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bioconductor.org packages
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VariantExperiment 1.18.0
A RangedSummarizedExperiment Container for VCF/GDS Data with GDS Backend3 versions - Latest release: 9 days ago - 4.98 thousand downloads total - 1 stars on GitHub - 1 maintainer
MPFE 1.38.0
Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data2 versions - Latest release: 6 months ago - 12.1 thousand downloads total - 1 maintainer
Top 6.9% on bioconductor.org
3 versions - Latest release: 7 days ago - 1 dependent package - 40.7 thousand downloads total - 27 stars on GitHub - 1 maintainer
M3Drop 1.30.0
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq3 versions - Latest release: 7 days ago - 1 dependent package - 40.7 thousand downloads total - 27 stars on GitHub - 1 maintainer
CNORode 1.44.0
ODE add-on to CellNOptR2 versions - Latest release: 6 months ago - 1 dependent package - 26.4 thousand downloads total - 1 maintainer
alabaster.se 1.2.0
Load and Save SummarizedExperiments from File2 versions - Latest release: 6 months ago - 4 dependent packages - 3.33 thousand downloads total - 1 maintainer
ribor 1.14.0
An R Interface for Ribo Files2 versions - Latest release: 6 months ago - 3.78 thousand downloads total - 1 maintainer
Top 6.8% on bioconductor.org
2 versions - Latest release: 6 months ago - 33.2 thousand downloads total - 1 maintainer
vbmp 1.70.0
Variational Bayesian Multinomial Probit Regression2 versions - Latest release: 6 months ago - 33.2 thousand downloads total - 1 maintainer
GOfuncR 1.22.2
Gene ontology enrichment using FUNC3 versions - Latest release: 3 months ago - 19.5 thousand downloads total - 1 maintainer
InTAD 1.22.0
Search for correlation between epigenetic signals and gene expression in TADs2 versions - Latest release: 6 months ago - 7.43 thousand downloads total - 1 maintainer
topdownr 1.24.0
Investigation of Fragmentation Conditions in Top-Down Proteomics2 versions - Latest release: 6 months ago - 8.03 thousand downloads total - 1 stars on GitHub - 1 maintainer
CytoPipelineGUI 1.0.0
GUI's for visualization of flow cytometry data analysis pipelines1 version - Latest release: 7 months ago - 564 downloads total - 1 maintainer
Top 8.9% on bioconductor.org
2 versions - Latest release: 6 months ago - 32.5 thousand downloads total - 1 maintainer
copa 1.70.0
Functions to perform cancer outlier profile analysis.2 versions - Latest release: 6 months ago - 32.5 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
3 versions - Latest release: 9 days ago - 1 dependent package - 49.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
pcaExplorer 2.30.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach3 versions - Latest release: 9 days ago - 1 dependent package - 49.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
nucleR 2.34.0
Nucleosome positioning package for R2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
InteractiveComplexHeatmap 1.10.0
Make Interactive Complex Heatmaps2 versions - Latest release: 6 months ago - 1 dependent package - 14.6 thousand downloads total - 112 stars on GitHub - 1 maintainer
mariner 1.2.0
Mariner: Explore the Hi-Cs2 versions - Latest release: 6 months ago - 1.04 thousand downloads total - 1 maintainer
rmspc 1.8.0
Multiple Sample Peak Calling2 versions - Latest release: 6 months ago - 2.17 thousand downloads total - 18 stars on GitHub - 1 maintainer
ComPrAn 1.10.0
Complexome Profiling Analysis package2 versions - Latest release: 6 months ago - 2.45 thousand downloads total - 1 maintainer
FunChIP 1.28.0
Clustering and Alignment of ChIP-Seq peaks based on their shapes2 versions - Latest release: 6 months ago - 9.49 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
2 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 maintainer
Rmagpie 1.58.0
MicroArray Gene-expression-based Program In Error rate estimation2 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 maintainer
ideal 1.28.0
Interactive Differential Expression AnaLysis3 versions - Latest release: 9 days ago - 14.5 thousand downloads total - 29 stars on GitHub - 1 maintainer
iSEEu 1.15.1
iSEE Universe3 versions - Latest release: 9 days ago - 6.84 thousand downloads total - 10 stars on GitHub - 1 maintainer
iSEEde 1.2.0
iSEE extension for panels related to differential expression analysis2 versions - Latest release: 9 days ago - 1 dependent package - 820 downloads total - 1 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
2 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
procoil 2.30.0
Prediction of Oligomerization of Coiled Coil Proteins2 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
StructuralVariantAnnotation 1.18.0
