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 3.0% on bioconductor.org
ChIPpeakAnno 3.38.0
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any expe...
4 versions - Latest release: 2 days ago - 8 dependent packages - 267 thousand downloads total - 4 maintainers
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets
2 versions - Latest release: 6 months ago - 2 dependent packages - 28.6 thousand downloads total - 4 maintainers
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
ASSIGN 1.38.0
Adaptive Signature Selection and InteGratioN (ASSIGN)
2 versions - Latest release: 6 months ago - 1 dependent package - 19.3 thousand downloads total - 2 stars on GitHub - 4 maintainers
BgeeDB 2.30.0
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities...
3 versions - Latest release: 8 days ago - 2 dependent packages - 17.4 thousand downloads total - 13 stars on GitHub - 4 maintainers
switchBox 1.38.0
Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair ...
2 versions - Latest release: 6 months ago - 1 dependent package - 17.8 thousand downloads total - 3 maintainers
Top 4.3% on bioconductor.org
crlmm 1.62.0
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumin...
3 versions - Latest release: 1 day ago - 3 dependent packages - 69.9 thousand downloads total - 3 maintainers
Top 1.7% on bioconductor.org
sva 3.52.0
Surrogate Variable Analysis
3 versions - Latest release: 7 days ago - 41 dependent packages - 800 thousand downloads total - 3 maintainers
DeepBlueR 1.27.0
DeepBlueR
2 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 3 maintainers
rcellminer 2.24.0
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
2 versions - Latest release: 6 months ago - 15.3 thousand downloads total - 3 maintainers
Top 3.3% on bioconductor.org
missMethyl 1.38.0
Analysing Illumina HumanMethylation BeadChip Data
3 versions - Latest release: 1 day ago - 5 dependent packages - 122 thousand downloads total - 3 maintainers
BioTIP 1.18.0
BioTIP: An R package for characterization of Biological Tipping-Point
3 versions - Latest release: 8 days ago - 5.78 thousand downloads total - 14 stars on GitHub - 3 maintainers
Top 6.2% on bioconductor.org
genomation 1.34.0
Summary, annotation and visualization of genomic data
2 versions - Latest release: 6 months ago - 5 dependent packages - 76.8 thousand downloads total - 3 maintainers
Top 2.3% on bioconductor.org
ReportingTools 2.44.0
Tools for making reports in various formats
4 versions - Latest release: 2 days ago - 5 dependent packages - 201 thousand downloads total - 3 maintainers
LOBSTAHS 1.28.0
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
2 versions - Latest release: 6 months ago - 10.3 thousand downloads total - 3 maintainers
RTNduals 1.26.0
Analysis of co-regulation and inference of 'dual regulons'
2 versions - Latest release: 6 months ago - 1 dependent package - 9.64 thousand downloads total - 2 maintainers
subSeq 1.32.0
Subsampling of high-throughput sequencing count data
2 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 19 stars on GitHub - 2 maintainers
splineTimeR 1.30.0
Time-course differential gene expression data analysis using spline regression models followed by...
2 versions - Latest release: 6 months ago - 12 thousand downloads total - 2 maintainers
Top 5.3% on bioconductor.org
LEA 3.16.0
LEA: an R package for Landscape and Ecological Association Studies
3 versions - Latest release: 1 day ago - 54.3 thousand downloads total - 2 maintainers
ArrayExpressHTS 1.50.0 removed
ArrayExpress High Throughput Sequencing Processing Pipeline
1 version - Latest release: 7 months ago - 17.8 thousand downloads total - 2 maintainers
Top 5.5% on bioconductor.org
dupRadar 1.34.0
Assessment of duplication rates in RNA-Seq datasets
3 versions - Latest release: 1 day ago - 51.4 thousand downloads total - 1 stars on GitHub - 2 maintainers
PathoStat 1.28.0
PathoStat Statistical Microbiome Analysis Package
2 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 8 stars on GitHub - 2 maintainers
DEsubs 1.28.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...
