bioconductor.org "bioinformatics" keyword
scMerge 1.28.0
scMerge: Merging multiple batches of scRNA-seq data7 versions - Latest release: 5 months ago - 2 dependent packages - 58.4 thousand downloads total - 72 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
8 versions - Latest release: 5 months ago - 8 dependent packages - 377 stars on GitHub - 1 maintainer
karyoploteR 1.38.0
Plot customizable linear genomes displaying arbitrary data8 versions - Latest release: 5 months ago - 8 dependent packages - 377 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
11 versions - Latest release: 3 months ago - 4 dependent packages - 111 thousand downloads total - 84 stars on GitHub - 1 maintainer
sesame 1.30.1
SEnsible Step-wise Analysis of DNA MEthylation BeadChips11 versions - Latest release: 3 months ago - 4 dependent packages - 111 thousand downloads total - 84 stars on GitHub - 1 maintainer
cTRAP 1.30.0
Identification of candidate causal perturbations from differential gene expression data8 versions - Latest release: 5 months ago - 29 thousand downloads total - 9 stars on GitHub - 1 maintainer
cfDNAPro 1.18.0
cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-fr...8 versions - Latest release: 5 months ago - 22.3 thousand downloads total - 44 stars on GitHub - 1 maintainer
gemma.R 3.8.1
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...20 versions - Latest release: 39 minutes ago - 19.7 thousand downloads total - 10 stars on GitHub - 1 maintainer
rWikiPathways 1.32.0
rWikiPathways - R client library for the WikiPathways API7 versions - Latest release: 5 months ago - 5 dependent packages - 91.2 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
10 versions - Latest release: 2 months ago - 30 dependent packages - 664 thousand downloads total - 139 stars on GitHub - 1 maintainer
MSnbase 2.38.1
Base Functions and Classes for Mass Spectrometry and Proteomics10 versions - Latest release: 2 months ago - 30 dependent packages - 664 thousand downloads total - 139 stars on GitHub - 1 maintainer
CopyNumberPlots 1.28.0
Create Copy-Number Plots using karyoploteR functionality8 versions - Latest release: 5 months ago - 2 dependent packages - 29.3 thousand downloads total - 7 stars on GitHub - 1 maintainer
drugfindR 1.0.0
Investigate iLINCS for candidate repurposable drugs1 version - Latest release: 5 months ago - 6.8 thousand downloads total - 13 stars on GitHub - 1 maintainer
signeR 2.14.0
Empirical Bayesian approach to mutational signature discovery7 versions - Latest release: 5 months ago - 36.9 thousand downloads total - 14 stars on GitHub - 1 maintainer
geneXtendeR 1.37.0
R/Bioconductor package for optimized functional annotation of ChIP-seq data7 versions - Latest release: 5 months ago - 33.1 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 3.5% on bioconductor.org
7 versions - Latest release: 5 months ago - 2 dependent packages - 944 thousand downloads total - 556 stars on GitHub - 1 maintainer
dada2 1.40.0
Accurate, high-resolution sample inference from amplicon sequencing data7 versions - Latest release: 5 months ago - 2 dependent packages - 944 thousand downloads total - 556 stars on GitHub - 1 maintainer
rTRM 1.50.0
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks7 versions - Latest release: 5 months ago - 1 dependent package - 37.7 thousand downloads total - 3 stars on GitHub - 1 maintainer
sevenbridges 1.42.0
Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R7 versions - Latest release: 4 months ago - 28 thousand downloads total - 37 stars on GitHub - 1 maintainer
SuperCellCyto 1.2.0
SuperCell For Cytometry Data2 versions - Latest release: 4 months ago - 5.26 thousand downloads total - 13 stars on GitHub - 1 maintainer
iModMix 1.2.0
Integrative Modules for Multi-Omics Data2 versions - Latest release: 5 months ago - 3.88 thousand downloads total - 4 stars on GitHub - 1 maintainer
DNEA 1.2.0
Differential Network Enrichment Analysis for Biological Data2 versions - Latest release: 5 months ago - 5.86 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
7 versions - Latest release: 6 months ago - 47 dependent packages - 2.61 million downloads total - 118 stars on GitHub - 1 maintainer
GEOquery 2.80.0
Get data from NCBI Gene Expression Omnibus (GEO)7 versions - Latest release: 6 months ago - 47 dependent packages - 2.61 million downloads total - 118 stars on GitHub - 1 maintainer
sparrow 1.18.0
Take command of set enrichment analyses through a unified interface8 versions - Latest release: 5 months ago - 1 dependent package - 30.9 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
7 versions - Latest release: 6 months ago - 9 dependent packages - 376 thousand downloads total - 503 stars on GitHub - 1 maintainer
maftools 2.28.0 💰
Summarize, Analyze and Visualize MAF Files7 versions - Latest release: 6 months ago - 9 dependent packages - 376 thousand downloads total - 503 stars on GitHub - 1 maintainer
Top 3.6% on bioconductor.org
21 versions - Latest release: 4 months ago - 11 dependent packages - 174 thousand downloads total - 49 stars on GitHub - 1 maintainer
SeqArray 1.52.1
Data management of large-scale whole-genome sequence variant calls using GDS files21 versions - Latest release: 4 months ago - 11 dependent packages - 174 thousand downloads total - 49 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
12 versions - Latest release: 3 months ago - 18 dependent packages - 374 thousand downloads total - 20 stars on GitHub - 1 maintainer
gdsfmt 1.48.2
R Interface to CoreArray Genomic Data Structure (GDS) Files12 versions - Latest release: 3 months ago - 18 dependent packages - 374 thousand downloads total - 20 stars on GitHub - 1 maintainer
decontam 1.32.0
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data7 versions - Latest release: 5 months ago - 1 dependent package - 172 thousand downloads total - 176 stars on GitHub - 1 maintainer
