downloads total - 60 stars on GitHub - 1 maintainer
scDesign3 1.0.1
A unified framework of realistic in silico data generation and statistical model inference for si...
2 versions - Latest release: 4 months ago - 610 downloads total - 59 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
PharmacoGx 3.6.0
Analysis of Large-Scale Pharmacogenomic Data
2 versions - Latest release: 6 months ago - 3 dependent packages - 25.9 thousand downloads total - 57 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: 9 days ago - 31 dependent packages - 787 thousand downloads total - 56 stars on GitHub - 1 maintainer
scDataviz 1.12.0
scDataviz: single cell dataviz and downstream analyses
2 versions - Latest release: 6 months ago - 4.42 thousand downloads total - 55 stars on GitHub - 1 maintainer
cardelino 1.4.0
Clone Identification from Single Cell Data
2 versions - Latest release: 6 months ago - 1.97 thousand downloads total - 54 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
ggcyto 1.32.0
Visualize Cytometry data with ggplot
4 versions - Latest release: 7 days ago - 9 dependent packages - 117 thousand downloads total - 53 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: 9 days ago - 7 dependent packages - 792 thousand downloads total - 53 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 2.30.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
3 versions - Latest release: 8 days ago - 1 dependent package - 49.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 4.0% on bioconductor.org
RTCGA 1.34.0
The Cancer Genome Atlas Data Integration
3 versions - Latest release: 1 day ago - 1 dependent package - 70 thousand downloads total - 52 stars on GitHub - 1 maintainer
CARNIVAL 2.12.0
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALu...
2 versions - Latest release: 6 months ago - 2 dependent packages - 8.44 thousand downloads total - 52 stars on GitHub - 1 maintainer
matter 2.6.0
Scientific computing for out-of-memory signals and images
4 versions - Latest release: 8 days ago - 2 dependent packages - 18.8 thousand downloads total - 52 stars on GitHub - 1 maintainer
scone 1.26.0
Single Cell Overview of Normalized Expression data
2 versions - Latest release: 6 months ago - 19.1 thousand downloads total - 52 stars on GitHub - 1 maintainer
cosmosR 1.10.0
COSMOS (Causal Oriented Search of Multi-Omic Space)
2 versions - Latest release: 6 months ago - 3.5 thousand downloads total - 52 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: 4 days ago - 2.56 thousand downloads total - 52 stars on GitHub - 1 maintainer