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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alpine 1.26.0 removed
alpine
1 version - Latest release: 7 months ago - 12.2 thousand downloads total - 1 maintainer
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
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
1 version - Latest release: 7 months ago - 3.82 thousand downloads total - 1 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
CBEA 1.3.0
Competitive Balances for Taxonomic Enrichment Analysis in R
2 versions - Latest release: 7 months ago - 2.37 thousand downloads total - 5 stars on GitHub - 1 maintainer
ChIC 1.19.0 removed
Quality Control Pipeline for ChIP-Seq Data
1 version - Latest release: 7 months ago - 6.47 thousand downloads total - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data
1 version - Latest release: 7 months ago - 7.34 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
copynumber 1.40.0 removed
Segmentation of single- and multi-track copy number data by penalized least squares regression.
1 version - Latest release: 7 months ago - 1 dependent package - 57 thousand downloads total - 1 maintainer
CopywriteR 2.32.0 removed
Copy number information from targeted sequencing using off-target reads
1 version - Latest release: 7 months ago - 18.3 thousand downloads total - 28 stars on GitHub - 1 maintainer
dasper 1.9.0 removed
Detecting abberant splicing events from RNA-sequencing data
1 version - Latest release: 7 months ago - 1 dependent package - 2.76 thousand downloads total - 14 stars on GitHub - 1 maintainer
epihet 1.16.0 removed
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
1 version - Latest release: 7 months ago - 4.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
GAPGOM 1.16.0 removed
GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
1 version - Latest release: 7 months ago - 3.72 thousand downloads total - 2 stars on GitHub - 1 maintainer
GeneAccord 1.18.0 removed
Detection of clonally exclusive gene or pathway pairs in a cohort of cancer patients
1 version - Latest release: 7 months ago - 4.41 thousand downloads total - 2 stars on GitHub - 1 maintainer
genotypeeval 1.31.1 removed
QA/QC of a gVCF or VCF file
1 version - Latest release: 7 months ago - 10.4 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
maanova 1.70.0 removed
Tools for analyzing Micro Array experiments
1 version - Latest release: 7 months ago - 36.5 thousand downloads total - 1 maintainer
metavizr 1.24.0 removed
R Interface to the metaviz web app for interactive metagenomics data analysis and visualization
1 version - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
MethCP 1.13.0 removed
Differential methylation anlsysis for bisulfite sequencing data
1 version - Latest release: 7 months ago - 2.97 thousand downloads total - 4 stars on GitHub - 1 maintainer
MIGSA 1.24.0 removed
Massive and Integrative Gene Set Analysis
1 version - Latest release: 7 months ago - 7.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
MIMOSA 1.37.0 removed
Mixture Models for Single-Cell Assays
1 version - Latest release: 7 months ago - 15.6 thousand downloads total - 1 maintainer
NanoStringQCPro 1.32.0 removed
Quality metrics and data processing methods for NanoString mRNA gene expression data
1 version - Latest release: 7 months ago - 18.7 thousand downloads total - 1 maintainer
NBSplice 1.18.0 removed
Negative Binomial Models to detect Differential Splicing
1 version - Latest release: 7 months ago - 5.1 thousand downloads total - 1 maintainer
netboxr 1.11.0 removed
netboxr
1 version - Latest release: 7 months ago - 2.92 thousand downloads total - 1 maintainer
NxtIRFcore 1.6.0 removed
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using ...
