Data

Tools

Indexes

Applications

Experiments

Packages

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

bioconductor.org "bioconductor" keyword

regutools 1.24.0
regutools: an R package for data extraction from RegulonDB
7 versions - Latest release: 5 months ago - 17.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
MDSvis 1.0.0
Plots of Multi Dimensional Scaling (MDS) results
1 version - Latest release: 5 months ago - 2.99 thousand downloads total - 0 stars on GitHub - 1 maintainer
scPCA 1.26.0
Sparse Contrastive Principal Component Analysis
7 versions - Latest release: 5 months ago - 25.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
nucleoSim 1.40.0
Generate synthetic nucleosome maps
7 versions - Latest release: 5 months ago - 1 dependent package - 23 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
recount 1.38.0
Explore and download data from the recount project
8 versions - Latest release: 5 months ago - 6 dependent packages - 84.7 thousand downloads total - 41 stars on GitHub - 1 maintainer
mistyR 1.20.0
Multiview Intercellular SpaTial modeling framework
8 versions - Latest release: 4 months ago - 19 thousand downloads total - 74 stars on GitHub - 1 maintainer
fedup 1.19.0
Fisher's Test for Enrichment and Depletion of User-Defined Pathways
7 versions - Latest release: 5 months ago - 13.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
visiumStitched 1.4.0
Enable downstream analysis of Visium capture areas stitched together with Fiji
3 versions - Latest release: 5 months ago - 7.41 thousand downloads total - 4 stars on GitHub - 1 maintainer
MotifPeeker 1.4.0
Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
3 versions - Latest release: 5 months ago - 6.29 thousand downloads total - 3 stars on GitHub - 1 maintainer
MsDataHub 1.12.1
Mass Spectrometry Data on ExperimentHub
8 versions - Latest release: about 1 month ago - 2 dependent packages - 17.9 thousand downloads total - 2 stars on GitHub - 1 maintainer
qsvaR 1.16.0
Generate Quality Surrogate Variable Analysis for Degradation Correction
7 versions - Latest release: 4 months ago - 14.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
tRNA 1.30.0
Analyzing tRNA sequences and structures
8 versions - Latest release: 5 months ago - 2 dependent packages - 25.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
MuData 1.16.0
Serialization for MultiAssayExperiment Objects
7 versions - Latest release: 5 months ago - 13.9 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
mia 1.20.0
Microbiome analysis
8 versions - Latest release: 5 months ago - 7 dependent packages - 250 thousand downloads total - 58 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
rpx 2.20.0
R Interface to the ProteomeXchange Repository
8 versions - Latest release: 5 months ago - 3 dependent packages - 86.5 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
GenomicDataCommons 1.36.0
NIH / NCI Genomic Data Commons Access
11 versions - Latest release: 5 months ago - 3 dependent packages - 243 thousand downloads total - 90 stars on GitHub - 1 maintainer
cTRAP 1.30.0
Identification of candidate causal perturbations from differential gene expression data
8 versions - Latest release: 4 months ago - 28.1 thousand downloads total - 9 stars on GitHub - 1 maintainer
recount3 1.22.0
Explore and download data from the recount3 project
7 versions - Latest release: 5 months ago - 59.4 thousand downloads total - 42 stars on GitHub - 1 maintainer
nullranges 1.18.0
Generation of null ranges via bootstrapping or covariate matching
8 versions - Latest release: 5 months ago - 1 dependent package - 22.9 thousand downloads total - 29 stars on GitHub - 1 maintainer
Top 9.0% on bioconductor.org
illuminaio 0.54.0
Parsing Illumina Microarray Output Files
7 versions - Latest release: 5 months ago - 12 dependent packages - 652 thousand downloads total - 5 stars on GitHub - 1 maintainer
scviR 1.12.0
experimental inferface from R to scvi-tools
7 versions - Latest release: 5 months ago - 8.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
RNAmodR 1.26.0
Detection of post-transcriptional modifications in high throughput sequencing data
7 versions - Latest release: 5 months ago - 3 dependent packages - 20.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
BiocHail 1.12.0
basilisk and hail
8 versions - Latest release: 5 months ago - 7.33 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