2 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 2 maintainers
OmaDB 2.18.0
R wrapper for the OMA REST API
2 versions - Latest release: 6 months ago - 2 dependent packages - 10.9 thousand downloads total - 1 stars on GitHub - 2 maintainers
swfdr 1.28.0
Estimation of the science-wise false discovery rate and the false discovery rate conditional on c...
2 versions - Latest release: 6 months ago - 8.35 thousand downloads total - 3 stars on GitHub - 2 maintainers
Top 3.2% on bioconductor.org
DSS 2.52.0
Dispersion shrinkage for sequencing data
4 versions - Latest release: 1 day ago - 10 dependent packages - 146 thousand downloads total - 2 maintainers
Top 2.9% on bioconductor.org
flowStats 4.16.0
Statistical methods for the analysis of flow cytometry data
4 versions - Latest release: about 23 hours ago - 9 dependent packages - 183 thousand downloads total - 15 stars on GitHub - 2 maintainers
Top 9.1% on bioconductor.org
codelink 1.70.0
Manipulation of Codelink microarray data
2 versions - Latest release: 6 months ago - 1 dependent package - 33.1 thousand downloads total - 0 stars on GitHub - 2 maintainers
MetaboSignal 1.32.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways
3 versions - Latest release: 5 months ago - 13.1 thousand downloads total - 2 maintainers
TCC 1.42.0
TCC: Differential expression analysis for tag count data with robust normalization strategies
2 versions - Latest release: 6 months ago - 1 dependent package - 50.4 thousand downloads total - 2 maintainers
RTNsurvival 1.26.0
Survival analysis using transcriptional networks inferred by the RTN package
2 versions - Latest release: 6 months ago - 8.45 thousand downloads total - 2 maintainers
DominoEffect 1.22.0
Identification and Annotation of Protein Hotspot Residues
2 versions - Latest release: 6 months ago - 7.11 thousand downloads total - 2 maintainers
groHMM 1.36.0
GRO-seq Analysis Pipeline
2 versions - Latest release: 6 months ago - 18.5 thousand downloads total - 1 stars on GitHub - 2 maintainers
MEB 1.16.0
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes ...
2 versions - Latest release: 6 months ago - 4.29 thousand downloads total - 2 maintainers
tRanslatome 1.40.0
Comparison between multiple levels of gene expression
2 versions - Latest release: 6 months ago - 19.5 thousand downloads total - 2 maintainers
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
CausalR 1.34.0
Causal network analysis methods
2 versions - Latest release: 6 months ago - 12.8 thousand downloads total - 2 maintainers
KEGGlincs 1.28.0
Visualize all edges within a KEGG pathway and overlay LINCS data
2 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 2 maintainers
pvac 1.50.0
PCA-based gene filtering for Affymetrix arrays
2 versions - Latest release: 6 months ago - 23 thousand downloads total - 2 maintainers
LowMACA 1.31.0
LowMACA - Low frequency Mutation Analysis via Consensus Alignment
2 versions - Latest release: 6 months ago - 12.2 thousand downloads total - 2 maintainers
MsBackendMgf 1.10.0
Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
2 versions - Latest release: 6 months ago - 3 dependent packages - 21.2 thousand downloads total - 4 stars on GitHub - 2 maintainers
GRmetrics 1.28.0
Calculate growth-rate inhibition (GR) metrics
2 versions - Latest release: 6 months ago - 15.2 thousand downloads total - 1 stars on GitHub - 2 maintainers
INDEED 2.16.0
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis...
