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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scatterHatch 1.8.0
Creates hatched patterns for scatterplots
2 versions - Latest release: 5 months ago - 1.78 thousand downloads total - 5 stars on GitHub - 1 maintainer
FindIT2 1.8.0
find influential TF and Target based on multi-omics data
2 versions - Latest release: 5 months ago - 2.46 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
bumphunter 1.44.0
Bump Hunter
2 versions - Latest release: 5 months ago - 15 dependent packages - 394 thousand downloads total - 15 stars on GitHub - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations
2 versions - Latest release: 5 months ago - 1 dependent package - 23.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
flowcatchR 1.36.0
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
2 versions - Latest release: 6 months ago - 15.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
diffUTR 1.10.0
diffUTR: Streamlining differential exon and 3' UTR usage
2 versions - Latest release: 5 months ago - 2.78 thousand downloads total - 6 stars on GitHub - 1 maintainer
Trendy 1.24.1
Breakpoint analysis of time-course expression data
3 versions - Latest release: 5 months ago - 8.18 thousand downloads total - 6 stars on GitHub - 1 maintainer
GenomAutomorphism 1.4.0
Compute the automorphisms between DNA's Abelian group representations
2 versions - Latest release: 5 months ago - 1.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
SpidermiR 1.32.0
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data
2 versions - Latest release: 5 months ago - 1 dependent package - 15.2 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: 6 months ago - 14 dependent packages - 1.04 million downloads total - 1 maintainer
primirTSS 1.20.0
Prediction of pri-miRNA Transcription Start Site
2 versions - Latest release: 5 months ago - 5.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
scAnnotatR 1.8.0
Pretrained learning models for cell type prediction on single cell RNA-sequencing data
2 versions - Latest release: 5 months ago - 4.09 thousand downloads total - 14 stars on GitHub - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
1 version - Latest release: 6 months ago - 563 downloads total - 0 stars on GitHub - 1 maintainer
autonomics 1.10.2
Generifying and intuifying cross-platform omics analysis
3 versions - Latest release: 6 months ago - 2.96 thousand 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: 6 months ago - 9 dependent packages - 616 thousand downloads total - 1 maintainer
iSEEindex 1.0.0
iSEE extension for a landing page to a custom collection of data sets
1 version - Latest release: 6 months ago - 715 downloads total - 1 stars on GitHub - 1 maintainer
BioCartaImage 1.0.0
BioCarta Pathway Images
1 version - Latest release: 6 months ago - 663 downloads total - 9 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: 5 months ago - 5 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
RBioFormats 1.2.0
R interface to Bio-Formats
2 versions - Latest release: 5 months ago - 1 dependent package - 2.22 thousand downloads total - 23 stars on GitHub - 1 maintainer
qPLEXanalyzer 1.20.0
Tools for quantitative proteomics data analysis
2 versions - Latest release: 5 months ago - 6.65 thousand downloads total - 1 stars on GitHub - 1 maintainer
SPLINTER 1.28.0
Splice Interpreter of Transcripts
2 versions - Latest release: 5 months ago - 9.93 thousand downloads total - 0 stars on GitHub - 1 maintainer
swfdr 1.28.0
Estimation of the science-wise false discovery rate and the false discovery rate conditional on c...
