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bioconductor.org

2,657

Packages

15,363

Versions

3,310

Maintainers

405,628,574

Downloads

iSEEfier 1.8.0
Streamlining the creation of initial states for starting an iSEE instance
5 versions - Latest release: 21 minutes ago - 5.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.4% on bioconductor.org
GeneRegionScan 1.68.0
GeneRegionScan
7 versions - Latest release: 37 minutes ago - 39.8 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
annotate 1.90.0
Annotation for microarrays
8 versions - Latest release: 13 days ago - 48 dependent packages - 4.84 million downloads total - 1 maintainer
topconfects 1.28.0
Top Confident Effect Sizes
7 versions - Latest release: about 1 hour ago - 3 dependent packages - 21.7 thousand downloads total - 15 stars on GitHub - 1 maintainer
vulcan 1.34.0
VirtUaL ChIP-Seq data Analysis using Networks
7 versions - Latest release: about 1 hour ago - 16.2 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.80.0
Variance stabilization and calibration for microarray data
8 versions - Latest release: 13 days ago - 30 dependent packages - 1.2 million downloads total - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.10.0
LC-MS and GC-MS Data Analysis
15 versions - Latest release: 11 days ago - 15 dependent packages - 984 thousand downloads total - 185 stars on GitHub - 1 maintainer
signeR 2.14.0
Empirical Bayesian approach to mutational signature discovery
7 versions - Latest release: about 2 hours ago - 24.2 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 1.1% on bioconductor.org
BiocParallel 1.46.0
Bioconductor facilities for parallel evaluation
12 versions - Latest release: 9 days ago - 377 dependent packages - 9.06 million downloads total - 63 stars on GitHub - 1 maintainer
tidysbml 1.6.0
Extract SBML's data into dataframes
4 versions - Latest release: about 2 hours ago - 4.28 thousand downloads total - 1 stars on GitHub - 1 maintainer
decontam 1.32.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
7 versions - Latest release: about 2 hours ago - 1 dependent package - 151 thousand downloads total - 163 stars on GitHub - 1 maintainer
GRENITS 1.64.0
Gene Regulatory Network Inference Using Time Series
7 versions - Latest release: about 2 hours ago - 31.8 thousand downloads total - 1 maintainer
RGraph2js 1.40.0
Convert a Graph into a D3js Script
7 versions - Latest release: about 3 hours ago - 18.9 thousand downloads total - 1 maintainer
StructuralVariantAnnotation 1.28.0
Variant annotations for structural variants
7 versions - Latest release: about 3 hours ago - 3 dependent packages - 32.8 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
HDF5Array 1.40.0
HDF5 datasets as array-like objects in R
9 versions - Latest release: 13 days ago - 54 dependent packages - 1.83 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GSEABase 1.74.0
Gene set enrichment data structures and methods
8 versions - Latest release: 12 days ago - 49 dependent packages - 1.44 million downloads total - 1 maintainer
MADSEQ 1.36.0 removed
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
6 versions - Latest release: 6 months ago - 15.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
goTools 1.86.0
Functions for Gene Ontology database
7 versions - Latest release: about 4 hours ago - 54.6 thousand downloads total - 1 maintainer
artMS 1.29.0
Analytical R tools for Mass Spectrometry
7 versions - Latest release: about 4 hours ago - 18.4 thousand downloads total - 1 maintainer
simplifyEnrichment 2.6.0
Simplify Functional Enrichment Results
9 versions - Latest release: about 5 hours ago - 4 dependent packages - 72.2 thousand downloads total - 117 stars on GitHub - 1 maintainer
ppcseq 1.20.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
7 versions - Latest release: about 5 hours ago - 10.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
diffuStats 1.32.0
Diffusion scores on biological networks
7 versions - Latest release: about 5 hours ago - 18.5 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.94.0
genefilter: methods for filtering genes from high-throughput experiments
7 versions - Latest release: 12 days ago - 66 dependent packages - 4.23 million downloads total - 1 maintainer
chevreulShiny 1.4.0
Tools for managing SingleCellExperiment objects as projects
4 versions - Latest release: about 5 hours ago - 3.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
EnhancedVolcano 1.30.0
Publication-ready volcano plots with enhanced colouring and labeling
8 versions - Latest release: 12 days ago - 525 thousand downloads total - 384 stars on GitHub - 1 maintainer
mfa 1.34.0
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