MsCoreUtils 1.24.0
Core Utils for Mass Spectrometry Data
10 versions - Latest release: 5 months ago - 19 dependent packages - 393 thousand downloads total - 17 stars on GitHub - 1 maintainer
Rarr 2.0.1
Read Zarr Files in R
9 versions - Latest release: 4 months ago - 26.1 thousand downloads total - 54 stars on GitHub - 1 maintainer
cmapR 1.24.0
CMap Tools in R
7 versions - Latest release: 4 months ago - 56.2 thousand downloads total - 94 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
regionReport 1.46.0
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
7 versions - Latest release: 5 months ago - 1 dependent package - 44.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
ProtGenerics 1.44.0
Generic infrastructure for Bioconductor mass spectrometry packages
7 versions - Latest release: 4 months ago - 20 dependent packages - 1.66 million downloads total - 8 stars on GitHub - 1 maintainer
TargetDecoy 1.18.0
Diagnostic Plots to Evaluate the Target Decoy Approach
7 versions - Latest release: 5 months ago - 14.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
rRDP 1.44.0 removed
Interface to the RDP Classifier
6 versions - Latest release: 11 months ago - 22.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
mimager 1.36.0
mimager: The Microarray Imager
7 versions - Latest release: 4 months ago - 22.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
cogena 1.46.0
co-expressed gene-set enrichment analysis
7 versions - Latest release: 5 months ago - 33.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
xcms 4.10.1
LC-MS and GC-MS Data Analysis
16 versions - Latest release: 3 months ago - 15 dependent packages - 1.02 million downloads total - 234 stars on GitHub - 1 maintainer
CTexploreR 1.8.0
Explores Cancer Testis Genes
5 versions - Latest release: 5 months ago - 10.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.42.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
7 versions - Latest release: 5 months ago - 3 dependent packages - 437 thousand downloads total - 1 stars on GitHub - 1 maintainer
TargetSearch 2.14.0
A package for the analysis of GC-MS metabolite profiling data
10 versions - Latest release: 5 months ago - 45.2 thousand downloads total - 4 stars on GitHub - 1 maintainer
TREG 1.16.0
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
7 versions - Latest release: 4 months ago - 12.8 thousand downloads total - 5 stars on GitHub - 1 maintainer
flowcatchR 1.46.0
Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
7 versions - Latest release: 4 months ago - 31 thousand downloads total - 4 stars on GitHub - 1 maintainer
GOexpress 1.46.0
Visualise microarray and RNAseq data using gene ontology annotations
7 versions - Latest release: 5 months ago - 1 dependent package - 41.8 thousand downloads total - 10 stars on GitHub - 1 maintainer
methylInheritance 1.36.0
Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multip...
8 versions - Latest release: 5 months ago - 1 dependent package - 23.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
derfinderHelper 1.46.0
derfinder helper package
7 versions - Latest release: 4 months ago - 1 dependent package - 98.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
splatter 1.36.0
Simple Simulation of Single-cell RNA Sequencing Data
7 versions - Latest release: 5 months ago - 6 dependent packages - 91.2 thousand downloads total - 205 stars on GitHub - 1 maintainer
tidybulk 2.2.0
Brings transcriptomics to the tidyverse
9 versions - Latest release: 5 months ago - 1 dependent package - 32.7 thousand downloads total - 182 stars on GitHub - 1 maintainer
simPIC 1.8.0
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
5 versions - Latest release: 5 months ago - 9.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
plotGrouper 1.30.0
Shiny app GUI wrapper for ggplot with built-in statistical analysis
7 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
similaRpeak 1.44.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles
7 versions - Latest release: 5 months ago - 1 dependent package - 29 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.68.0
Quality metrics report for microarray data sets
8 versions - Latest release: 5 months ago - 226 thousand downloads total - 1 stars on GitHub - 1 maintainer
GeneTonic 3.6.0
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional ...