2 versions - Latest release: 5 months ago - 8.35 thousand downloads total - 3 stars on GitHub - 2 maintainers
Top 3.5% on bioconductor.org
biocViews 1.70.0
Categorized views of R package repositories
2 versions - Latest release: 5 months ago - 8 dependent packages - 428 thousand downloads total - 1 maintainer
lefser 1.12.1
R implementation of the LEfSE method for microbiome biomarker discovery
3 versions - Latest release: 4 months ago - 16.4 thousand downloads total - 31 stars on GitHub - 1 maintainer
gDRcore 1.0.1
Processing functions and interface to process and analyze drug dose-response data
2 versions - Latest release: 2 months ago - 1 dependent package - 1.29 thousand downloads total - 1 maintainer
Rarr 1.2.0
Read Zarr Files in R
2 versions - Latest release: 6 months ago - 2.07 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
recount 1.28.0
Explore and download data from the recount project
2 versions - Latest release: 5 months ago - 6 dependent packages - 52.4 thousand downloads total - 41 stars on GitHub - 1 maintainer
erccdashboard 1.36.0
Assess Differential Gene Expression Experiments with ERCC Controls
2 versions - Latest release: 5 months ago - 18.7 thousand downloads total - 7 stars on GitHub - 1 maintainer
MEAT 1.14.0
Muscle Epigenetic Age Test
2 versions - Latest release: 5 months ago - 4.16 thousand downloads total - 0 stars on GitHub - 1 maintainer
nipalsMCIA 1.0.0
Multiple Co-Inertia Analysis via the NIPALS Method
1 version - Latest release: 6 months ago - 635 downloads total - 6 stars on GitHub - 1 maintainer
DEsingle 1.22.0
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
2 versions - Latest release: 5 months ago - 1 dependent package - 23.6 thousand downloads total - 28 stars on GitHub - 1 maintainer
BioNetStat 1.22.0
Biological Network Analysis
2 versions - Latest release: 5 months ago - 8.52 thousand downloads total - 7 stars on GitHub - 1 maintainer
RNAmodR 1.16.0
Detection of post-transcriptional modifications in high throughput sequencing data
2 versions - Latest release: 5 months ago - 3 dependent packages - 6.54 thousand downloads total - 2 stars on GitHub - 1 maintainer
mirIntegrator 1.32.0
Integrating microRNA expression into signaling pathways for pathway analysis
2 versions - Latest release: 5 months ago - 11.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
PFP 1.10.0
Pathway Fingerprint Framework in R
2 versions - Latest release: 5 months ago - 1.82 thousand downloads total - 0 stars on GitHub - 1 maintainer
SAIGEgds 2.2.1
Scalable Implementation of Generalized mixed models using GDS files in Phenome-Wide Association S...
3 versions - Latest release: 2 months ago - 7.28 thousand downloads total - 7 stars on GitHub - 1 maintainer
vidger 1.22.0
Create rapid visualizations of RNAseq data in R
2 versions - Latest release: 5 months ago - 11.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
GenomicScores 2.14.3
Infrastructure to work with genomewide position-specific scores
5 versions - Latest release: 3 months ago - 6 dependent packages - 54.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 3.1% on bioconductor.org
Rhtslib 2.4.1
HTSlib high-throughput sequencing library as an R package
3 versions - Latest release: 3 months ago - 5 dependent packages - 2.45 million downloads total - 1 maintainer
DNABarcodeCompatibility 1.18.0
A Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Genera...
2 versions - Latest release: 5 months ago - 5.01 thousand downloads total - 7 stars on GitHub - 1 maintainer
CNVMetrics 1.6.0
Copy Number Variant Metrics
2 versions - Latest release: 5 months ago - 1.86 thousand downloads total - 5 stars on GitHub - 1 maintainer
TimiRGeN 1.11.0
Time sensitive microRNA-mRNA integration, analysis and network generation tool
2 versions - Latest release: 6 months ago - 1 dependent package - 3.71 thousand downloads total - 2 stars on GitHub - 1 maintainer
SOMNiBUS 1.10.0
Smooth modeling of bisulfite sequencing
2 versions - Latest release: 5 months ago - 2.75 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
microbiome 1.24.0
Microbiome Analytics
2 versions - Latest release: 5 months ago - 1 dependent package - 113 thousand downloads total - 270 stars on GitHub - 1 maintainer
matter 2.4.1
Out-of-memory dense and sparse signal arrays
3 versions - Latest release: about 1 month ago - 2 dependent packages - 18.5 thousand downloads total - 52 stars on GitHub - 1 maintainer
pipeFrame 1.18.0
Pipeline framework for bioinformatics in R
2 versions - Latest release: 5 months ago - 2 dependent packages - 9.86 thousand downloads total - 1 stars on GitHub - 1 maintainer
alabaster.files 1.0.0
Wrappers to Save Common File Formats
1 version - Latest release: 6 months ago - 695 downloads total - 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
TREG 1.6.0
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
2 versions - Latest release: 5 months ago - 1.69 thousand downloads total - 4 stars on GitHub - 1 maintainer
CardinalIO 1.0.0
Read and write mass spectrometry imaging files
1 version - Latest release: 6 months ago - 1 dependent package - 1.78 thousand downloads total - 1 maintainer
APL 1.6.1
Association Plots
3 versions - Latest release: 2 months ago - 2.77 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
Gviz 1.46.1
Plotting data and annotation information along genomic coordinates
3 versions - Latest release: 5 months ago - 55 dependent packages - 832 thousand downloads total - 66 stars on GitHub - 1 maintainer
MoonlightR 1.28.0
Identify oncogenes and tumor suppressor genes from omics data
2 versions - Latest release: 5 months ago - 11.5 thousand downloads total - 16 stars on GitHub - 1 maintainer
msPurity 1.28.0
Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabol...
