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

bioconductor.org "Software" keyword

CalibraCurve 1.0.0
Calibration curves for targeted proteomics, lipidomics and metabolomics data
1 version - Latest release: 4 months ago - 971 downloads total - 5 stars on GitHub - 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: 4 months ago - 740 dependent packages - 11.2 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: 4 months ago - 54 dependent packages - 1.74 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: 4 months ago - 47 dependent packages - 2.35 million downloads total - 105 stars on GitHub - 1 maintainer
Top 0.7% on bioconductor.org
graph 1.88.1
graph: A package to handle graph data structures
8 versions - Latest release: 3 months ago - 101 dependent packages - 3.49 million downloads total - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.54.0
Provides plotting capabilities for R graph objects
6 versions - Latest release: 4 months ago - 61 dependent packages - 1.93 million downloads total - 1 maintainer
epihet 1.16.0 removed
Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data
1 version - Latest release: over 2 years ago - 4.09 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.86.0
utilities for ROC, with microarray focus
6 versions - Latest release: 4 months ago - 6 dependent packages - 319 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
fgsea 1.36.2
Fast Gene Set Enrichment Analysis
10 versions - Latest release: about 2 months ago - 38 dependent packages - 2.28 million downloads total - 345 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
RBGL 1.86.0
An interface to the BOOST graph library
6 versions - Latest release: 4 months ago - 33 dependent packages - 1.92 million downloads total - 1 maintainer
infinityFlow 1.20.2
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
7 versions - Latest release: about 1 month ago - 11 thousand downloads total - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 4 months ago - 44 dependent packages - 1.98 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: 4 months ago - 36 dependent packages - 9.46 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 4 months ago - 74 dependent packages - 2.25 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: 4 months ago - 201 dependent packages - 2.03 million downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.88.0
Annotation for microarrays
7 versions - Latest release: 4 months ago - 48 dependent packages - 4.74 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: 4 months ago - 66 dependent packages - 4.16 million downloads total - 1 maintainer
flowMeans 1.70.0
Non-parametric Flow Cytometry Data Gating
6 versions - Latest release: 3 months ago - 2 dependent packages - 59 thousand downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.36.0
A unified framework for working transparently with on-disk and in-memory array-like datasets
8 versions - Latest release: 4 months ago - 111 dependent packages - 7.81 million 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: 4 months ago - 10 dependent packages - 406 thousand downloads total - 1 maintainer
RTNduals 1.34.1
Analysis of co-regulation and inference of 'dual regulons'
7 versions - Latest release: about 9 hours ago - 1 dependent package - 17.4 thousand downloads total - 2 maintainers
Top 1.5% on bioconductor.org
maftools 2.26.0 💰
Summarize, Analyze and Visualize MAF Files
6 versions - Latest release: 4 months ago - 9 dependent packages - 337 thousand downloads total - 485 stars on GitHub - 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: 4 months ago - 183 dependent packages - 4.3 million downloads total - 1 maintainer
wavClusteR 2.44.0
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
6 versions - Latest release: 3 months ago - 25.8 thousand downloads total - 1 maintainer
MatrixRider 1.42.0
Obtain total affinity and occupancies for binding site matrices on a given sequence
6 versions - Latest release: 3 months ago - 20 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
goTools 1.84.0
Functions for Gene Ontology database
6 versions - Latest release: 4 months ago - 52.9 thousand downloads total - 1 maintainer
notame 1.0.1
Workflow for non-targeted LC-MS metabolic profiling
2 versions - Latest release: about 2 months ago - 1.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.1% on bioconductor.org
Biobase 2.70.0
Biobase: Base functions for Bioconductor
6 versions - Latest release: 4 months ago - 518 dependent packages - 11.2 million downloads total - 1 maintainer
Coralysis 1.0.0
Coralysis sensitive identification of imbalanced cell types and states in single-cell data via mu...