7 versions - Latest release: 5 months ago - 1 dependent package - 28.8 thousand downloads total - 83 stars on GitHub - 1 maintainer
iSEEpathways 1.10.0
iSEE extension for panels related to pathway analysis
6 versions - Latest release: 5 months ago - 11.2 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.6% on bioconductor.org
biomaRt 2.68.0
Interface to BioMart databases (i.e. Ensembl)
13 versions - Latest release: 4 months ago - 124 dependent packages - 5.5 million downloads total - 51 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
rhdf5 2.56.1
R Interface to HDF5
13 versions - Latest release: 19 days ago - 69 dependent packages - 3.67 million downloads total - 74 stars on GitHub - 1 maintainer
DiscoRhythm 1.28.0
Interactive Workflow for Discovering Rhythmicity in Biological Data
7 versions - Latest release: 5 months ago - 19.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
iSEEhex 1.14.0
iSEE extension for summarising data points in hexagonal bins
7 versions - Latest release: 5 months ago - 1 dependent package - 14.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
crisprBwa 1.16.0
BWA-based alignment of CRISPR gRNA spacer sequences
7 versions - Latest release: 5 months ago - 1 dependent package - 12.2 thousand downloads total - 2 stars on GitHub - 1 maintainer
categoryCompare 1.56.0
Meta-analysis of high-throughput experiments using feature annotations
7 versions - Latest release: 4 months ago - 40.1 thousand downloads total - 6 stars on GitHub - 1 maintainer
crisprViz 1.14.0
Visualization Functions for CRISPR gRNAs
7 versions - Latest release: 4 months ago - 2 dependent packages - 16.5 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
MSnbase 2.38.1
Base Functions and Classes for Mass Spectrometry and Proteomics
10 versions - Latest release: about 2 months ago - 30 dependent packages - 660 thousand downloads total - 138 stars on GitHub - 1 maintainer
tidySummarizedExperiment 1.22.0
Brings SummarizedExperiment to the Tidyverse
8 versions - Latest release: 5 months ago - 5 dependent packages - 30.1 thousand downloads total - 31 stars on GitHub - 1 maintainer
orthogene 1.18.1
Gene mapping made easy
9 versions - Latest release: 5 months ago - 1 dependent package - 39.5 thousand downloads total - 58 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
dada2 1.40.0
Accurate, high-resolution sample inference from amplicon sequencing data
7 versions - Latest release: 5 months ago - 2 dependent packages - 941 thousand downloads total - 558 stars on GitHub - 1 maintainer
derfinderPlot 1.46.0
Plotting functions for derfinder
7 versions - Latest release: 5 months ago - 3 dependent packages - 40.1 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 3.6.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
7 versions - Latest release: 5 months ago - 2 dependent packages - 75.5 thousand downloads total - 56 stars on GitHub - 1 maintainer
miaViz 1.20.0
Microbiome Analysis Plotting and Visualization
8 versions - Latest release: 4 months ago - 2 dependent packages - 31.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
tximport 1.40.0
Import and summarize transcript-level estimates for transcript- and gene-level analysis
9 versions - Latest release: 4 months ago - 13 dependent packages - 617 thousand downloads total - 145 stars on GitHub - 1 maintainer
fishpond 2.18.0
Fishpond: downstream methods and tools for expression data
7 versions - Latest release: 5 months ago - 1 dependent package - 71.9 thousand downloads total - 32 stars on GitHub - 1 maintainer
iSEEindex 1.10.0
iSEE extension for a landing page to a custom collection of data sets
6 versions - Latest release: 4 months ago - 9.61 thousand downloads total - 2 stars on GitHub - 1 maintainer
Voyager 1.14.0
From geospatial to spatial omics
7 versions - Latest release: 5 months ago - 24.6 thousand downloads total - 105 stars on GitHub - 1 maintainer
NormalyzerDE 1.30.0