2 versions - Latest release: 5 months ago - 12.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
RAIDS 1.0.0
Accurate Inference of Genetic Ancestry from Cancer Sequences
1 version - Latest release: 6 months ago - 708 downloads total - 5 stars on GitHub - 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: 6 months ago - 3 dependent packages - 619 thousand downloads total - 1 maintainer
adverSCarial 1.0.0
adverSCarial, generate and analyze the vulnerability of scRNA-seq classifiers to adversarial attacks
1 version - Latest release: 6 months ago - 634 downloads total - 1 maintainer
groHMM 1.36.0
GRO-seq Analysis Pipeline
2 versions - Latest release: 5 months ago - 18.5 thousand downloads total - 1 stars on GitHub - 2 maintainers
Top 2.0% on bioconductor.org
DNAcopy 1.76.0
DNA Copy Number Data Analysis
2 versions - Latest release: 6 months ago - 29 dependent packages - 592 thousand downloads total - 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: 17 days ago - 11 dependent packages - 85.4 thousand downloads total - 42 stars on GitHub - 1 maintainer
HilbertCurve 1.32.0
Making 2D Hilbert Curve
2 versions - Latest release: 5 months ago - 1 dependent package - 15.4 thousand downloads total - 40 stars on GitHub - 1 maintainer
ndexr 1.24.0
NDEx R client library
2 versions - Latest release: 5 months ago - 9.9 thousand downloads total - 8 stars on GitHub - 1 maintainer
shinyMethyl 1.38.0
Interactive visualization for Illumina methylation arrays
2 versions - Latest release: 5 months ago - 23.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
BiocFileCache 2.10.2
Manage Files Across Sessions
4 versions - Latest release: about 22 hours ago - 88 dependent packages - 1.85 million downloads total - 11 stars on GitHub - 1 maintainer
famat 1.12.0
Functional analysis of metabolic and transcriptomic data
2 versions - Latest release: 5 months ago - 3.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
RNAmodR.AlkAnilineSeq 1.16.0
Detection of m7G, m3C and D modification by AlkAnilineSeq
2 versions - Latest release: 5 months ago - 1 dependent package - 5.04 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
GenomicInteractions 1.36.0
Utilities for handling genomic interaction data
2 versions - Latest release: 5 months ago - 7 dependent packages - 42.9 thousand downloads total - 6 stars on GitHub - 1 maintainer
CytoGLMM 1.10.0
Conditional Differential Analysis for Flow and Mass Cytometry Experiments
2 versions - Latest release: 5 months ago - 1 dependent package - 3.66 thousand downloads total - 2 stars on GitHub - 1 maintainer
CluMSID 1.18.0
Clustering of MS2 Spectra for Metabolite Identification
2 versions - Latest release: 5 months ago - 6.52 thousand downloads total - 9 stars on GitHub - 1 maintainer
planttfhunter 1.2.0
Identification and classification of plant transcription factors
2 versions - Latest release: 6 months ago - 949 downloads total - 0 stars on GitHub - 1 maintainer
NBAMSeq 1.18.0
Negative Binomial Additive Model for RNA-Seq Data
2 versions - Latest release: 5 months ago - 5.45 thousand downloads total - 2 stars on GitHub - 1 maintainer
Qtlizer 1.16.0
Comprehensive QTL annotation of GWAS results
2 versions - Latest release: 5 months ago - 6.25 thousand downloads total - 3 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: 6 months ago - 2 dependent packages - 375 thousand downloads total - 1 maintainer
countsimQC 1.20.0
Compare Characteristic Features of Count Data Sets
2 versions - Latest release: 5 months ago - 1 dependent package - 8.69 thousand downloads total - 27 stars on GitHub - 1 maintainer
decontX 1.0.0
Decontamination of single cell genomics data
1 version - Latest release: 6 months ago - 1.69 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.10.0
Microbiome analysis
2 versions - Latest release: 6 months ago - 5 dependent packages - 47.1 thousand downloads total - 43 stars on GitHub - 1 maintainer
GA4GHclient 1.26.0
A Bioconductor package for accessing GA4GH API data servers
2 versions - Latest release: 5 months ago - 1 dependent package - 9.94 thousand downloads total - 1 stars on GitHub - 1 maintainer