7 versions - Latest release: about 6 hours ago - 1 dependent package - 21.3 thousand downloads total - 1 maintainer
epistasisGA 1.14.0
An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
7 versions - Latest release: about 6 hours ago - 8.17 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.0% on bioconductor.org
Rgraphviz 2.56.0
Provides plotting capabilities for R graph objects
7 versions - Latest release: 13 days ago - 61 dependent packages - 1.97 million downloads total - 1 maintainer
Top 4.1% on bioconductor.org
Rdisop 1.72.0
Decomposition of Isotopic Patterns
7 versions - Latest release: about 6 hours ago - 2 dependent packages - 149 thousand downloads total - 5 stars on GitHub - 1 maintainer
BayesKnockdown 1.38.0
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
7 versions - Latest release: about 6 hours ago - 19.2 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
VariantAnnotation 1.58.0
Annotation of Genetic Variants
9 versions - Latest release: 13 days ago - 93 dependent packages - 2.12 million downloads total - 1 maintainer
Top 0.5% on bioconductor.org
DESeq2 1.52.0
Differential gene expression analysis based on the negative binomial distribution
12 versions - Latest release: 13 days ago - 146 dependent packages - 4.36 million downloads total - 330 stars on GitHub - 1 maintainer
Top 0.6% on bioconductor.org
GenomicAlignments 1.48.0
Representation and manipulation of short genomic alignments
9 versions - Latest release: 13 days ago - 132 dependent packages - 5.08 million downloads total - 1 maintainer
HIBAG 1.48.0
HLA Genotype Imputation with Attribute Bagging
9 versions - Latest release: about 7 hours ago - 32.3 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 4.6.0
Disease Ontology Semantic and Enrichment analysis
14 versions - Latest release: 13 days ago - 27 dependent packages - 2.34 million downloads total - 1 maintainer
maPredictDSC 1.50.0
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Dia...
7 versions - Latest release: about 7 hours ago - 26.5 thousand downloads total - 1 maintainer
scGraphVerse 1.2.0
scGraphVerse: A Gene Network Analysis Package
2 versions - Latest release: about 8 hours ago - 1.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
tidySingleCellExperiment 1.22.0
Brings SingleCellExperiment to the Tidyverse
8 versions - Latest release: about 8 hours ago - 4 dependent packages - 23.7 thousand downloads total - 36 stars on GitHub - 1 maintainer
pageRank 1.22.0
Temporal and Multiplex PageRank for Gene Regulatory Network Analysis
7 versions - Latest release: about 8 hours ago - 10.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
FGNet 3.46.0
Functional Gene Networks derived from biological enrichment analyses
7 versions - Latest release: about 8 hours ago - 1 dependent package - 37.2 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
MatrixGenerics 1.24.0
S4 Generic Summary Statistic Functions that Operate on Matrix-Like Objects
8 versions - Latest release: 13 days ago - 45 dependent packages - 5.69 million downloads total - 1 maintainer
kissDE 1.32.0
Retrieves Condition-Specific Variants in RNA-Seq Data
7 versions - Latest release: about 8 hours ago - 16.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
granulator 1.20.0
Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
7 versions - Latest release: about 9 hours ago - 1 dependent package - 13.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
affyPLM 1.88.0
Methods for fitting probe-level models
7 versions - Latest release: about 10 hours ago - 9 dependent packages - 642 thousand downloads total - 0 stars on GitHub - 1 maintainer
MSstatsTMT 2.20.0
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tande...
9 versions - Latest release: about 10 hours ago - 2 dependent packages - 35 thousand downloads total - 1 maintainer
orthogene 1.18.1
Gene mapping made easy
9 versions - Latest release: about 10 hours ago - 1 dependent package - 32.6 thousand downloads total - 45 stars on GitHub - 1 maintainer
ReducedExperiment 1.4.0
Containers and tools for dimensionally-reduced -omics representations
4 versions - Latest release: about 12 hours ago - 4.04 thousand downloads total - 3 stars on GitHub - 1 maintainer
ClusterSignificance 1.40.0
The ClusterSignificance package provides tools to assess if class clusters in dimensionality redu...
7 versions - Latest release: about 7 hours ago - 19.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
ShortRead 1.70.0
FASTQ input and manipulation
8 versions - Latest release: 12 days ago - 36 dependent packages - 2.01 million downloads total - 1 maintainer
Top 0.1% on bioconductor.org
GenomicRanges 1.64.0
Representation and manipulation of genomic intervals
