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

bioconductor.org "Software" keyword

Top 7.9% on bioconductor.org
quantro 1.44.0
A test for when to use quantile normalization
6 versions - Latest release: 4 months ago - 3 dependent packages - 50.7 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.46.2
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
21 versions - Latest release: 4 months ago - 342 dependent packages - 10.7 million downloads total - 1 maintainer
Top 8.9% on bioconductor.org
CRImage 1.58.0
CRImage a package to classify cells and calculate tumour cellularity
6 versions - Latest release: 4 months ago - 43.2 thousand downloads total - 2 maintainers
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 5 months ago - 44 dependent packages - 2 million downloads total - 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 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: 3 months ago - 38 dependent packages - 2.33 million downloads total - 345 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.44.0
Bioconductor facilities for parallel evaluation
10 versions - Latest release: 5 months ago - 377 dependent packages - 8.89 million downloads total - 63 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.5
an R package for visualization of tree and annotation data
13 versions - Latest release: 17 days ago - 28 dependent packages - 2.36 million downloads total - 1 maintainer
onlineFDR 2.18.0
Online error rate control
6 versions - Latest release: 5 months ago - 11.2 thousand downloads total - 14 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 - 2.27 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.18.4
A universal enrichment tool for interpreting omics data
19 versions - Latest release: 4 months ago - 59 dependent packages - 2.46 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 5 months ago - 47 dependent packages - 2.37 million downloads total - 109 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 5 months ago - 49 dependent packages - 1.41 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.36.1
A unified framework for working transparently with on-disk and in-memory array-like datasets
9 versions - Latest release: 2 days ago - 111 dependent packages - 7.93 million downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.92.0
genefilter: methods for filtering genes from high-throughput experiments
6 versions - Latest release: 5 months ago - 66 dependent packages - 4.19 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 5 months ago - 37 dependent packages - 2.66 million downloads total - 1 maintainer
SpatialFeatureExperiment 1.12.1
Integrating SpatialExperiment with Simple Features in sf
13 versions - Latest release: 5 months ago - 1 dependent package - 18 thousand downloads total - 57 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: 13 days ago - 96 dependent packages - 1.09 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
GenomicFeatures 1.62.0
Query the gene models of a given organism/assembly
9 versions - Latest release: 5 months ago - 183 dependent packages - 4.34 million downloads total - 1 maintainer
Top 3.8% on bioconductor.org
ropls 1.42.0
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data
6 versions - Latest release: 5 months ago - 9 dependent packages - 143 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 4 months ago - 101 dependent packages - 3.53 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 5 months ago - 36 dependent packages - 1.99 million downloads total - 1 maintainer
h5vc 2.44.0
Managing alignment tallies using a hdf5 backend
7 versions - Latest release: 4 months ago - 38.1 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 5 months ago - 43 dependent packages - 1.19 million downloads total - 3 maintainers
Top 0.2% on bioconductor.org
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays
7 versions - Latest release: 5 months ago - 632 dependent packages - 7.83 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.50.2
Differential gene expression analysis based on the negative binomial distribution
11 versions - Latest release: 5 months ago - 146 dependent packages - 4.27 million downloads total - 330 stars on GitHub - 1 maintainer
sigsquared 1.42.0
Gene signature generation for functionally validated signaling pathways
6 versions - Latest release: 5 months ago - 19.8 thousand downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 5 months ago - 15.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.46.0
Representation and manipulation of short genomic alignments
8 versions - Latest release: 5 months ago - 132 dependent packages - 4.99 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
EnhancedVolcano 1.28.2
Publication-ready volcano plots with enhanced colouring and labeling
7 versions - Latest release: 4 months ago - 512 thousand downloads total - 384 stars on GitHub - 1 maintainer
Top 0.4% on bioconductor.org
rtracklayer 1.70.1
R interface to genome annotation files and the UCSC genome browser
7 versions - Latest release: 3 months ago - 251 dependent packages - 5.22 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 - 9.59 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.1
Variance stabilization and calibration for microarray data
7 versions - Latest release: 2 months ago - 30 dependent packages - 1.19 million downloads total - 1 maintainer
seqArchR 1.14.0
Identify Different Architectures of Sequence Elements
6 versions - Latest release: 5 months ago - 1 dependent package - 8.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
Rhdf5lib 1.32.0
hdf5 library as an R package
8 versions - Latest release: 5 months ago - 3 dependent packages - 3.18 million downloads total - 6 stars on GitHub - 1 maintainer
batchCorr 1.0.0
Within And Between Batch Correction Of LC-MS Metabolomics Data
1 version - Latest release: 5 months ago - 1.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
Rsubread 2.24.0
Mapping, quantification and variant analysis of sequencing data
8 versions - Latest release: 5 months ago - 14 dependent packages - 421 thousand downloads total - 2 maintainers
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 5 months ago - 333 dependent packages - 9.51 million 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
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 5 months ago - 93 dependent packages - 2.1 million downloads total - 1 maintainer
BioCartaImage 1.8.1
BioCarta Pathway Images
6 versions - Latest release: about 1 month ago - 6.22 thousand downloads total - 11 stars on GitHub - 1 maintainer
MEIGOR 1.44.0
MEIGOR - MEtaheuristics for bIoinformatics Global Optimization
8 versions - Latest release: 4 months ago - 2 dependent packages - 25.2 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
oligoClasses 1.72.0
Classes for high-throughput arrays supported by oligo and crlmm
6 versions - Latest release: 5 months ago - 12 dependent packages - 444 thousand downloads total - 1 maintainer
BaalChIP 1.36.0
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
6 versions - Latest release: 5 months ago - 21.9 thousand downloads total - 1 maintainer
DepInfeR 1.14.0
Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and...