1 version - Latest release: 4 months ago - 1.96 thousand downloads total - 1 stars on GitHub - 1 maintainer
DspikeIn 1.0.0
Estimating Absolute Abundance from Microbial Spike-in Controls
2 versions - Latest release: 3 months ago - 933 downloads total - 16 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 4 months ago - 31 dependent packages - 942 thousand downloads total - 63 stars on GitHub - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 4 months ago - 37 dependent packages - 2.63 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: 3 months ago - 59 dependent packages - 2.41 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: 4 months ago - 563 dependent packages - 11.7 million downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 4 months ago - 14.5 thousand downloads total - 12 stars on GitHub - 1 maintainer
schex 1.24.0
Hexbin plots for single cell omics data
7 versions - Latest release: 4 months ago - 3 dependent packages - 23.1 thousand downloads total - 74 stars on GitHub - 1 maintainer
interacCircos 1.20.0
The Generation of Interactive Circos Plot
6 versions - Latest release: 3 months ago - 9.45 thousand downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.4.0
Disease Ontology Semantic and Enrichment analysis
13 versions - Latest release: 4 months ago - 27 dependent packages - 2.22 million downloads total - 1 maintainer
Top 0.2% on bioconductor.org
Biostrings 2.78.0
Efficient manipulation of biological strings
11 versions - Latest release: 4 months ago - 333 dependent packages - 9.4 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: 4 months ago - 30 dependent packages - 592 thousand downloads total - 123 stars on GitHub - 1 maintainer
MetaDICT 1.0.0
Microbiome data integration method via shared dictionary learning
1 version - Latest release: 4 months ago - 933 downloads total - 2 stars on GitHub - 1 maintainer
iModMix 1.0.0
Integrative Modules for Multi-Omics Data
1 version - Latest release: 4 months ago - 936 downloads total - 2 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.54.1
R Interface to HDF5
11 versions - Latest release: 3 months ago - 69 dependent packages - 3.28 million downloads total - 72 stars on GitHub - 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: 4 months ago - 146 dependent packages - 4.21 million downloads total - 330 stars on GitHub - 1 maintainer
nondetects 2.40.0
Non-detects in qPCR data
7 versions - Latest release: 3 months ago - 24.8 thousand downloads total - 1 maintainer
pRolocGUI 2.20.0
Interactive visualisation of spatial proteomics data
6 versions - Latest release: 4 months ago - 27.8 thousand downloads total - 8 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: 4 months ago - 15 dependent packages - 973 thousand downloads total - 185 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: 4 months ago - 132 dependent packages - 4.93 million 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 18 hours ago - 4 dependent packages - 190 thousand downloads total - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.38.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
9 versions - Latest release: 4 months ago - 96 dependent packages - 1.06 million downloads total - 1 maintainer
Top 9.1% on bioconductor.org
lapmix 1.76.0
Laplace Mixture Model in Microarray Experiments
6 versions - Latest release: 3 months ago - 33.6 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.56.0
Annotation of Genetic Variants
8 versions - Latest release: 4 months ago - 93 dependent packages - 2.08 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
ggtree 4.0.4
an R package for visualization of tree and annotation data
12 versions - Latest release: about 2 months ago - 28 dependent packages - 2.27 million downloads total - 1 maintainer
FinfoMDS 1.0.0
Multidimensional Scaling with F-ratio for microbiome visualization
1 version - Latest release: 4 months ago - 988 downloads total - 2 stars on GitHub - 1 maintainer
vulcan 1.32.0
VirtUaL ChIP-Seq data Analysis using Networks
6 versions - Latest release: 3 months ago - 15.1 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.72.0
Gene set enrichment data structures and methods
7 versions - Latest release: 4 months ago - 49 dependent packages - 1.39 million downloads total - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.68.0
FASTQ input and manipulation
7 versions - Latest release: 4 months ago - 36 dependent packages - 1.98 million downloads total - 1 maintainer
Top 0.8% on bioconductor.org
flowCore 2.22.1
