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 3.8% on bioconductor.org
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data
3 versions - Latest release: 1 day ago - 6 dependent packages - 122 thousand downloads total - 1 maintainer
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
timeOmics 1.16.0
Time-Course Multi-Omics data integration
3 versions - Latest release: 1 day ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
OCplus 1.78.0
Operating characteristics plus sample size and local fdr for microarray experiments
3 versions - Latest release: 1 day ago - 41.6 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
Top 4.6% on bioconductor.org
sangerseqR 1.40.0
Tools for Sanger Sequencing Data in R
3 versions - Latest release: 1 day ago - 3 dependent packages - 63.7 thousand downloads total - 1 maintainer
Top 3.5% on bioconductor.org
Ringo 1.66.0 removed
R Investigation of ChIP-chip Oligoarrays
2 versions - Latest release: 6 months ago - 2 dependent packages - 86.1 thousand downloads total - 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
Top 4.6% on bioconductor.org
chipseq 1.54.0
chipseq: A package for analyzing chipseq data
3 versions - Latest release: 1 day ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
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 5.6% on bioconductor.org
PICS 2.48.0
Probabilistic inference of ChIP-seq
3 versions - Latest release: 1 day ago - 1 dependent package - 42.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
bamsignals 1.36.0
Extract read count signals from bam files
3 versions - Latest release: 1 day ago - 7 dependent packages - 93.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
HMMcopy 1.46.0
Copy number prediction with correction for GC and mappability bias for HTS data
3 versions - Latest release: 1 day ago - 1 dependent package - 64.3 thousand downloads total - 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 4.9% on bioconductor.org
rsbml 2.62.0
R support for SBML, using libsbml
3 versions - Latest release: 1 day ago - 3 dependent packages - 52.4 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
beadarray 2.54.0
Quality assessment and low-level analysis for Illumina BeadArray data
3 versions - Latest release: 1 day ago - 5 dependent packages - 196 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
DECIPHER 3.0.0
Tools for curating, analyzing, and manipulating biological sequences
3 versions - Latest release: 1 day ago - 7 dependent packages - 208 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
regioneR 1.36.0
Association analysis of genomic regions based on permutation tests
3 versions - Latest release: 1 day ago - 12 dependent packages - 217 thousand downloads total - 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
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
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
Top 3.8% on bioconductor.org
MLInterfaces 1.84.0
Uniform interfaces to R machine learning procedures for data in Bioconductor containers
3 versions - Latest release: 1 day ago - 2 dependent packages - 96.7 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
gwascat 2.36.0
representing and modeling data in the EMBL-EBI GWAS catalog
3 versions - Latest release: 1 day ago - 7 dependent packages - 64.9 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
DEGseq 1.58.0
Identify Differentially Expressed Genes from RNA-seq data
3 versions - Latest release: 1 day ago - 98.9 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
HilbertVis 1.62.0
Hilbert curve visualization
3 versions - Latest release: 1 day ago - 3 dependent packages - 66.4 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
RankProd 3.30.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis
3 versions - Latest release: 1 day ago - 4 dependent packages - 106 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
globaltest 5.58.0
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications...
3 versions - Latest release: 1 day ago - 6 dependent packages - 220 thousand downloads total - 1 maintainer
Top 3.4% on bioconductor.org
rGADEM 2.52.0
de novo motif discovery
3 versions - Latest release: 1 day ago - 1 dependent package - 89.7 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
STRINGdb 2.16.0
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment Analysis
4 versions - Latest release: 1 day ago - 12 dependent packages - 99.9 thousand downloads total - 1 maintainer
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
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 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
Top 3.5% on bioconductor.org
Glimma 2.14.0
Interactive visualizations for gene expression analysis
3 versions - Latest release: 1 day ago - 1 dependent package - 134 thousand downloads total - 22 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
zinbwave 1.26.0
Zero-Inflated Negative Binomial Model for RNA-Seq Data