biobtreeR 1.14.0
Using biobtree tool from R
2 versions - Latest release: 5 months ago - 4.9 thousand downloads total - 3 stars on GitHub - 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: 6 months ago - 3 dependent packages - 793 thousand downloads total - 1 maintainer
HIPPO 1.14.0
Heterogeneity-Induced Pre-Processing tOol
2 versions - Latest release: 5 months ago - 4.09 thousand downloads total - 16 stars on GitHub - 1 maintainer
RNAAgeCalc 1.14.0
A multi-tissue transcriptional age calculator
2 versions - Latest release: 5 months ago - 4.88 thousand downloads total - 6 stars on GitHub - 1 maintainer
NetPathMiner 1.38.0
NetPathMiner for Biological Network Construction, Path Mining and Visualization
2 versions - Latest release: 5 months ago - 19.1 thousand downloads total - 7 stars on GitHub - 1 maintainer
ctsGE 1.28.0
Clustering of Time Series Gene Expression data
2 versions - Latest release: 5 months ago - 10.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
snpStats 1.52.0
SnpMatrix and XSnpMatrix classes and methods
2 versions - Latest release: 5 months ago - 15 dependent packages - 395 thousand downloads total - 1 maintainer
SeqGate 1.12.0
Filtering of Lowly Expressed Features
2 versions - Latest release: 5 months ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
derfinderPlot 1.36.0
Plotting functions for derfinder
2 versions - Latest release: 5 months ago - 3 dependent packages - 21.3 thousand downloads total - 2 stars on GitHub - 1 maintainer
plotgardener 1.8.3
Coordinate-Based Genomic Visualization Package for R
5 versions - Latest release: 21 days ago - 3 dependent packages - 9.28 thousand downloads total - 276 stars on GitHub - 1 maintainer
SummarizedBenchmark 2.20.0
Classes and methods for performing benchmark comparisons
2 versions - Latest release: 5 months ago - 7.78 thousand downloads total - 15 stars on GitHub - 1 maintainer
methylSig 1.14.0
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
2 versions - Latest release: 5 months ago - 5.02 thousand downloads total - 15 stars on GitHub - 1 maintainer
bigPint 1.18.1
BIG multivariate data Plotted INTeractively
3 versions - Latest release: 2 months ago - 6.52 thousand downloads total - 20 stars on GitHub - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing
2 versions - Latest release: 5 months ago - 4.26 thousand downloads total - 0 stars on GitHub - 1 maintainer
methylCC 1.16.0
Estimate the cell composition of whole blood in DNA methylation samples
2 versions - Latest release: 5 months ago - 6.03 thousand downloads total - 20 stars on GitHub - 1 maintainer
sevenC 1.22.0
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
2 versions - Latest release: 5 months ago - 7.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
oncoscanR 1.4.0
Secondary analyses of CNV data (HRD and more)
2 versions - Latest release: 5 months ago - 1.32 thousand downloads total - 2 stars on GitHub - 1 maintainer
MSstatsBig 1.0.1
MSstats Preprocessing for Larger than Memory Data
2 versions - Latest release: 1 day ago - 637 downloads total - 1 maintainer
Top 9.9% on bioconductor.org
affyio 1.72.0
Tools for parsing Affymetrix data files
2 versions - Latest release: 6 months ago - 12 dependent packages - 1.52 million downloads total - 3 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
Category 2.68.0
Category Analysis
2 versions - Latest release: 5 months ago - 13 dependent packages - 513 thousand downloads total - 1 maintainer
MOGAMUN 1.12.0
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
2 versions - Latest release: 5 months ago - 3.45 thousand downloads total - 12 stars on GitHub - 1 maintainer
DMCFB 1.16.1
Differentially Methylated Cytosines via a Bayesian Functional Approach
3 versions - Latest release: 2 months ago - 4.61 thousand downloads total - 0 stars on GitHub - 1 maintainer
motifbreakR 2.16.0
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription F...
2 versions - Latest release: 5 months ago - 19.6 thousand downloads total - 24 stars on GitHub - 1 maintainer