Variant annotations for structural variants2 versions - Latest release: 6 months ago - 2 dependent packages - 14.6 thousand downloads total - 1 maintainer
iPath 1.8.0
iPath pipeline for detecting perturbed pathways at individual level2 versions - Latest release: 6 months ago - 1.97 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
2 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
r3Cseq 1.48.0
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)2 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
diffUTR 1.10.0
diffUTR: Streamlining differential exon and 3' UTR usage2 versions - Latest release: 6 months ago - 2.78 thousand downloads total - 6 stars on GitHub - 1 maintainer
h5vc 2.36.0
Managing alignment tallies using a hdf5 backend2 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
SDAMS 1.22.0
Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequen...2 versions - Latest release: 6 months ago - 7.06 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 34.2 thousand downloads total - 1 maintainer
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data2 versions - Latest release: 6 months ago - 34.2 thousand downloads total - 1 maintainer
fastLiquidAssociation 1.38.0
functions for genome-wide application of Liquid Association2 versions - Latest release: 6 months ago - 15 thousand downloads total - 1 maintainer
alabaster.vcf 1.2.0
Save and Load Variant Data to/from File2 versions - Latest release: 6 months ago - 1 dependent package - 1.44 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
2 versions - Latest release: 6 months ago - 28.5 thousand downloads total - 1 maintainer
CORREP 1.68.0
Multivariate Correlation Estimator and Statistical Inference Procedures.2 versions - Latest release: 6 months ago - 28.5 thousand downloads total - 1 maintainer
Top 9.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 2 dependent packages - 27 thousand downloads total - 1 maintainer
ROntoTools 2.30.0
R Onto-Tools suite2 versions - Latest release: 6 months ago - 2 dependent packages - 27 thousand downloads total - 1 maintainer
CoSIA 1.2.0
An Investigation Across Different Species and Tissues2 versions - Latest release: 6 months ago - 908 downloads total - 1 maintainer
scTHI 1.14.0
Indentification of significantly activated ligand-receptor interactions across clusters of cells ...2 versions - Latest release: 6 months ago - 3.72 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
2 versions - Latest release: 6 months ago - 2 dependent packages - 194 thousand downloads total - 5 stars on GitHub - 1 maintainer
MassSpecWavelet 1.68.0 💰
Peak Detection for Mass Spectrometry data using wavelet-based algorithms2 versions - Latest release: 6 months ago - 2 dependent packages - 194 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
3 versions - Latest release: 2 days ago - 1 dependent package - 61.6 thousand downloads total - 1 maintainer
microRNA 1.62.0
Data and functions for dealing with microRNAs3 versions - Latest release: 2 days ago - 1 dependent package - 61.6 thousand downloads total - 1 maintainer
BindingSiteFinder 2.0.0
Binding site defintion based on iCLIP data2 versions - Latest release: 6 months ago - 2.49 thousand downloads total - 3 stars on GitHub - 1 maintainer
svaNUMT 1.8.0
NUMT detection from structural variant calls2 versions - Latest release: 6 months ago - 2.08 thousand downloads total - 3 stars on GitHub - 1 maintainer
SubCellBarCode 1.18.0
SubCellBarCode: Integrated workflow for robust mapping and visualizing whole human spatial proteome2 versions - Latest release: 6 months ago - 4.96 thousand downloads total - 1 maintainer
HybridMTest 1.46.0
Hybrid Multiple Testing2 versions - Latest release: 6 months ago - 1 dependent package - 24.1 thousand downloads total - 1 maintainer
SBGNview 1.16.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"2 versions - Latest release: 6 months ago - 7.48 thousand downloads total - 23 stars on GitHub - 1 maintainer
dagLogo 1.40.0
dagLogo: a Bioconductor package for visualizing conserved amino acid sequence pattern in groups b...2 versions - Latest release: 6 months ago - 18.3 thousand downloads total - 1 maintainer
parglms 1.34.0
support for parallelized estimation of GLMs/GEEs2 versions - Latest release: 6 months ago - 11.4 thousand downloads total - 1 maintainer
TMixClust 1.24.0
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines2 versions - Latest release: 6 months ago - 9.26 thousand downloads total - 1 maintainer
eds 1.4.0
eds: Low-level reader for Alevin EDS format2 versions - Latest release: 6 months ago - 2 dependent packages - 12.6 thousand downloads total - 0 stars on GitHub - 1 maintainer
SISPA 1.32.0