3 versions - Latest release: 1 day ago - 6 dependent packages - 83.5 thousand downloads total - 41 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
mixOmics 6.28.0
Omics Data Integration Project
3 versions - Latest release: 1 day ago - 8 dependent packages - 214 thousand downloads total - 1 maintainer
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
Top 6.0% on bioconductor.org
widgetTools 1.82.0
Creates an interactive tcltk widget
3 versions - Latest release: 1 day ago - 3 dependent packages - 201 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
GlobalAncova 4.22.0
Global test for groups of variables via model comparisons
3 versions - Latest release: 1 day ago - 98.3 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
cqn 1.50.0
Conditional quantile normalization
3 versions - Latest release: 1 day ago - 4 dependent packages - 50.5 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
bsseq 1.40.0
Analyze, manage and store bisulfite sequencing data
3 versions - Latest release: 1 day ago - 12 dependent packages - 201 thousand downloads total - 34 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
GLAD 2.68.0
Gain and Loss Analysis of DNA
3 versions - Latest release: 1 day ago - 5 dependent packages - 83.4 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
DirichletMultinomial 1.46.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
3 versions - Latest release: 1 day ago - 5 dependent packages - 267 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
plier 1.74.0
Implements the Affymetrix PLIER algorithm
3 versions - Latest release: 1 day ago - 1 dependent package - 65 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
affycomp 1.80.0
Graphics Toolbox for Assessment of Affymetrix Expression Measures
3 versions - Latest release: 1 day ago - 58.2 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.10.0
Illumina 450 and EPIC methylation array normalization and metrics
3 versions - Latest release: 1 day ago - 5 dependent packages - 132 thousand downloads total - 1 maintainer
Top 5.1% on bioconductor.org
ACME 2.60.0
Algorithms for Calculating Microarray Enrichment (ACME)
3 versions - Latest release: 1 day ago - 1 dependent package - 41.6 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
RaggedExperiment 1.28.0
Representation of Sparse Experiments and Assays Across Samples
3 versions - Latest release: 1 day ago - 12 dependent packages - 72.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
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
Top 4.5% on bioconductor.org
TFBSTools 1.42.0
Software Package for Transcription Factor Binding Site (TFBS) Analysis
3 versions - Latest release: 1 day ago - 17 dependent packages - 288 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 5.9% on bioconductor.org
systemPipeR 2.10.0
systemPipeR: workflow management and report generation environment
3 versions - Latest release: 1 day ago - 3 dependent packages - 204 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
GenomicFiles 1.40.0
Distributed computing by file or by range
3 versions - Latest release: 1 day ago - 12 dependent packages - 154 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
OmicCircos 1.42.0
High-quality circular visualization of omics data
3 versions - Latest release: 1 day ago - 44.5 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
BeadDataPackR 1.56.0
Compression of Illumina BeadArray data
3 versions - Latest release: 1 day ago - 1 dependent package - 145 thousand downloads total - 1 maintainer
Top 3.4% on bioconductor.org
Mfuzz 2.64.0
Soft clustering of time series gene expression data
3 versions - Latest release: 1 day ago - 5 dependent packages - 122 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
qrqc 1.56.0 removed
Quick Read Quality Control
2 versions - Latest release: 6 months ago - 39 thousand downloads total - 20 stars on GitHub - 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
Top 4.5% on bioconductor.org
convert 1.80.0
Convert Microarray Data Objects
3 versions - Latest release: 1 day ago - 4 dependent packages - 69.5 thousand downloads total - 1 maintainer
Top 4.1% on bioconductor.org
GWASTools 1.50.0
Tools for Genome Wide Association Studies
3 versions - Latest release: 1 day ago - 4 dependent packages - 95.1 thousand downloads total - 13 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
SparseSignatures 2.14.0
SparseSignatures
3 versions - Latest release: 4 days ago - 7.65 thousand downloads total - 10 stars on GitHub - 1 maintainer
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
Top 4.0% on bioconductor.org
ALDEx2 1.36.0
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
3 versions - Latest release: 1 day ago - 3 dependent packages - 75.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
ropls 1.36.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
3 versions - Latest release: 1 day ago - 9 dependent packages - 83.4 thousand downloads total - 1 maintainer
mitoClone2 1.10.0
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Muta...
4 versions - Latest release: 1 day ago - 2.32 thousand downloads total - 0 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
OUTRIDER 1.22.0
OUTRIDER - OUTlier in RNA-Seq fInDER
3 versions - Latest release: 1 day ago - 1 dependent package - 15.7 thousand downloads total - 45 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
fabia 2.50.0
FABIA: Factor Analysis for Bicluster Acquisition
3 versions - Latest release: 1 day ago - 3 dependent packages - 48.5 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
muscle 3.46.0
Multiple Sequence Alignment with MUSCLE
3 versions - Latest release: 1 day ago - 44.2 thousand downloads total - 1 maintainer
Top 2.4% on bioconductor.org
DEXSeq 1.50.0
Inference of differential exon usage in RNA-Seq
3 versions - Latest release: 1 day ago - 9 dependent packages - 234 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
chromVAR 1.26.0
Chromatin Variation Across Regions
3 versions - Latest release: 1 day ago - 1 dependent package - 85.1 thousand downloads total - 1 maintainer
Top 2.9% on bioconductor.org
openCyto 2.16.0
Hierarchical Gating Pipeline for flow cytometry data
3 versions - Latest release: 1 day ago - 8 dependent packages - 144 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
ChemmineOB 1.42.0
R interface to a subset of OpenBabel functionalities
3 versions - Latest release: 1 day ago - 2 dependent packages - 217 thousand downloads total - 9 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 4.8% on bioconductor.org
mygene 1.40.0
Access MyGene.Info_ services
3 versions - Latest release: 1 day ago - 1 dependent package - 57.8 thousand downloads total - 1 maintainer
escheR 1.3.2
Unified multi-dimensional visualizations with Gestalt principles
3 versions - Latest release: 1 day ago - 1.93 thousand downloads total - 3 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
iSEEhex 1.6.0
iSEE extension for summarising data points in hexagonal bins
3 versions - Latest release: 1 day ago - 1 dependent package - 3.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.36.0
Generic infrastructure for Bioconductor mass spectrometry packages
3 versions - Latest release: 1 day ago - 19 dependent packages - 979 thousand downloads total - 7 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 5.6% on bioconductor.org
RDRToolbox 1.54.0
A package for nonlinear dimension reduction with Isomap and LLE.
3 versions - Latest release: 1 day ago - 42.3 thousand downloads total - 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 5.0% on bioconductor.org
hopach 2.64.0
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
3 versions - Latest release: 1 day ago - 5 dependent packages - 64 thousand downloads total - 1 maintainer
Top 6.0% on bioconductor.org
cn.mops 1.50.0
cn.mops - Mixture of Poissons for CNV detection in NGS data
3 versions - Latest release: 1 day ago - 3 dependent packages - 54.7 thousand downloads total - 1 maintainer
fishpond 2.10.0
Fishpond: downstream methods and tools for expression data
3 versions - Latest release: 1 day ago - 1 dependent package - 27.1 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
MEDIPS 1.56.0
DNA IP-seq data analysis
3 versions - Latest release: 1 day ago - 48.6 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
IHW 1.32.0
Independent Hypothesis Weighting
3 versions - Latest release: 1 day ago - 5 dependent packages - 98 thousand downloads total - 1 maintainer
martini 1.24.0
GWAS Incorporating Networks
3 versions - Latest release: 1 day ago - 7.58 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
easyRNASeq 2.38.0
Count summarization and normalization for RNA-Seq data
2 versions - Latest release: 6 months ago - 1 dependent package - 53 thousand downloads total - 1 maintainer
Top 2.6% on bioconductor.org
ConsensusClusterPlus 1.68.0
ConsensusClusterPlus
3 versions - Latest release: 1 day ago - 7 dependent packages - 314 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
EBSeq 2.2.0
An R package for gene and isoform differential expression analysis of RNA-seq data
3 versions - Latest release: 1 day ago - 6 dependent packages - 85.6 thousand downloads total - 1 maintainer
mitch 1.16.0
Multi-Contrast Gene Set Enrichment Analysis
3 versions - Latest release: 8 days ago - 5.04 thousand downloads total - 14 stars on GitHub - 1 maintainer
bettr 1.0.0
A Better Way To Explore What Is Best
1 version - Latest release: 9 days ago - 230 downloads total - 3 stars on GitHub - 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
smartid 1.0.0
Scoring and Marker Selection Method Based on Modified TF-IDF
1 version - Latest release: 9 days ago - 185 downloads total - 0 stars on GitHub - 1 maintainer
Top 5.7% on bioconductor.org
GreyListChIP 1.36.0
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
3 versions - Latest release: 1 day ago - 2 dependent packages - 60.6 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
preprocessCore 1.66.0
A collection of pre-processing functions
3 versions - Latest release: 1 day ago - 50 dependent packages - 2.16 million downloads total - 14 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
cytolib 2.16.0
C++ infrastructure for representing and interacting with the gated cytometry data
4 versions - Latest release: 1 day ago - 3 dependent packages - 208 thousand downloads total - 1 maintainer
Top 3.4% on bioconductor.org
FlowSOM 2.12.0
Using self-organizing maps for visualization and interpretation of cytometry data
3 versions - Latest release: 1 day ago - 3 dependent packages - 128 thousand downloads total - 1 maintainer
Top 3.6% on bioconductor.org
CNEr 1.40.0
CNE Detection and Visualization
3 versions - Latest release: 1 day ago - 1 dependent package - 198 thousand downloads total - 3 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