Evaluation of normalization methods and calculation of differential expression analysis statistics
7 versions - Latest release: 4 months ago - 38.7 thousand downloads total - 26 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.80.0
Get data from NCBI Gene Expression Omnibus (GEO)
7 versions - Latest release: 5 months ago - 47 dependent packages - 2.61 million downloads total - 118 stars on GitHub - 1 maintainer
dar 1.8.0
Differential Abundance Analysis by Consensus
5 versions - Latest release: 4 months ago - 10.2 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
karyoploteR 1.38.0
Plot customizable linear genomes displaying arbitrary data
8 versions - Latest release: 5 months ago - 8 dependent packages - 169 thousand downloads total - 377 stars on GitHub - 1 maintainer
ramr 1.20.2
Detection of Rare Aberrantly Methylated Regions in Array and NGS Data
8 versions - Latest release: 10 days ago - 20.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
rBLAST 1.8.0
R Interface for the Basic Local Alignment Search Tool
5 versions - Latest release: 5 months ago - 15.7 thousand downloads total - 115 stars on GitHub - 1 maintainer
BiocPkgTools 1.30.1
Collection of simple tools for learning about Bioconductor Packages
11 versions - Latest release: about 2 months ago - 40.7 thousand downloads total - 22 stars on GitHub - 1 maintainer
crisprDesign 1.14.0
Comprehensive design of CRISPR gRNAs for nucleases and base editors
7 versions - Latest release: 5 months ago - 3 dependent packages - 24.8 thousand downloads total - 33 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
TCGAbiolinks 2.40.0
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
9 versions - Latest release: 5 months ago - 7 dependent packages - 652 thousand downloads total - 355 stars on GitHub - 2 maintainers
biocthis 1.22.0
Automate package and project setup for Bioconductor packages
7 versions - Latest release: 5 months ago - 2 dependent packages - 53.5 thousand downloads total - 56 stars on GitHub - 1 maintainer
RJMCMCNucleosomes 1.36.0
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-rea...
5 versions - Latest release: about 2 months ago - 22.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
SingleR 2.14.2
Reference-Based Single-Cell RNA-Seq Annotation
10 versions - Latest release: 16 days ago - 5 dependent packages - 468 thousand downloads total - 204 stars on GitHub - 1 maintainer
scp 1.22.0
Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
7 versions - Latest release: 4 months ago - 31.5 thousand downloads total - 33 stars on GitHub - 1 maintainer
rTRM 1.50.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
7 versions - Latest release: 5 months ago - 1 dependent package - 37.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
bambu 3.14.0
Context-Aware Transcript Quantification from Long Read RNA-Seq data
12 versions - Latest release: 5 months ago - 1 dependent package - 46.7 thousand downloads total - 259 stars on GitHub - 1 maintainer
epialleleR 1.20.0
Fast, Accurate, Epiallele-Aware Methylation Caller and Reporter
7 versions - Latest release: 5 months ago - 19.9 thousand downloads total - 7 stars on GitHub - 1 maintainer
crisprScore 1.16.0
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
7 versions - Latest release: 5 months ago - 3 dependent packages - 25.4 thousand downloads total - 31 stars on GitHub - 1 maintainer
Top 3.3% on bioconductor.org
ensembldb 2.36.1
Utilities to create and use Ensembl-based annotation databases
9 versions - Latest release: 2 months ago - 40 dependent packages - 1.73 million downloads total - 36 stars on GitHub - 1 maintainer
RLSeq 1.6.0 removed
RLSeq: An analysis package for R-loop mapping data
3 versions - Latest release: almost 3 years ago - 2.67 thousand downloads total - 2 stars on GitHub - 1 maintainer
esATAC 1.34.0
An Easy-to-use Systematic pipeline for ATACseq data analysis
7 versions - Latest release: 4 months ago - 42.9 thousand downloads total - 24 stars on GitHub - 1 maintainer
DeconvoBuddies 1.4.0