SISPA: Method for Sample Integrated Set Profile Analysis2 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
scGPS 1.16.0
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing t...2 versions - Latest release: 6 months ago - 4.96 thousand downloads total - 4 stars on GitHub - 1 maintainer
biodbExpasy 1.6.0
biodbExpasy, a library for connecting to Expasy ENZYME database.2 versions - Latest release: 6 months ago - 1.56 thousand downloads total - 1 maintainer
ChIPanalyser 1.24.0
ChIPanalyser: Predicting Transcription Factor Binding Sites2 versions - Latest release: 6 months ago - 7.86 thousand downloads total - 1 maintainer
CSSQ 1.14.0
Chip-seq Signal Quantifier Pipeline2 versions - Latest release: 6 months ago - 3.91 thousand downloads total - 1 maintainer
STdeconvolve 1.6.0
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data2 versions - Latest release: 6 months ago - 3.13 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
2 versions - Latest release: 6 months ago - 2 dependent packages - 28.8 thousand downloads total - 1 maintainer
MLP 1.50.0
Mean Log P Analysis2 versions - Latest release: 6 months ago - 2 dependent packages - 28.8 thousand downloads total - 1 maintainer
RiboDiPA 1.10.0
Differential pattern analysis for Ribo-seq data2 versions - Latest release: 6 months ago - 2.87 thousand downloads total - 1 maintainer
Top 5.7% on bioconductor.org
3 versions - Latest release: 2 days ago - 43.5 thousand downloads total - 1 maintainer
OrderedList 1.76.0
Similarities of Ordered Gene Lists3 versions - Latest release: 2 days ago - 43.5 thousand downloads total - 1 maintainer
HPAStainR 1.12.0
Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes2 versions - Latest release: 6 months ago - 2.37 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
2 versions - Latest release: 6 months ago - 5 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
annotatr 1.28.0
Annotation of Genomic Regions to Genomic Annotations2 versions - Latest release: 6 months ago - 5 dependent packages - 57.5 thousand downloads total - 25 stars on GitHub - 1 maintainer
memes 1.12.0
motif matching, comparison, and de novo discovery using the MEME Suite3 versions - Latest release: 3 days ago - 8.72 thousand downloads total - 43 stars on GitHub - 1 maintainer
octad 1.4.0
Open Cancer TherApeutic Discovery (OCTAD)2 versions - Latest release: 6 months ago - 1.39 thousand downloads total - 1 maintainer
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data2 versions - Latest release: 6 months ago - 21 thousand downloads total - 1 maintainer
Rarr 1.4.0
Read Zarr Files in R3 versions - Latest release: 5 days ago - 2.25 thousand downloads total - 24 stars on GitHub - 1 maintainer
flowMap 1.40.0
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-R...2 versions - Latest release: 6 months ago - 17.7 thousand downloads total - 1 maintainer
OncoSimulR 4.4.0
Forward Genetic Simulation of Cancer Progression with Epistasis2 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
biodbHmdb 1.8.0
biodbHmdb, a library for connecting to the HMDB Database2 versions - Latest release: 6 months ago - 2.21 thousand downloads total - 2 stars on GitHub - 1 maintainer
CNORfuzzy 1.44.0
Addon to CellNOptR: Fuzzy Logic2 versions - Latest release: 6 months ago - 20.8 thousand downloads total - 1 maintainer
Top 3.7% on bioconductor.org
3 versions - Latest release: 3 days ago - 2 dependent packages - 81.3 thousand downloads total - 1 maintainer
safe 3.44.0
Significance Analysis of Function and Expression3 versions - Latest release: 3 days ago - 2 dependent packages - 81.3 thousand downloads total - 1 maintainer
microSTASIS 1.2.0
Microbiota STability ASsessment via Iterative cluStering2 versions - Latest release: 6 months ago - 1.09 thousand downloads total - 1 maintainer
mina 1.10.0
Microbial community dIversity and Network Analysis2 versions - Latest release: 6 months ago - 2.44 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.2% on bioconductor.org
2 versions - Latest release: 6 months ago - 5 dependent packages - 76.8 thousand downloads total - 3 maintainers
genomation 1.34.0
Summary, annotation and visualization of genomic data2 versions - Latest release: 6 months ago - 5 dependent packages - 76.8 thousand downloads total - 3 maintainers
fmrs 1.12.0
Variable Selection in Finite Mixture of AFT Regression and FMR Models2 versions - Latest release: 6 months ago - 5 thousand downloads total - 3 stars on GitHub - 1 maintainer
eiR 1.44.0
Accelerated similarity searching of small molecules3 versions - Latest release: 9 days ago - 15.5 thousand downloads total - 3 stars on GitHub - 1 maintainer
TCseq 1.26.0
Time course sequencing data analysis2 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 1 maintainer