flowCore: Basic structures for flow cytometry data
9 versions - Latest release: about 2 months ago - 51 dependent packages - 4.95 million downloads total - 1 maintainer
metaSeq 1.50.0
Meta-analysis of RNA-Seq count data in multiple studies
6 versions - Latest release: 4 months ago - 26.9 thousand downloads total - 1 maintainer
cytoviewer 1.10.0
An interactive multi-channel image viewer for R
6 versions - Latest release: 4 months ago - 8.49 thousand downloads total - 7 stars on GitHub - 1 maintainer
HelloRanges 1.36.0
Introduce *Ranges to bedtools users
6 versions - Latest release: 3 months ago - 2 dependent packages - 32.1 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
lpsymphony 1.38.0
Symphony integer linear programming solver in R
6 versions - Latest release: 3 months ago - 1 dependent package - 201 thousand downloads total - 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: 2 months ago - 181 dependent packages - 4.28 million downloads total - 4 maintainers
scrapper 1.4.0
Bindings to C++ Libraries for Single-Cell Analysis
6 versions - Latest release: 3 months ago - 19.1 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 4 months ago - 43 dependent packages - 1.18 million downloads total - 3 maintainers
Top 2.6% on bioconductor.org
Category 2.76.0
Category Analysis
6 versions - Latest release: 3 months ago - 13 dependent packages - 605 thousand downloads total - 1 maintainer
iCARE 1.38.0
Individualized Coherent Absolute Risk Estimation (iCARE)
6 versions - Latest release: 3 months ago - 21.6 thousand downloads total - 1 maintainer
stageR 1.32.0
stageR: stage-wise analysis of high throughput gene expression data in R
7 versions - Latest release: 3 months ago - 2 dependent packages - 34 thousand downloads total - 1 maintainer
LOLA 1.40.1
Locus overlap analysis for enrichment of genomic ranges
7 versions - Latest release: about 1 month ago - 5 dependent packages - 42.2 thousand downloads total - 1 maintainer
Rcwl 1.26.0
An R interface to the Common Workflow Language
6 versions - Latest release: 3 months ago - 2 dependent packages - 16.9 thousand downloads total - 1 maintainer
bacon 1.38.0
Controlling bias and inflation in association studies using the empirical null distribution
6 versions - Latest release: 3 months ago - 30.3 thousand downloads total - 1 maintainer
EBcoexpress 1.54.0
EBcoexpress for Differential Co-Expression Analysis
6 versions - Latest release: 4 months ago - 1 dependent package - 31.7 thousand downloads total - 1 maintainer
Pviz 1.44.0
Peptide Annotation and Data Visualization using Gviz
6 versions - Latest release: 3 months ago - 1 dependent package - 25.2 thousand downloads total - 1 maintainer
unifiedWMWqPCR 1.46.0
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
6 versions - Latest release: 3 months ago - 21.7 thousand downloads total - 1 maintainer
scQTLtools 1.2.4
scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of singl...
6 versions - Latest release: 1 day ago - 2.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
getDEE2 1.20.0
Programmatic access to the DEE2 RNA expression dataset
7 versions - Latest release: 4 months ago - 10.4 thousand downloads total - 4 stars on GitHub - 1 maintainer
veloviz 1.16.0
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
6 versions - Latest release: 3 months ago - 7.7 thousand downloads total - 1 maintainer
twilight 1.86.0
Estimation of local false discovery rate
6 versions - Latest release: 3 months ago - 1 dependent package - 55.6 thousand downloads total - 1 maintainer
rawrr 1.18.0
Direct Access to Orbitrap Data and Beyond
8 versions - Latest release: 4 months ago - 1 dependent package - 20 thousand downloads total - 57 stars on GitHub - 1 maintainer
MCbiclust 1.34.0
Massive correlating biclusters for gene expression data and associated methods
6 versions - Latest release: 3 months ago - 18.5 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
GeneticsPed 1.72.0
Pedigree and genetic relationship functions
6 versions - Latest release: 4 months ago - 49.1 thousand downloads total - 1 maintainer
GloScope 2.0.1
Population-level Representation on scRNA-Seq data
6 versions - Latest release: 3 months ago - 6.39 thousand downloads total - 1 stars on GitHub - 1 maintainer
SigCheck 2.42.0
Check a gene signature's prognostic performance against random signatures, known signatures, and ...
6 versions - Latest release: 3 months ago - 21.4 thousand downloads total - 1 maintainer
Top 5.2% on bioconductor.org
GENESIS 2.40.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...