1 version - Latest release: 7 months ago - 1.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
ODER 1.6.0 removed
Optimising the Definition of Expressed Regions
1 version - Latest release: 7 months ago - 1.01 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.1% on bioconductor.org
pkgDepTools 1.66.0 removed
Package Dependency Tools
1 version - Latest release: 7 months ago - 32.1 thousand downloads total - 1 maintainer
PrecisionTrialDrawer 1.16.0 removed
A Tool to Analyze and Design NGS Based Custom Gene Panels
1 version - Latest release: 7 months ago - 3.87 thousand downloads total - 1 maintainer
proBatch 1.15.1 removed
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
1 version - Latest release: 7 months ago - 5.93 thousand downloads total - 14 stars on GitHub - 1 maintainer
proFIA 1.26.0 removed
Preprocessing of FIA-HRMS data
1 version - Latest release: 7 months ago - 8.96 thousand downloads total - 1 maintainer
pulsedSilac 1.14.0 removed
Analysis of pulsed-SILAC quantitative proteomics data
1 version - Latest release: 7 months ago - 3.16 thousand downloads total - 1 maintainer
RLSeq 1.6.0
RLSeq: An analysis package for R-loop mapping data
2 versions - Latest release: 7 months ago - 2.28 thousand downloads total - 2 stars on GitHub - 1 maintainer
savR 1.37.0 removed
Parse and analyze Illumina SAV files
1 version - Latest release: 7 months ago - 17.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 5.1% on bioconductor.org
sigPathway 1.68.0 removed
Pathway Analysis
1 version - Latest release: 7 months ago - 44.9 thousand downloads total - 1 maintainer
STAN 2.28.0 removed
The Genomic STate ANnotation Package
1 version - Latest release: 7 months ago - 14.8 thousand downloads total - 1 maintainer
TarSeqQC 1.29.0 removed
TARgeted SEQuencing Experiment Quality Control
1 version - Latest release: 7 months ago - 10.2 thousand downloads total - 1 maintainer
tscR 1.11.0 removed
A time series clustering package combining slope and Frechet distances
1 version - Latest release: 7 months ago - 3.57 thousand downloads total - 1 maintainer
ExploreModelMatrix 1.14.0
Graphical Exploration of Design Matrices
2 versions - Latest release: 7 months ago - 7.69 thousand downloads total - 37 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
annaffy 1.74.0
Annotation tools for Affymetrix biological metadata
2 versions - Latest release: 7 months ago - 2 dependent packages - 375 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
affyio 1.72.0
Tools for parsing Affymetrix data files
2 versions - Latest release: 7 months ago - 12 dependent packages - 1.52 million downloads total - 3 stars on GitHub - 1 maintainer
adverSCarial 1.0.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks
1 version - Latest release: 7 months ago - 634 downloads total - 1 maintainer
beachmat.hdf5 1.0.0
beachmat bindings for HDF5-backed matrices
1 version - Latest release: 7 months ago - 842 downloads total - 1 maintainer
CardinalIO 1.0.0
Read and write mass spectrometry imaging files
1 version - Latest release: 7 months ago - 1 dependent package - 1.78 thousand downloads total - 1 maintainer
alabaster.files 1.0.0
Wrappers to Save Common File Formats
1 version - Latest release: 7 months ago - 695 downloads total - 1 maintainer
DCATS 1.0.0
Differential Composition Analysis Transformed by a Similarity matrix
1 version - Latest release: 7 months ago - 748 downloads total - 1 maintainer
BioCartaImage 1.0.0
BioCarta Pathway Images
1 version - Latest release: 7 months ago - 663 downloads total - 9 stars on GitHub - 1 maintainer
iSEEindex 1.0.0
iSEE extension for a landing page to a custom collection of data sets
1 version - Latest release: 7 months ago - 715 downloads total - 1 stars on GitHub - 1 maintainer
demuxSNP 1.0.0
scRNAseq demultiplexing using cell hashing and SNPs
1 version - Latest release: 7 months ago - 658 downloads total - 4 stars on GitHub - 1 maintainer
MICSQTL 1.0.0
MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
1 version - Latest release: 7 months ago - 709 downloads total - 1 maintainer
regionalpcs 1.0.0
Summarizing Regional Methylation with Regional Principal Components Analysis
1 version - Latest release: 7 months ago - 534 downloads total - 0 stars on GitHub - 1 maintainer