6 versions - Latest release: 5 months ago - 7.57 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 5 months ago - 48 dependent packages - 4.78 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
BSgenome 1.78.0
Software infrastructure for efficient representation of full genomes and their SNPs
8 versions - Latest release: 5 months ago - 129 dependent packages - 2.82 million downloads total - 1 maintainer
SEraster 1.2.0
Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis
2 versions - Latest release: 4 months ago - 3 thousand downloads total - 19 stars on GitHub - 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 - 7.05 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
S4Vectors 0.48.0
Foundation of vector-like and list-like containers in Bioconductor
9 versions - Latest release: 5 months ago - 740 dependent packages - 11.3 million downloads total - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 5 months ago - 6 dependent packages - 322 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
rols 3.6.1
An R interface to the Ontology Lookup Service
9 versions - Latest release: 4 months ago - 3 dependent packages - 85.2 thousand downloads total - 11 stars on GitHub - 1 maintainer
hermes 1.14.0 💰
Preprocessing, analyzing, and reporting of RNA-seq data
8 versions - Latest release: 5 months ago - 13 thousand downloads total - 12 stars on GitHub - 1 maintainer
easylift 1.8.0
An R package to perform genomic liftover
5 versions - Latest release: 4 months ago - 6.33 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
basilisk 1.22.0
Freezing Python Dependencies Inside Bioconductor Packages
8 versions - Latest release: 5 months ago - 27 dependent packages - 311 thousand downloads total - 24 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
rpx 2.18.0
R Interface to the ProteomeXchange Repository
7 versions - Latest release: 4 months ago - 3 dependent packages - 78 thousand downloads total - 6 stars on GitHub - 1 maintainer
atSNP 1.26.0
Affinity test for identifying regulatory SNPs
6 versions - Latest release: 4 months ago - 16.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.8.0
LC-MS and GC-MS Data Analysis
13 versions - Latest release: 5 months ago - 15 dependent packages - 978 thousand downloads total - 185 stars on GitHub - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.1
flowCore: Basic structures for flow cytometry data
9 versions - Latest release: 3 months ago - 51 dependent packages - 4.96 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 5 months ago - 33 dependent packages - 1.94 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.38.0
HDF5 datasets as array-like objects in R
8 versions - Latest release: 5 months ago - 54 dependent packages - 1.77 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.32.0
S4 Classes for Single Cell Data
8 versions - Latest release: 5 months ago - 201 dependent packages - 2.07 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.44.0
Foundation of integer range manipulation in Bioconductor
8 versions - Latest release: 5 months ago - 563 dependent packages - 11.8 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 5 months ago - 45 dependent packages - 2.44 million downloads total - 106 stars on GitHub - 2 maintainers
marr 1.20.0
Maximum rank reproducibility
6 versions - Latest release: 5 months ago - 10 thousand downloads total - 2 stars on GitHub - 1 maintainer
immApex 1.4.3
Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
9 versions - Latest release: 3 months ago - 7.48 thousand downloads total - 12 stars on GitHub - 1 maintainer
Summix 2.16.0
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
6 versions - Latest release: 5 months ago - 8.17 thousand downloads total - 1 maintainer
anglemania 1.0.0
Feature Extraction for scRNA-seq Dataset Integration
1 version - Latest release: 5 months ago - 1.31 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
MatrixGenerics 1.22.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
7 versions - Latest release: 5 months ago - 45 dependent packages - 5.55 million downloads total - 1 maintainer
arrayMvout 1.68.0
multivariate outlier detection for expression array QA
6 versions - Latest release: 5 months ago - 46.3 thousand downloads total - 1 maintainer
crisprBwa 1.14.0
BWA-based alignment of CRISPR gRNA spacer sequences
6 versions - Latest release: 4 months ago - 1 dependent package - 8.93 thousand downloads total - 1 stars on GitHub - 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 - 409 thousand downloads total - 1 maintainer
MsFeatures 1.18.0
Functionality for Mass Spectrometry Features
6 versions - Latest release: 5 months ago - 2 dependent packages - 146 thousand downloads total - 7 stars on GitHub - 1 maintainer
ontoProc 2.4.0
processing of ontologies of anatomy, cell lines, and so on
8 versions - Latest release: 5 months ago - 3 dependent packages - 26.3 thousand downloads total - 5 stars on GitHub - 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 - 9.43 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