11 versions - Latest release: 13 days ago - 604 dependent packages - 9.58 million downloads total - 1 maintainer
ideal 2.6.0
Interactive Differential Expression AnaLysis
7 versions - Latest release: about 8 hours ago - 25.2 thousand downloads total - 29 stars on GitHub - 1 maintainer
HarmonizR 1.10.0
Handles missing values and makes more data available
6 versions - Latest release: about 8 hours ago - 7.69 thousand downloads total - 1 maintainer
compSPOT 1.10.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
6 versions - Latest release: about 8 hours ago - 6.24 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
GeneOverlap 1.48.0
Test and visualize gene overlaps
7 versions - Latest release: about 8 hours ago - 1 dependent package - 73 thousand downloads total - 1 maintainer
flowSpecs 1.26.0
Tools for processing of high-dimensional cytometry data
7 versions - Latest release: about 8 hours ago - 14 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 0.2% on bioconductor.org
GenomeInfoDb 1.48.0
Utilities for manipulating chromosome names, including modifying them to follow a particular nami...
22 versions - Latest release: 13 days ago - 342 dependent packages - 10.8 million downloads total - 1 maintainer
Top 4.4% on bioconductor.org
PROcess 1.88.0
Ciphergen SELDI-TOF Processing
7 versions - Latest release: about 8 hours ago - 70.3 thousand downloads total - 1 maintainer
branchpointer 1.38.0
Prediction of intronic splicing branchpoints
8 versions - Latest release: about 8 hours ago - 19.5 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
GraphAT 1.84.0
Graph Theoretic Association Tests
7 versions - Latest release: about 8 hours ago - 41 thousand downloads total - 1 maintainer
BUS 1.68.0
Gene network reconstruction
7 versions - Latest release: about 8 hours ago - 37.8 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
qvalue 2.44.0
Q-value estimation for false discovery rate control
7 versions - Latest release: 13 days ago - 45 dependent packages - 2.5 million downloads total - 106 stars on GitHub - 2 maintainers
Top 1.0% on bioconductor.org
fgsea 1.38.0
Fast Gene Set Enrichment Analysis
11 versions - Latest release: 12 days ago - 38 dependent packages - 2.4 million downloads total - 345 stars on GitHub - 1 maintainer
MetaCyto 1.34.0
MetaCyto: A package for meta-analysis of cytometry data
7 versions - Latest release: about 8 hours ago - 18.5 thousand downloads total - 1 maintainer
BPRMeth 1.38.0
Model higher-order methylation profiles
7 versions - Latest release: about 8 hours ago - 1 dependent package - 22.4 thousand downloads total - 1 maintainer
Top 8.5% on bioconductor.org
geneRecommender 1.84.0
A gene recommender algorithm to identify genes coexpressed with a query set of genes
7 versions - Latest release: about 8 hours ago - 40.5 thousand downloads total - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.90.0
Methods for Affymetrix Oligonucleotide Arrays
7 versions - Latest release: 11 days ago - 74 dependent packages - 2.28 million downloads total - 1 maintainer
Top 1.8% on bioconductor.org
oligoClasses 1.74.0
Classes for high-throughput arrays supported by oligo and crlmm
7 versions - Latest release: 13 days ago - 12 dependent packages - 450 thousand downloads total - 1 maintainer
Top 4.0% on bioconductor.org
apeglm 1.34.0
Approximate posterior estimation for GLM coefficients
8 versions - Latest release: about 10 hours ago - 11 dependent packages - 512 thousand downloads total - 1 maintainer
ASAFE 1.38.0
Ancestry Specific Allele Frequency Estimation
7 versions - Latest release: about 10 hours ago - 18.8 thousand downloads total - 1 maintainer
CAFE 1.48.0
Chromosmal Aberrations Finder in Expression data
7 versions - Latest release: about 11 hours ago - 28.4 thousand downloads total - 1 maintainer
Top 0.1% on bioconductor.org
IRanges 2.46.0
Foundation of integer range manipulation in Bioconductor
9 versions - Latest release: 13 days ago - 563 dependent packages - 12 million downloads total - 1 maintainer
NetSAM 1.52.0
Network Seriation And Modularization
7 versions - Latest release: about 13 hours ago - 27.4 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
splots 1.78.0
Visualization of high-throughput assays in microtitre plate or slide format
7 versions - Latest release: about 13 hours ago - 2 dependent packages - 66 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
multiscan 1.72.0
R package for combining multiple scans
7 versions - Latest release: about 13 hours ago - 36.1 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.66.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
7 versions - Latest release: about 13 hours ago - 36.5 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.64.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