Helper Functions for LIBD Deconvolution
3 versions - Latest release: 5 months ago - 12.1 thousand downloads total - 11 stars on GitHub - 1 maintainer
Top 8.6% on bioconductor.org
Spectra 1.22.2
Spectra Infrastructure for Mass Spectrometry Data
13 versions - Latest release: 3 months ago - 15 dependent packages - 198 thousand downloads total - 47 stars on GitHub - 1 maintainer
Top 4.3% on bioconductor.org
plyranges 1.32.0
A fluent interface for manipulating GenomicRanges
7 versions - Latest release: 5 months ago - 22 dependent packages - 173 thousand downloads total - 156 stars on GitHub - 1 maintainer
brainflowprobes 1.20.0 removed
Plots and annotation for choosing BrainFlow target probe sequence
4 versions - Latest release: almost 2 years ago - 5.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
crisprBase 1.16.0
Base functions and classes for CRISPR gRNA design
7 versions - Latest release: 5 months ago - 6 dependent packages - 23.7 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
pRoloc 1.52.0
A unifying bioinformatics framework for spatial proteomics
9 versions - Latest release: 4 months ago - 3 dependent packages - 94.5 thousand downloads total - 16 stars on GitHub - 1 maintainer
ImmuneSpaceR 1.32.0 removed
A Thin Wrapper around the ImmuneSpace Data and Tools Portal
3 versions - Latest release: over 2 years ago - 12.5 thousand downloads total - 24 stars on GitHub - 1 maintainer
ideal 2.6.0
Interactive Differential Expression AnaLysis
7 versions - Latest release: 5 months ago - 37.1 thousand downloads total - 34 stars on GitHub - 1 maintainer
dce 1.13.0 removed
Pathway Enrichment Based on Differential Causal Effects
4 versions - Latest release: almost 2 years ago - 6.79 thousand downloads total - 14 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data
1 version - Latest release: almost 3 years ago - 7.34 thousand downloads total - 5 stars on GitHub - 1 maintainer
SpotSweeper 1.8.0
Spatially-aware quality control for spatial transcriptomics
9 versions - Latest release: 5 months ago - 16.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
signeR 2.14.0
Empirical Bayesian approach to mutational signature discovery
7 versions - Latest release: 5 months ago - 32.8 thousand downloads total - 14 stars on GitHub - 1 maintainer
Modstrings 1.28.0
Working with modified nucleotide sequences
7 versions - Latest release: 5 months ago - 4 dependent packages - 30.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Related Keywords
Software 133 r 63 Sequencing 39 Visualization 38 GeneExpression 36 DataImport 36 ImmunoOncology 29 Infrastructure 29 DifferentialExpression 29 rstats 27 RNASeq 26 bioinformatics 26 Transcriptomics 19 QualityControl 17 Transcription 15 Coverage 15 bioconductor-package 14 SingleCell 14 MultipleComparison 13 MassSpectrometry 13 r-package 12 Normalization 11 mass-spectrometry 11 Proteomics 11 proteomics 10 FunctionalGenomics 10 Clustering 10 Genetics 9 GUI 9 Microarray 9 DataRepresentation 9 genomics 9 Pathways 9 GeneSetEnrichment 9 Epigenetics 9 Alignment 9 ChIPSeq 8 Classification 8 Preprocessing 8 rnaseq 8 ReportWriting 7 OneChannel 7 shiny 7 Network 7 Annotation 7 StatisticalMethod 7 crispr 6 transcriptomics 6 crispr-design 6 GO 6 ShinyApps 6 Metabolomics 6 grna 6 derfinder 6 grna-sequence 6 WorkflowStep 6 grna-sequences 6 metabolomics 6 CRISPR 6 Regression 6 DNAMethylation 5 hacktoberfest 5 deseq2 5 package 5 PrincipalComponent 5 sgrna-design 5 sgrna 5 rna 5 sequences 5 crispr-target 5 crispr-cas9 5 Microbiome 5 Spatial 5 FlowCytometry 4 ATACSeq 4 DifferentialMethylation 4 scrna-seq 4 data-visualization 4 gene-expression 4 SequenceMatching 4 GeneTarget 4 TwoChannel 4 chip-seq 4 DifferentialPeakCalling 4 HistoneModification 4 structures 4 GeneRegulation 4 spatial-transcriptomics 4 microbiome 4 BiologicalQuestion 4 rna-seq-analysis 4 user-friendly 4 MethylSeq 4 BiomedicalInformatics 3 iseeu 3 human 3 DNASeq 3 rnamodr 3 DNaseSeq 3 modifications 3