2 versions - Latest release: 6 months ago - 5.16 thousand downloads total - 4 stars on GitHub - 2 maintainers
DeMAND 1.32.0
DeMAND
2 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 2 maintainers
NanoStringDiff 1.32.0
Differential Expression Analysis of NanoString nCounter Data
2 versions - Latest release: 6 months ago - 1 dependent package - 15.9 thousand downloads total - 2 maintainers
RImmPort 1.30.0
RImmPort: Enabling Ready-for-analysis Immunology Research Data
2 versions - Latest release: 6 months ago - 9.47 thousand downloads total - 2 maintainers
edge 2.34.0
Extraction of Differential Gene Expression
2 versions - Latest release: 6 months ago - 21.7 thousand downloads total - 20 stars on GitHub - 2 maintainers
Top 2.7% on bioconductor.org
goseq 1.56.0
Gene Ontology analyser for RNA-seq and other length biased data
3 versions - Latest release: 1 day ago - 5 dependent packages - 218 thousand downloads total - 2 maintainers
PAIRADISE 1.18.0
PAIRADISE: Paired analysis of differential isoform expression
2 versions - Latest release: 6 months ago - 6.79 thousand downloads total - 2 maintainers
rfaRm 1.14.2
An R interface to the Rfam database
4 versions - Latest release: 3 months ago - 4.05 thousand downloads total - 2 maintainers
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 11 hours ago - 6 dependent packages - 364 thousand downloads total - 274 stars on GitHub - 2 maintainers
Top 1.8% on bioconductor.org
Rsubread 2.18.0
Mapping, quantification and variant analysis of sequencing data
4 versions - Latest release: 4 days ago - 14 dependent packages - 311 thousand downloads total - 2 maintainers
anota2seq 1.24.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
2 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 2 maintainers
Top 6.1% on bioconductor.org
ChIPQC 1.38.0
Quality metrics for ChIPseq data
2 versions - Latest release: 6 months ago - 57.4 thousand downloads total - 2 maintainers
CancerInSilico 2.22.0
An R interface for computational modeling of tumor progression
2 versions - Latest release: 6 months ago - 8.84 thousand downloads total - 2 maintainers
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 6.2% on bioconductor.org
iClusterPlus 1.38.0
Integrative clustering of multi-type genomic data
2 versions - Latest release: 6 months ago - 1 dependent package - 47.7 thousand downloads total - 2 maintainers
RCASPAR 1.48.0
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
2 versions - Latest release: 6 months ago - 20.9 thousand downloads total - 2 maintainers
nethet 1.34.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
2 versions - Latest release: 6 months ago - 12.9 thousand downloads total - 2 maintainers
STATegRa 1.38.0
Classes and methods for multi-omics data integration
2 versions - Latest release: 6 months ago - 15 thousand downloads total - 2 maintainers
GSAR 1.36.0
Gene Set Analysis in R
2 versions - Latest release: 6 months ago - 22.6 thousand downloads total - 2 maintainers
pandaR 1.34.0
PANDA Algorithm
2 versions - Latest release: 6 months ago - 1 dependent package - 16.2 thousand downloads total - 2 maintainers
BubbleTree 2.32.0
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic m...
2 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 2 maintainers
Top 9.9% on bioconductor.org
polyester 1.38.0
Simulate RNA-seq reads
2 versions - Latest release: 6 months ago - 25.6 thousand downloads total - 2 maintainers
divergence 1.18.0
Divergence: Functionality for assessing omics data by divergence with respect to a baseline
2 versions - Latest release: 6 months ago - 4.75 thousand downloads total - 2 maintainers
NADfinder 1.26.0
Call wide peaks for sequencing data
2 versions - Latest release: 6 months ago - 9.39 thousand downloads total - 2 maintainers
GSReg 1.36.0
Gene Set Regulation (GS-Reg)
2 versions - Latest release: 6 months ago - 14 thousand downloads total - 2 maintainers
INSPEcT 1.32.1
Modeling RNA synthesis, processing and degradation with RNA-seq data
3 versions - Latest release: 4 months ago - 13.8 thousand downloads total - 2 maintainers
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...
2 versions - Latest release: 6 months ago - 35.7 thousand downloads total - 2 maintainers
matchBox 1.44.0
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. di...