TSAR 1.0.0
Thermal Shift Analysis in R
1 version - Latest release: 7 months ago - 604 downloads total - 1 maintainer
HarmonizR 1.0.0
Handles missing values and makes more data available
1 version - Latest release: 7 months ago - 702 downloads total - 1 maintainer
HERON 1.0.0
Hierarchical Epitope pROtein biNding
1 version - Latest release: 7 months ago - 607 downloads total - 1 stars on GitHub - 1 maintainer
decontX 1.0.0
Decontamination of single cell genomics data
1 version - Latest release: 7 months ago - 1.69 thousand downloads total - 1 maintainer
CytoPipelineGUI 1.0.0
GUI's for visualization of flow cytometry data analysis pipelines
1 version - Latest release: 7 months ago - 564 downloads total - 1 maintainer
CCPlotR 1.0.0
Plots For Visualising Cell-Cell Interactions
1 version - Latest release: 7 months ago - 738 downloads total - 22 stars on GitHub - 1 maintainer
phantasusLite 1.0.0
Loading and annotation RNA-Seq counts matrices
1 version - Latest release: 7 months ago - 523 downloads total - 2 stars on GitHub - 1 maintainer
multiWGCNA 1.0.0
multiWGCNA
1 version - Latest release: 7 months ago - 938 downloads total - 1 maintainer
tadar 1.0.0
Transcriptome Analysis of Differential Allelic Representation
1 version - Latest release: 7 months ago - 652 downloads total - 0 stars on GitHub - 1 maintainer
hoodscanR 1.0.0
Spatial cellular neighbourhood scanning in R
1 version - Latest release: 7 months ago - 577 downloads total - 0 stars on GitHub - 1 maintainer
gDRstyle 1.0.0
A package with style requirements for the gDR suite
1 version - Latest release: 7 months ago - 4 dependent packages - 1.15 thousand downloads total - 1 maintainer
enrichViewNet 1.0.0
From functional enrichment results to biological networks
1 version - Latest release: 7 months ago - 644 downloads total - 5 stars on GitHub - 1 maintainer
gDRimport 1.0.0
Package for handling the import of dose-response data
1 version - Latest release: 7 months ago - 2 dependent packages - 1.3 thousand downloads total - 1 maintainer
QTLExperiment 1.0.0
S4 classes for QTL summary statistics and metadata
1 version - Latest release: 7 months ago - 486 downloads total - 1 stars on GitHub - 1 maintainer
SARC 1.0.0
Statistical Analysis of Regions with CNVs
1 version - Latest release: 7 months ago - 634 downloads total - 0 stars on GitHub - 1 maintainer
BiocBook 1.0.0
Write, containerize, publish and version Quarto books with Bioconductor
1 version - Latest release: 7 months ago - 679 downloads total - 1 maintainer
partCNV 1.0.0
Infer locally aneuploid cells using single cell RNA-seq data
1 version - Latest release: 7 months ago - 659 downloads total - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
1 version - Latest release: 7 months ago - 563 downloads total - 0 stars on GitHub - 1 maintainer
gDR 1.0.0
Umbrella package for R packages in the gDR suite
1 version - Latest release: 7 months ago - 680 downloads total - 1 maintainer
gatom 1.0.0
Finding an Active Metabolic Module in Atom Transition Network
1 version - Latest release: 7 months ago - 748 downloads total - 5 stars on GitHub - 1 maintainer
RAIDS 1.0.0
Accurate Inference of Genetic Ancestry from Cancer Sequences
1 version - Latest release: 7 months ago - 708 downloads total - 5 stars on GitHub - 1 maintainer
Rvisdiff 1.0.0
Interactive Graphs for Differential Expression
1 version - Latest release: 7 months ago - 466 downloads total - 0 stars on GitHub - 1 maintainer
gDRutils 1.0.0
A package with helper functions for processing drug response data
1 version - Latest release: 7 months ago - 3 dependent packages - 1.61 thousand downloads total - 1 maintainer
ClustIRR 1.0.0
Clustering of immune receptor repertoires
1 version - Latest release: 7 months ago - 534 downloads total - 2 stars on GitHub - 1 maintainer
GloScope 1.0.0
Population-level Representation on scRNA-Seq data
1 version - Latest release: 7 months ago - 591 downloads total - 1 stars on GitHub - 1 maintainer
GNOSIS 1.0.0
Genomics explorer using statistical and survival analysis in R
1 version - Latest release: 7 months ago - 705 downloads total - 2 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
plasmut 1.0.0
Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic,...