6 versions - Latest release: 4 months ago - 1 dependent package - 83.9 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.42.0
Q-value estimation for false discovery rate control
6 versions - Latest release: 4 months ago - 45 dependent packages - 2.4 million downloads total - 106 stars on GitHub - 2 maintainers
Top 9.8% on bioconductor.org
metaMS 1.46.0
MS-based metabolomics annotation pipeline
6 versions - Latest release: 3 months ago - 1 dependent package - 32.5 thousand downloads total - 15 stars on GitHub - 1 maintainer
rfPred 1.48.0
Assign rfPred functional prediction scores to a missense variants list
6 versions - Latest release: 3 months ago - 25.5 thousand downloads total - 1 maintainer
SpatialCPie 1.26.0
Cluster analysis of Spatial Transcriptomics data
6 versions - Latest release: 4 months ago - 14 thousand downloads total - 1 maintainer
biotmle 1.34.0
Targeted Learning with Moderated Statistics for Biomarker Discovery
7 versions - Latest release: 3 months ago - 19.6 thousand downloads total - 1 maintainer
Top 0.2% on bioconductor.org
SummarizedExperiment 1.40.0
A container (S4 class) for matrix-like assays
7 versions - Latest release: 4 months ago - 632 dependent packages - 7.72 million downloads total - 1 maintainer
Top 4.2% on bioconductor.org
bluster 1.20.0
Clustering Algorithms for Bioconductor
6 versions - Latest release: 3 months ago - 12 dependent packages - 586 thousand downloads total - 1 maintainer
AnVILPublish 1.20.0
Publish Packages and Other Resources to AnVIL Workspaces
6 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 1 maintainer
derfinderPlot 1.44.0
Plotting functions for derfinder
6 versions - Latest release: 4 months ago - 3 dependent packages - 32.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
CRISPRball 1.6.0
Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filte...
5 versions - Latest release: about 1 month ago - 4.96 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
gpls 1.82.0
Classification using generalized partial least squares
6 versions - Latest release: 3 months ago - 1 dependent package - 67.4 thousand downloads total - 1 maintainer
coGPS 1.54.0
cancer outlier Gene Profile Sets
6 versions - Latest release: 3 months ago - 29.4 thousand downloads total - 1 maintainer
ADAMgui 1.26.0
Activity and Diversity Analysis Module Graphical User Interface
6 versions - Latest release: 3 months ago - 15 thousand downloads total - 1 maintainer
profileplyr 1.26.1
Visualization and annotation of read signal over genomic ranges with profileplyr
8 versions - Latest release: about 1 month ago - 1 dependent package - 25.9 thousand downloads total - 2 maintainers
ggspavis 1.16.0
Visualization functions for spatial transcriptomics data
10 versions - Latest release: 3 months ago - 1 dependent package - 17.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
OUTRIDER 1.28.1
OUTRIDER - OUTlier in RNA-Seq fInDER
10 versions - Latest release: 1 day ago - 1 dependent package - 28.9 thousand downloads total - 53 stars on GitHub - 1 maintainer
Related Keywords
GeneExpression 664 Sequencing 659 Visualization 482 ImmunoOncology 460 RNASeq 438 DifferentialExpression 420 Microarray 375 DataImport 368 SingleCell 341 Clustering 320 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 CellBasedAssays 73 FlowCytometry 73 CellBiology 72 OneChannel 72 GUI 71 NetworkInference 69 KEGG 69 FeatureExtraction 69 DifferentialMethylation 67 TwoChannel 64 TimeCourse 61 Microbiome 60 GenomeAnnotation 58 bioconductor-package 58 PrincipalComponent 58 SequenceMatching 57 NetworkEnrichment 57 GeneTarget 56 AlternativeSplicing 55 GeneticVariability 47 MethylationArray 47 WorkflowStep 47 Survival 47 DNASeq 44 ReportWriting 44 rstats 43 GenomicVariation 43 WholeGenome 43 Metagenomics 41 GenomeWideAssociation 41 ShinyApps 41 MethylSeq 40 ATACSeq 39 DifferentialSplicing 39 ThirdPartyClient 39 VariantAnnotation 37 ExperimentalDesign 36 r-package 35 FunctionalPrediction 35 HiC 35 BiologicalQuestion 35 GenePrediction 31 Reactome 30 Technology 29 genomics 28 SomaticMutation 28 mRNAMicroarray 28 mass-spectrometry 27 PeakDetection 27 CRISPR 26 MotifAnnotation 25