singleCellTK 2.12.2
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data3 versions - Latest release: 3 months ago - 1 dependent package - 17 thousand downloads total - 1 maintainer
pageRank 1.14.0
Temporal and Multiplex PageRank for Gene Regulatory Network Analysis3 versions - Latest release: 3 days ago - 3.5 thousand downloads total - 0 stars on GitHub - 1 maintainer
flowTime 1.26.0
Annotation and analysis of biological dynamical systems using flow cytometry2 versions - Latest release: 6 months ago - 8.89 thousand downloads total - 1 maintainer
RSeqAn 1.22.0
R SeqAn2 versions - Latest release: 6 months ago - 1 dependent package - 7.53 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 7.1% on bioconductor.org
2 versions - Latest release: 6 months ago - 31.5 thousand downloads total - 1 maintainer
SLqPCR 1.68.0
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH2 versions - Latest release: 6 months ago - 31.5 thousand downloads total - 1 maintainer
EasyCellType 1.4.0
Annotate cell types for scRNA-seq data2 versions - Latest release: 6 months ago - 1.21 thousand downloads total - 1 maintainer
nipalsMCIA 1.2.0
Multiple Co-Inertia Analysis via the NIPALS Method2 versions - Latest release: 9 days ago - 790 downloads total - 6 stars on GitHub - 1 maintainer
cbpManager 1.12.0
Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Canc...3 versions - Latest release: 5 days ago - 3.21 thousand downloads total - 6 stars on GitHub - 1 maintainer
DMRcaller 1.34.0
Differentially Methylated Regions caller2 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
contiBAIT 1.30.0
Improves Early Build Genome Assemblies using Strand-Seq Data2 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 1 maintainer
meshr 2.8.0
Tools for conducting enrichment analysis of MeSH2 versions - Latest release: 6 months ago - 1 dependent package - 24.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
demuxmix 1.4.0
Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models2 versions - Latest release: 6 months ago - 1 dependent package - 4.05 thousand downloads total - 4 stars on GitHub - 1 maintainer
BUSpaRse 1.16.1
kallisto | bustools R utilities3 versions - Latest release: about 1 month ago - 15.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
alabaster.base 1.2.1
Save Bioconductor Objects To File2 versions - Latest release: 6 months ago - 11 dependent packages - 4.21 thousand downloads total - 1 maintainer
syntenet 1.4.2
Inference And Analysis Of Synteny Networks3 versions - Latest release: 20 days ago - 1 dependent package - 2.85 thousand downloads total - 14 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
3 versions - Latest release: 2 days ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
chipseq 1.54.0
chipseq: A package for analyzing chipseq data3 versions - Latest release: 2 days ago - 4 dependent packages - 115 thousand downloads total - 1 maintainer
Mergeomics 1.30.0
Integrative network analysis of omics data2 versions - Latest release: 6 months ago - 10.9 thousand downloads total - 1 maintainer
RESOLVE 1.6.0
RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes3 versions - Latest release: 5 days ago - 1.58 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.7% on bioconductor.org
2 versions - Latest release: 6 months ago - 30.6 thousand downloads total - 1 maintainer
idiogram 1.78.0
idiogram2 versions - Latest release: 6 months ago - 30.6 thousand downloads total - 1 maintainer
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering2 versions - Latest release: 6 months ago - 1.29 thousand downloads total - 1 maintainer
TSCAN 1.40.1
Tools for Single-Cell Analysis3 versions - Latest release: 3 months ago - 3 dependent packages - 40.5 thousand downloads total - 1 maintainer
paircompviz 1.40.0
Multiple comparison test visualization2 versions - Latest release: 6 months ago - 17 thousand downloads total - 1 maintainer
mfa 1.24.0
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations2 versions - Latest release: 6 months ago - 1 dependent package - 10.3 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
3 versions - Latest release: 3 days ago - 6 dependent packages - 232 thousand downloads total - 1 maintainer
ChIPseeker 1.40.0
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization3 versions - Latest release: 3 days ago - 6 dependent packages - 232 thousand downloads total - 1 maintainer
IVAS 2.22.0
Identification of genetic Variants affecting Alternative Splicing2 versions - Latest release: 6 months ago - 1 dependent package - 14 thousand downloads total - 1 maintainer
netDx 1.14.0
Network-based patient classifier2 versions - Latest release: 6 months ago - 4.03 thousand downloads total - 1 maintainer