7 versions - Latest release: 13 days ago - 10 dependent packages - 413 thousand downloads total - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.56.0
Reactome Pathway Analysis
7 versions - Latest release: about 14 hours ago - 15 dependent packages - 627 thousand downloads total - 1 maintainer
Top 2.0% on bioconductor.org
ROC 1.88.0
utilities for ROC, with microarray focus
7 versions - Latest release: 13 days ago - 6 dependent packages - 327 thousand downloads total - 1 maintainer
Top 4.9% on bioconductor.org
CATALYST 1.36.0
Cytometry dATa anALYSis Tools
12 versions - Latest release: about 14 hours ago - 5 dependent packages - 87.6 thousand downloads total - 70 stars on GitHub - 1 maintainer
concordexR 1.12.0
Identify Spatial Homogeneous Regions with concordex
7 versions - Latest release: about 14 hours ago - 8.26 thousand downloads total - 10 stars on GitHub - 1 maintainer
ncRNAtools 1.22.1
An R toolkit for non-coding RNA
7 versions - Latest release: about 14 hours ago - 10.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
pandaR 1.44.0
PANDA Algorithm
7 versions - Latest release: about 15 hours ago - 1 dependent package - 27.1 thousand downloads total - 2 maintainers
Top 8.2% on bioconductor.org
XDE 2.58.0
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
7 versions - Latest release: about 15 hours ago - 41.4 thousand downloads total - 1 maintainer
GenomicInteractionNodes 1.16.0
A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data
7 versions - Latest release: about 15 hours ago - 8.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
MsBackendMsp 1.16.0
Mass Spectrometry Data Backend for NIST msp Files
7 versions - Latest release: about 16 hours ago - 20.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
RUCova 1.4.0
Removes unwanted covariance from mass cytometry data
3 versions - Latest release: about 16 hours ago - 3.66 thousand downloads total - 2 stars on GitHub - 1 maintainer
spicyR 1.24.0
Spatial analysis of in situ cytometry data
14 versions - Latest release: about 16 hours ago - 2 dependent packages - 21.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
rfaRm 1.23.0
An R interface to the Rfam database
9 versions - Latest release: about 16 hours ago - 11.7 thousand downloads total - 2 maintainers
Top 6.6% on bioconductor.org
RbcBook1 1.80.0
Support for Springer monograph on Bioconductor
7 versions - Latest release: about 16 hours ago - 51.7 thousand downloads total - 1 maintainer
similaRpeak 1.44.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles
7 versions - Latest release: about 16 hours ago - 1 dependent package - 23.4 thousand downloads total - 7 stars on GitHub - 1 maintainer
ssrch 1.28.0
a simple search engine
7 versions - Latest release: about 16 hours ago - 1 dependent package - 12.9 thousand downloads total - 1 maintainer
MineICA 1.52.0
Analysis of an ICA decomposition obtained on genomics data
7 versions - Latest release: about 16 hours ago - 33.1 thousand downloads total - 1 maintainer
DEsubs 1.38.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...
7 versions - Latest release: about 17 hours ago - 20.6 thousand downloads total - 2 maintainers
Top 5.8% on bioconductor.org
fabia 2.58.0
FABIA: Factor Analysis for Bicluster Acquisition
7 versions - Latest release: about 17 hours ago - 3 dependent packages - 61.6 thousand downloads total - 1 maintainer
rebook 1.22.0
Re-using Content in Bioconductor Books
7 versions - Latest release: about 17 hours ago - 17.5 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
Rqc 1.46.0
Quality Control Tool for High-Throughput Sequencing Data
7 versions - Latest release: about 17 hours ago - 50.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.5% on bioconductor.org
DelayedArray 0.38.1
A unified framework for working transparently with on-disk and in-memory array-like datasets
11 versions - Latest release: 10 days ago - 111 dependent packages - 8.11 million downloads total - 1 maintainer
Top 5.2% on bioconductor.org
GENESIS 2.42.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...
7 versions - Latest release: about 18 hours ago - 1 dependent package - 87.3 thousand downloads total - 40 stars on GitHub - 1 maintainer
Top 6.4% on bioconductor.org
annaffy 1.84.0
Annotation tools for Affymetrix biological metadata
7 versions - Latest release: about 18 hours ago - 2 dependent packages - 397 thousand downloads total - 1 maintainer
Top 2.1% on bioconductor.org
scuttle 1.22.0
Legacy Utilities for Single-Cell RNA-Seq Analysis
7 versions - Latest release: about 18 hours ago - 41 dependent packages - 1.14 million downloads total - 1 maintainer