seqLogo 1.76.0
Sequence logos for DNA sequence alignments
6 versions - Latest release: 5 months ago - 15 dependent packages - 515 thousand downloads total - 4 stars on GitHub - 1 maintainer
fedup 1.18.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
6 versions - Latest release: 5 months ago - 9.32 thousand downloads total - 7 stars on GitHub - 1 maintainer
pmp 1.22.1
Peak Matrix Processing and signal batch correction for metabolomics datasets
7 versions - Latest release: 5 months ago - 2 dependent packages - 17.5 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 4 months ago - 69 dependent packages - 3.33 million downloads total - 72 stars on GitHub - 1 maintainer
lineagespot 1.14.0
Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
6 versions - Latest release: 4 months ago - 7.86 thousand downloads total - 2 stars on GitHub - 1 maintainer
MetaboAnnotation 1.14.0
Utilities for Annotation of Metabolomics Data
9 versions - Latest release: 5 months ago - 20.8 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R
26 versions - Latest release: 3 months ago - 181 dependent packages - 4.32 million downloads total - 4 maintainers
prebs 1.50.0
Probe region expression estimation for RNA-seq data for improved microarray comparability
6 versions - Latest release: 5 months ago - 28.7 thousand downloads total - 1 maintainer
DiscoRhythm 1.26.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
6 versions - Latest release: 5 months ago - 14.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
tpSVG 1.6.0
Thin plate models to detect spatially variable genes
5 versions - Latest release: 5 months ago - 5.25 thousand downloads total - 2 stars on GitHub - 1 maintainer
BAGS 2.50.0
A Bayesian Approach for Geneset Selection
6 versions - Latest release: 5 months ago - 29.4 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 5 months ago - 74 dependent packages - 2.26 million downloads total - 1 maintainer
timeOmics 1.22.0
Time-Course Multi-Omics data integration
6 versions - Latest release: 5 months ago - 1 dependent package - 13 thousand downloads total - 21 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
RUVSeq 1.44.0
Remove Unwanted Variation from RNA-Seq Data
6 versions - Latest release: 5 months ago - 7 dependent packages - 203 thousand downloads total - 14 stars on GitHub - 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 - 2.3 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 - 599 thousand downloads total - 123 stars on GitHub - 1 maintainer
BgeeCall 1.26.0
Automatic RNA-Seq present/absent gene expression calls generation
9 versions - Latest release: 4 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
scmap 1.32.0
A tool for unsupervised projection of single cell RNA-seq data
6 versions - Latest release: 5 months ago - 50.2 thousand downloads total - 86 stars on GitHub - 1 maintainer
adSplit 1.80.0
Annotation-Driven Clustering
6 versions - Latest release: 5 months ago - 50.2 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 - 950 thousand downloads total - 63 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 5 months ago - 61 dependent packages - 1.95 million downloads total - 1 maintainer
rWikiPathways 1.30.0
rWikiPathways - R client library for the WikiPathways API
6 versions - Latest release: 4 months ago - 5 dependent packages - 78.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
biocmake 1.2.0
CMake for Bioconductor
3 versions - Latest release: 5 months ago - 16.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.38.2
Import and summarize transcript-level estimates for transcript- and gene-level analysis
8 versions - Latest release: 2 months ago - 13 dependent packages - 563 thousand downloads total - 141 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
beachmat 2.26.0
Compiling Bioconductor to Handle Each Matrix Type
7 versions - Latest release: 4 months ago - 15 dependent packages - 1.82 million downloads total - 5 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 Network 189 Normalization 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 BiomedicalInformatics 96 SNP 96 DimensionReduction 94 GO 84 Spatial 80 BatchEffect 79 CopyNumberVariation 78 bioinformatics 75 FlowCytometry 73 CellBasedAssays 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 WorkflowStep 47 Survival 47 MethylationArray 47 GeneticVariability 47 ReportWriting 44 rstats 44 DNASeq 44 WholeGenome 43 GenomicVariation 43 ShinyApps 41 Metagenomics 41 GenomeWideAssociation 41 MethylSeq 40 ThirdPartyClient 39 ATACSeq 39 DifferentialSplicing 39 VariantAnnotation 37 ExperimentalDesign 36 FunctionalPrediction 35 r-package 35 HiC 35 BiologicalQuestion 35 GenePrediction 31 Reactome 30 Technology 29 mRNAMicroarray 28 mass-spectrometry 28 SomaticMutation 28 genomics 28 PeakDetection 27 CRISPR 26 MotifAnnotation 25