2 versions - Latest release: 6 months ago - 18.9 thousand downloads total - 2 maintainers
Top 7.7% on bioconductor.org
flowFP 1.60.0
Fingerprinting for Flow Cytometry
2 versions - Latest release: 6 months ago - 2 dependent packages - 34.3 thousand downloads total - 2 maintainers
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
PloGO2 1.14.0
Plot Gene Ontology and KEGG pathway Annotation and Abundance
2 versions - Latest release: 6 months ago - 4.48 thousand downloads total - 2 maintainers
banocc 1.26.0
Bayesian ANalysis Of Compositional Covariance
2 versions - Latest release: 6 months ago - 9.33 thousand downloads total - 2 maintainers
PROMISE 1.54.0
PRojection Onto the Most Interesting Statistical Evidence
2 versions - Latest release: 6 months ago - 1 dependent package - 24.4 thousand downloads total - 2 maintainers
MWASTools 1.26.0
MWASTools: an integrated pipeline to perform metabolome-wide association studies
2 versions - Latest release: 6 months ago - 1 dependent package - 13.1 thousand downloads total - 2 maintainers
Top 8.6% on bioconductor.org
flagme 1.58.0
Analysis of Metabolomics GC/MS Data
2 versions - Latest release: 6 months ago - 29.3 thousand downloads total - 2 maintainers
BiGGR 1.38.0
Constraint based modeling in R using metabolic reconstruction databases
2 versions - Latest release: 6 months ago - 25 thousand downloads total - 2 maintainers
FISHalyseR 1.36.0
FISHalyseR a package for automated FISH quantification
2 versions - Latest release: 6 months ago - 12 thousand downloads total - 2 maintainers
profileplyr 1.18.0
Visualization and annotation of read signal over genomic ranges with profileplyr
2 versions - Latest release: 6 months ago - 1 dependent package - 13 thousand downloads total - 2 maintainers
Top 8.9% on bioconductor.org
CRImage 1.50.0
CRImage a package to classify cells and calculate tumour cellularity
2 versions - Latest release: 6 months ago - 31.6 thousand downloads total - 2 maintainers
SMITE 1.30.0
Significance-based Modules Integrating the Transcriptome and Epigenome
2 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 stars on GitHub - 2 maintainers
Top 3.0% on bioconductor.org
flowClust 3.42.0
Clustering for Flow Cytometry
3 versions - Latest release: 1 day ago - 7 dependent packages - 157 thousand downloads total - 2 maintainers
IntEREst 1.26.0
Intron-Exon Retention Estimator
2 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 2 maintainers
PAA 1.36.0
PAA (Protein Array Analyzer)
2 versions - Latest release: 6 months ago - 17.1 thousand downloads total - 2 maintainers
iasva 1.20.0
Iteratively Adjusted Surrogate Variable Analysis
2 versions - Latest release: 6 months ago - 6.09 thousand downloads total - 2 maintainers
Rarr 1.4.0
Read Zarr Files in R
3 versions - Latest release: 4 days ago - 2.25 thousand downloads total - 24 stars on GitHub - 1 maintainer
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data
2 versions - Latest release: 6 months ago - 21 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data
2 versions - Latest release: 6 months ago - 34.2 thousand downloads total - 1 maintainer
octad 1.4.0
Open Cancer TherApeutic Discovery (OCTAD)
2 versions - Latest release: 6 months ago - 1.39 thousand downloads total - 1 maintainer
memes 1.12.0
motif matching, comparison, and de novo discovery using the MEME Suite
3 versions - Latest release: 2 days ago - 8.72 thousand downloads total - 43 stars on GitHub - 1 maintainer
SDAMS 1.22.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...
2 versions - Latest release: 6 months ago - 7.06 thousand downloads total - 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
Top 6.8% on bioconductor.org
annotatr 1.28.0
Annotation of Genomic Regions to Genomic Annotations
2 versions - Latest release: 6 months ago - 5 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
HPAStainR 1.12.0
Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes
2 versions - Latest release: 6 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 1 maintainer
h5vc 2.36.0
Managing alignment tallies using a hdf5 backend
2 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
OrderedList 1.76.0
Similarities of Ordered Gene Lists
3 versions - Latest release: 1 day ago - 43.5 thousand downloads total - 1 maintainer
RiboDiPA 1.10.0
Differential pattern analysis for Ribo-seq data
2 versions - Latest release: 6 months ago - 2.87 thousand downloads total - 1 maintainer
diffUTR 1.10.0
diffUTR: Streamlining differential exon and 3' UTR usage
2 versions - Latest release: 6 months ago - 2.78 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
nucleR 2.34.0
Nucleosome positioning package for R
2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer