An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "Software" keyword

VariantFiltering 1.46.0
Filtering of coding and non-coding genetic variants
6 versions - Latest release: 5 months ago - 35.1 thousand downloads total - 4 stars on GitHub - 1 maintainer
DominoEffect 1.30.0
Identification and Annotation of Protein Hotspot Residues
6 versions - Latest release: 4 months ago - 14.8 thousand downloads total - 2 maintainers
SEtools 1.24.0
SEtools: tools for working with SummarizedExperiment
6 versions - Latest release: 4 months ago - 15.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.1
Single-Cell Analysis Toolkit for Gene Expression Data in R
10 versions - Latest release: 17 days ago - 96 dependent packages - 1.09 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.36.0
Base Functions and Classes for Mass Spectrometry and Proteomics
8 versions - Latest release: 5 months ago - 30 dependent packages - 600 thousand downloads total - 123 stars on GitHub - 1 maintainer
rfPred 1.48.0
Assign rfPred functional prediction scores to a missense variants list
6 versions - Latest release: 4 months ago - 26.4 thousand downloads total - 1 maintainer
scTHI 1.22.0
Indentification of significantly activated ligand-receptor interactions across clusters of cells ...
6 versions - Latest release: 4 months ago - 10.3 thousand downloads total - 4 stars on GitHub - 1 maintainer
pogos 1.30.0
PharmacOGenomics Ontology Support
6 versions - Latest release: 4 months ago - 1 dependent package - 15.4 thousand downloads total - 1 maintainer
SWATH2stats 1.40.1
Transform and Filter SWATH Data for Statistical Packages
8 versions - Latest release: 2 months ago - 22.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
omicsPrint 1.30.0
Cross omic genetic fingerprinting
6 versions - Latest release: 4 months ago - 16 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.48.1
Foundation of vector-like and list-like containers in Bioconductor
10 versions - Latest release: 2 days ago - 740 dependent packages - 11.4 million downloads total - 1 maintainer
cellity 1.38.0
Quality Control for Single-Cell RNA-seq Data
6 versions - Latest release: 4 months ago - 21.5 thousand downloads total - 1 maintainer
SIMAT 1.42.0
GC-SIM-MS data processing and alaysis tool
6 versions - Latest release: 4 months ago - 21.1 thousand downloads total - 1 maintainer
musicatk 2.4.0
Mutational Signature Comprehensive Analysis Toolkit
9 versions - Latest release: 4 months ago - 12.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
coRdon 1.28.0
Codon Usage Analysis and Prediction of Gene Expressivity
6 versions - Latest release: 5 months ago - 25.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
signeR 2.12.0
Empirical Bayesian approach to mutational signature discovery
6 versions - Latest release: 4 months ago - 23.3 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
SGSeq 1.44.0
Splice event prediction and quantification from RNA-seq data
7 versions - Latest release: 4 months ago - 3 dependent packages - 61.3 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
survcomp 1.60.1
Performance Assessment and Comparison for Survival Analysis
7 versions - Latest release: about 1 month ago - 4 dependent packages - 193 thousand downloads total - 1 maintainer
MSstatsBig 1.8.1
MSstats Preprocessing for Larger than Memory Data
7 versions - Latest release: 3 months ago - 6.75 thousand downloads total - 1 maintainer
h5mread 1.2.1
A fast HDF5 reader
3 versions - Latest release: 4 months ago - 220 thousand downloads total - 1 maintainer
anota 1.58.0
ANalysis Of Translational Activity (ANOTA).
6 versions - Latest release: 4 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 5 months ago - 322 dependent packages - 7.06 million downloads total - 1 maintainer
Pigengene 1.36.0
Infers biological signatures from gene expression data
7 versions - Latest release: about 3 hours ago - 1 dependent package - 22.2 thousand downloads total - 1 maintainer
RiboDiPA 1.18.0
Differential pattern analysis for Ribo-seq data
6 versions - Latest release: 4 months ago - 10.3 thousand downloads total - 1 maintainer
nethet 1.42.0
A bioconductor package for high-dimensional exploration of biological network heterogeneity
6 versions - Latest release: 4 months ago - 21.7 thousand downloads total - 2 maintainers
RcwlPipelines 1.26.0
Bioinformatics pipelines based on Rcwl
7 versions - Latest release: 4 months ago - 1 dependent package - 14.6 thousand downloads total - 1 maintainer
profileplyr 1.26.1
Visualization and annotation of read signal over genomic ranges with profileplyr
8 versions - Latest release: 2 months ago - 1 dependent package - 26.5 thousand downloads total - 2 maintainers
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 4 months ago - 69 dependent packages - 3.34 million downloads total - 72 stars on GitHub - 1 maintainer
flowMatch 1.46.0
Matching and meta-clustering in flow cytometry
6 versions - Latest release: 5 months ago - 26.5 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
csaw 1.44.0
ChIP-Seq Analysis with Windows
7 versions - Latest release: 4 months ago - 8 dependent packages - 107 thousand downloads total - 1 maintainer
quantiseqr 1.18.0
Quantification of the Tumor Immune contexture from RNA-seq data
6 versions - Latest release: 4 months ago - 2 dependent packages - 38.1 thousand downloads total - 1 maintainer
metapone 1.16.0
Conducts pathway test of metabolomics data using a weighted permutation test
6 versions - Latest release: 4 months ago - 9.04 thousand downloads total - 1 maintainer
DCATS 1.8.0
Differential Composition Analysis Transformed by a Similarity matrix
5 versions - Latest release: 4 months ago - 7.1 thousand downloads total - 1 maintainer
beer 1.14.1
Bayesian Enrichment Estimation in R
6 versions - Latest release: 5 months ago - 9.4 thousand downloads total - 11 stars on GitHub - 1 maintainer
primirTSS 1.28.0
Prediction of pri-miRNA Transcription Start Site
6 versions - Latest release: 4 months ago - 12.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
alabaster.sfe 1.2.0
Language agnostic on disk serialization of SpatialFeatureExperiment
2 versions - Latest release: 5 months ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
BiocGenerics 0.56.0
S4 generic functions used in Bioconductor
7 versions - Latest release: 5 months ago - 729 dependent packages - 12.2 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
XVector 0.50.0
Foundation of external vector representation and manipulation in Bioconductor
6 versions - Latest release: 5 months ago - 36 dependent packages - 9.6 million downloads total - 1 maintainer
RAIDS 1.8.0
Robust Ancestry Inference using Data Synthesis
5 versions - Latest release: 4 months ago - 5.77 thousand downloads total - 5 stars on GitHub - 1 maintainer
gVenn 1.0.0
Proportional Venn and UpSet Diagrams for Gene Sets and Genomic Regions
1 version - Latest release: 5 months ago - 1.46 thousand downloads total - 0 stars on GitHub - 1 maintainer
mariner 1.10.2
Mariner: Explore the Hi-Cs
8 versions - Latest release: 2 months ago - 7.42 thousand downloads total - 1 maintainer
GenomicOZone 1.24.0
Delineate outstanding genomic zones of differential gene activity
6 versions - Latest release: 4 months ago - 12.2 thousand downloads total - 1 maintainer
HelloRanges 1.36.0
Introduce *Ranges to bedtools users
6 versions - Latest release: 4 months ago - 2 dependent packages - 33.1 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 5 months ago - 518 dependent packages - 11.4 million downloads total - 1 maintainer
BayesSpace 1.20.2
Clustering and Resolution Enhancement of Spatial Transcriptomes
10 versions - Latest release: 2 months ago - 1 dependent package - 33.5 thousand downloads total - 154 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.26.0
Platform for integrative analysis of omics data
6 versions - Latest release: 4 months ago - 3 dependent packages - 107 thousand downloads total - 1 maintainer
a4Classif 1.58.0
Automated Affymetrix Array Analysis Classification Package
6 versions - Latest release: 5 months ago - 1 dependent package - 48.8 thousand downloads total - 1 maintainer
treekoR 1.18.0
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
6 versions - Latest release: 5 months ago - 10.5 thousand downloads total - 1 maintainer
scTreeViz 1.16.0
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with h...
7 versions - Latest release: 4 months ago - 9.04 thousand downloads total - 1 maintainer
CAEN 1.18.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
6 versions - Latest release: 4 months ago - 8.85 thousand downloads total - 1 maintainer
Doscheda 1.32.0
A DownStream Chemo-Proteomics Analysis Pipeline
6 versions - Latest release: 4 months ago - 16.6 thousand downloads total - 1 maintainer
iasva 1.28.0
Iteratively Adjusted Surrogate Variable Analysis
6 versions - Latest release: 4 months ago - 14.8 thousand downloads total - 2 maintainers
assorthead 1.4.0
Assorted Header-Only C++ Libraries
4 versions - Latest release: 4 months ago - 364 thousand downloads total - 1 stars on GitHub - 1 maintainer
RCyjs 2.32.0
Display and manipulate graphs in cytoscape.js
6 versions - Latest release: 4 months ago - 22.5 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
DirichletMultinomial 1.52.0
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
6 versions - Latest release: 4 months ago - 5 dependent packages - 516 thousand downloads total - 10 stars on GitHub - 1 maintainer
GloScope 2.0.1
Population-level Representation on scRNA-Seq data
6 versions - Latest release: 4 months ago - 6.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
nnNorm 2.74.0
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
6 versions - Latest release: 4 months ago - 38.2 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SpeCond 1.64.0
Condition specific detection from expression data
6 versions - Latest release: 4 months ago - 41.9 thousand downloads total - 1 maintainer
LymphoSeq 1.38.0
Analyze high-throughput sequencing of T and B cell receptors
6 versions - Latest release: 4 months ago - 20.4 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
enrichplot 1.30.5
Visualization of Functional Enrichment Result
21 versions - Latest release: about 1 month ago - 15 dependent packages - 2.31 million downloads total - 1 maintainer
Top 6.9% on bioconductor.org
biocGraph 1.72.0
Graph examples and use cases in Bioinformatics
6 versions - Latest release: 4 months ago - 1 dependent package - 65.1 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 5 months ago - 10 dependent packages - 410 thousand downloads total - 1 maintainer
SMAD 1.26.0
Statistical Modelling of AP-MS Data (SMAD)
6 versions - Latest release: 4 months ago - 11.6 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.64.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
6 versions - Latest release: 4 months ago - 35.6 thousand downloads total - 1 maintainer
consensus 1.28.0
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
6 versions - Latest release: 4 months ago - 13 thousand downloads total - 1 maintainer
tRNAscanImport 1.30.0
Importing a tRNAscan-SE result file as GRanges object
6 versions - Latest release: 4 months ago - 2 dependent packages - 15.8 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.2% on bioconductor.org
genomation 1.42.0
Summary, annotation and visualization of genomic data
7 versions - Latest release: 4 months ago - 6 dependent packages - 127 thousand downloads total - 3 maintainers
CBNplot 1.10.0
plot bayesian network inferred from gene expression data based on enrichment analysis results
8 versions - Latest release: 4 months ago - 9.99 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 5 months ago - 27 dependent packages - 2.28 million downloads total - 1 maintainer
GARS 1.30.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...
6 versions - Latest release: 4 months ago - 15.9 thousand downloads total - 1 maintainer
seqsetvis 1.30.2
Set Based Visualizations for Next-Gen Sequencing Data
8 versions - Latest release: about 1 month ago - 20.3 thousand downloads total - 1 maintainer
spicyR 1.22.0
Spatial analysis of in situ cytometry data
13 versions - Latest release: 5 months ago - 2 dependent packages - 20.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
AnVILPublish 1.20.0
Publish Packages and Other Resources to AnVIL Workspaces
6 versions - Latest release: 5 months ago - 10.6 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
GeneMeta 1.82.0
MetaAnalysis for High Throughput Experiments
6 versions - Latest release: 4 months ago - 2 dependent packages - 53.1 thousand downloads total - 1 maintainer
DEsubs 1.36.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...
6 versions - Latest release: 4 months ago - 19.7 thousand downloads total - 2 maintainers
PPInfer 1.36.0
Inferring functionally related proteins using protein interaction networks
6 versions - Latest release: 4 months ago - 1 dependent package - 21.5 thousand downloads total - 1 maintainer
InteractiveComplexHeatmap 1.18.1
Make Interactive Complex Heatmaps
7 versions - Latest release: about 1 month ago - 4 dependent packages - 41.9 thousand downloads total - 138 stars on GitHub - 1 maintainer
HiLDA 1.24.0
Conducting statistical inference on comparing the mutational exposures of mutational signatures b...
6 versions - Latest release: 5 months ago - 1 dependent package - 13.3 thousand downloads total - 3 stars on GitHub - 1 maintainer
hypeR 2.8.2
An R Package For Geneset Enrichment Workflows
7 versions - Latest release: 4 months ago - 19 thousand downloads total - 79 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.20.0
Single-Cell RNA-Seq Analysis Utilities
6 versions - Latest release: 4 months ago - 41 dependent packages - 1.11 million downloads total - 1 maintainer
appreci8R 1.28.0
appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity an...
7 versions - Latest release: 4 months ago - 15.2 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
GenomicRanges 1.62.1
Representation and manipulation of genomic intervals
10 versions - Latest release: 4 months ago - 604 dependent packages - 9.44 million downloads total - 1 maintainer
RbowtieCuda 1.2.0
An R Wrapper for nvBowtie and nvBWT, a rewritten version of Bowtie2 for cuda
5 versions - Latest release: 4 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 1 maintainer
HIREewas 1.28.0
Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
6 versions - Latest release: 4 months ago - 13.1 thousand downloads total - 1 maintainer
SigCheck 2.42.0
Check a gene signature's prognostic performance against random signatures, known signatures, and ...
6 versions - Latest release: 4 months ago - 22.2 thousand downloads total - 1 maintainer
RRHO 1.50.0
Inference on agreement between ordered lists
6 versions - Latest release: 4 months ago - 29.8 thousand downloads total - 1 maintainer
AGDEX 1.58.0
Agreement of Differential Expression Analysis
6 versions - Latest release: 4 months ago - 38.2 thousand downloads total - 1 maintainer
GateFinder 1.30.0
Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
6 versions - Latest release: 4 months ago - 15.2 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
CAMERA 1.66.0
Collection of annotation related methods for mass spectrometry data
6 versions - Latest release: 4 months ago - 8 dependent packages - 144 thousand downloads total - 1 maintainer
strandCheckR 1.28.0
Calculate strandness information of a bam file
6 versions - Latest release: 5 months ago - 13.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
RCy3 2.30.1
Functions to Access and Control Cytoscape
8 versions - Latest release: 4 months ago - 15 dependent packages - 122 thousand downloads total - 54 stars on GitHub - 1 maintainer
MsQuality 1.10.0
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
9 versions - Latest release: 4 months ago - 8.23 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
methylKit 1.36.0
DNA methylation analysis from high-throughput bisulfite sequencing results
7 versions - Latest release: 4 months ago - 3 dependent packages - 154 thousand downloads total - 247 stars on GitHub - 2 maintainers
scry 1.22.0
Small-Count Analysis Methods for High-Dimensional Data
6 versions - Latest release: 4 months ago - 29.4 thousand downloads total - 1 maintainer
Harman 1.38.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
6 versions - Latest release: 4 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 5 months ago - 31 dependent packages - 953 thousand downloads total - 63 stars on GitHub - 1 maintainer
Rbwa 1.14.0
R wrapper for BWA-backtrack and BWA-MEM aligners
6 versions - Latest release: 4 months ago - 2 dependent packages - 9.31 thousand downloads total - 1 maintainer
iSEEhex 1.12.0
iSEE extension for summarising data points in hexagonal bins
6 versions - Latest release: 5 months ago - 1 dependent package - 10.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
HDTD 1.44.0
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Trans...
6 versions - Latest release: 5 months ago - 20.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.50.0
a tool set for pathway based data integration and visualization
6 versions - Latest release: 5 months ago - 9 dependent packages - 706 thousand downloads total - 41 stars on GitHub - 1 maintainer
Related Keywords
GeneExpression 664 Sequencing 659 Visualization 482 ImmunoOncology 460 RNASeq 438 DifferentialExpression 421 Microarray 375 DataImport 368 SingleCell 341 Clustering 321 Transcriptomics 297 Preprocessing 290 Infrastructure 268 QualityControl 255 Genetics 227 Proteomics 208 Transcription 200 Classification 195 MultipleComparison 194 Normalization 189 Network 189 StatisticalMethod 183 GeneSetEnrichment 179 Coverage 175 Pathways 168 DataRepresentation 167 Regression 157 Annotation 156 MassSpectrometry 156 GraphAndNetwork 151 r 130 bioconductor 127 Metabolomics 125 DNAMethylation 124 GeneRegulation 123 SystemsBiology 113 FunctionalGenomics 109 Alignment 107 Epigenetics 106 ChIPSeq 100 Bayesian 98 SNP 96 BiomedicalInformatics 96 DimensionReduction 94 GO 84 Spatial 80 BatchEffect 79 CopyNumberVariation 78 bioinformatics 75 CellBasedAssays 73 FlowCytometry 73 CellBiology 72 OneChannel 72 GUI 71 NetworkInference 69 KEGG 69 FeatureExtraction 69 DifferentialMethylation 67 TwoChannel 64 TimeCourse 61 Microbiome 60 bioconductor-package 59 GenomeAnnotation 58 PrincipalComponent 58 NetworkEnrichment 57 SequenceMatching 57 GeneTarget 56 AlternativeSplicing 55 GeneticVariability 47 MethylationArray 47 Survival 47 WorkflowStep 47 rstats 44 ReportWriting 44 DNASeq 44 WholeGenome 43 GenomicVariation 43 Metagenomics 41 GenomeWideAssociation 41 ShinyApps 41 MethylSeq 40 ThirdPartyClient 39 ATACSeq 39 DifferentialSplicing 39 VariantAnnotation 37 ExperimentalDesign 36 FunctionalPrediction 35 HiC 35 BiologicalQuestion 35 r-package 35 GenePrediction 31 Reactome 30 Technology 29 genomics 28 mRNAMicroarray 28 mass-spectrometry 28 SomaticMutation 28 PeakDetection 27 CRISPR 26 MotifAnnotation 25