1 version - Latest release: 7 months ago - 518 downloads total - 1 maintainer
iSEEpathways 1.0.0
iSEE extension for panels related to pathway analysis
1 version - Latest release: 7 months ago - 677 downloads total - 1 stars on GitHub - 1 maintainer
easylift 1.0.0
An R package to perform genomic liftover
1 version - Latest release: 7 months ago - 623 downloads total - 3 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
gcrma 2.74.0
Background Adjustment Using Sequence Information
2 versions - Latest release: 7 months ago - 9 dependent packages - 616 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
geneplotter 1.80.0
Graphics related functions for Bioconductor
2 versions - Latest release: 7 months ago - 9 dependent packages - 2.29 million downloads total - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.80.0
Exploratory analysis for two-color spotted microarray data
2 versions - Latest release: 7 months ago - 21 dependent packages - 547 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.46.0
Handling and analysis of high-throughput microbiome census data
2 versions - Latest release: 7 months ago - 21 dependent packages - 687 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.12.0
Single-Cell RNA-Seq Analysis Utilities
2 versions - Latest release: 7 months ago - 29 dependent packages - 533 thousand downloads total - 1 maintainer
brendaDb 1.16.0
The BRENDA Enzyme Database
2 versions - Latest release: 7 months ago - 5.12 thousand downloads total - 2 stars on GitHub - 1 maintainer
crisprBase 1.6.0
Base functions and classes for CRISPR gRNA design
2 versions - Latest release: 7 months ago - 5 dependent packages - 4.34 thousand downloads total - 2 stars on GitHub - 1 maintainer
BEclear 2.18.0
Correction of batch effects in DNA methylation data
2 versions - Latest release: 7 months ago - 14.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
bayNorm 1.20.0
Single-cell RNA sequencing data normalization
2 versions - Latest release: 7 months ago - 9.06 thousand downloads total - 9 stars on GitHub - 1 maintainer
ontoProc 1.24.0
processing of ontologies of anatomy, cell lines, and so on
2 versions - Latest release: 7 months ago - 3 dependent packages - 13.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
biovizBase 1.50.0
Basic graphic utilities for visualization of genomic data.
2 versions - Latest release: 7 months ago - 14 dependent packages - 1.04 million downloads total - 1 maintainer
Top 2.0% on bioconductor.org
DNAcopy 1.76.0
DNA Copy Number Data Analysis
2 versions - Latest release: 7 months ago - 29 dependent packages - 592 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
ComplexHeatmap 2.18.0
Make Complex Heatmaps
2 versions - Latest release: 7 months ago - 87 dependent packages - 1.02 million downloads total - 21 stars on GitHub - 1 maintainer
cummeRbund 2.44.0
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
2 versions - Latest release: 7 months ago - 575 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
DynDoc 1.80.0
Dynamic document tools
2 versions - Latest release: 7 months ago - 1 dependent package - 390 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
interactiveDisplayBase 1.40.0
Base package for enabling powerful shiny web displays of Bioconductor objects
2 versions - Latest release: 7 months ago - 3 dependent packages - 793 thousand downloads total - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.68.0
Tools for manipulating GO and microarrays
2 versions - Latest release: 7 months ago - 23 dependent packages - 501 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.46.0
Reactome Pathway Analysis
2 versions - Latest release: 7 months ago - 12 dependent packages - 439 thousand downloads total - 1 maintainer
Top 5.1% on bioconductor.org
MeSHDbi 1.38.0
DBI to construct MeSH-related package from sqlite file
2 versions - Latest release: 7 months ago - 3 dependent packages - 619 thousand downloads total - 1 maintainer
Top 3.5% on bioconductor.org
pcaMethods 1.94.0
A collection of PCA methods
2 versions - Latest release: 7 months ago - 19 dependent packages - 579 thousand downloads total - 44 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
KEGGgraph 1.62.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
2 versions - Latest release: 7 months ago - 12 dependent packages - 535 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
OrganismDbi 1.44.0
Software to enable the smooth interfacing of different database packages
2 versions - Latest release: 7 months ago - 6 dependent packages - 428 thousand downloads total - 1 maintainer