scruff 1.30.0
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)8 versions - Latest release: 5 months ago - 22.8 thousand downloads total - 8 stars on GitHub - 1 maintainer
pathlinkR 1.8.0
Analyze and interpret RNA-Seq results6 versions - Latest release: 5 months ago - 11.2 thousand downloads total - 33 stars on GitHub - 1 maintainer
CellBench 1.28.0
Construct Benchmarks for Single Cell Analysis Methods7 versions - Latest release: 5 months ago - 2 dependent packages - 24.6 thousand downloads total - 33 stars on GitHub - 1 maintainer
ClustIRR 1.10.0
Clustering of Immune Receptor Repertoires6 versions - Latest release: 5 months ago - 10.6 thousand downloads total - 5 stars on GitHub - 1 maintainer
ReducedExperiment 1.4.0
Containers and tools for dimensionally-reduced -omics representations4 versions - Latest release: 5 months ago - 7.65 thousand downloads total - 3 stars on GitHub - 1 maintainer
ggseqalign 1.6.0
Minimal Visualization of Sequence Alignments4 versions - Latest release: 4 months ago - 8.36 thousand downloads total - 0 stars on GitHub - 1 maintainer
packFinder 1.24.0
de novo Annotation of Pack-TYPE Transposable Elements7 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 7 stars on GitHub - 1 maintainer
TDbasedUFE 1.12.0
Tensor Decomposition Based Unsupervised Feature Extraction7 versions - Latest release: 5 months ago - 1 dependent package - 11.2 thousand downloads total - 5 stars on GitHub - 1 maintainer
methrix 1.26.0
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing8 versions - Latest release: 6 months ago - 1 dependent package - 23.6 thousand downloads total - 36 stars on GitHub - 1 maintainer
biobtreeR 1.24.0
Using biobtree tool from R7 versions - Latest release: 5 months ago - 16.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
netSmooth 1.32.0
Network smoothing for scRNAseq7 versions - Latest release: 5 months ago - 1 dependent package - 22.6 thousand downloads total - 30 stars on GitHub - 1 maintainer
Top 6.8% on bioconductor.org
8 versions - Latest release: 4 months ago - 3 dependent packages - 148 thousand downloads total - 51 stars on GitHub - 1 maintainer
singscore 1.32.0
Rank-based single-sample gene set scoring method8 versions - Latest release: 4 months ago - 3 dependent packages - 148 thousand downloads total - 51 stars on GitHub - 1 maintainer
Top 4.1% on bioconductor.org
11 versions - Latest release: 5 months ago - 3 dependent packages - 243 thousand downloads total - 90 stars on GitHub - 1 maintainer
GenomicDataCommons 1.36.0
NIH / NCI Genomic Data Commons Access11 versions - Latest release: 5 months ago - 3 dependent packages - 243 thousand downloads total - 90 stars on GitHub - 1 maintainer
miaDash 1.4.0
Dashboard for the interactive analysis and exploration of microbiome data3 versions - Latest release: 5 months ago - 6.49 thousand downloads total - 1 stars on GitHub - 1 maintainer
koinar 1.6.0
KoinaR - Remote machine learning inference using Koina5 versions - Latest release: 5 months ago - 10.1 thousand downloads total - 57 stars on GitHub - 1 maintainer
RandomWalkRestartMH 1.26.0 removed
Random walk with restart on multiplex and heterogeneous Networks4 versions - Latest release: almost 2 years ago - 1 dependent package - 10.7 thousand downloads total - 23 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
7 versions - Latest release: 5 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
graphite 1.58.0
GRAPH Interaction from pathway Topological Environment7 versions - Latest release: 5 months ago - 11 dependent packages - 459 thousand downloads total - 8 stars on GitHub - 1 maintainer
hypeR 2.10.0
An R Package For Geneset Enrichment Workflows8 versions - Latest release: 5 months ago - 22.9 thousand downloads total - 79 stars on GitHub - 1 maintainer
cmapR 1.24.0
CMap Tools in R7 versions - Latest release: 5 months ago - 56.2 thousand downloads total - 94 stars on GitHub - 1 maintainer
rRDP 1.44.0 removed
Interface to the RDP Classifier6 versions - Latest release: 11 months ago - 22.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
mimager 1.36.0
mimager: The Microarray Imager7 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 analysis7 versions - Latest release: 5 months ago - 33.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
epistack 1.18.0
Heatmaps of Stack Profiles from Epigenetic Signals7 versions - Latest release: 5 months ago - 14.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
DEWSeq 1.26.0
Differential Expressed Windows Based on Negative Binomial Distribution7 versions - Latest release: 6 months ago - 18.5 thousand downloads total - 5 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
tidytof 1.6.0
Analyze High-dimensional Cytometry Data Using Tidy Data Principles4 versions - Latest release: 5 months ago - 3.42 thousand downloads total - 20 stars on GitHub - 1 maintainer
vissE 1.20.0
Visualising Set Enrichment Analysis Results7 versions - Latest release: 5 months ago - 17.4 thousand downloads total - 19 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
7 versions - Latest release: 5 months ago - 6 dependent packages - 91.2 thousand downloads total - 205 stars on GitHub - 1 maintainer
splatter 1.36.0
Simple Simulation of Single-cell RNA Sequencing Data7 versions - Latest release: 5 months ago - 6 dependent packages - 91.2 thousand downloads total - 205 stars on GitHub - 1 maintainer
simPIC 1.8.0
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data5 versions - Latest release: 5 months ago - 9.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
ontoProc 2.6.0
processing of ontologies of anatomy, cell lines, and so on9 versions - Latest release: 5 months ago - 3 dependent packages - 32.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
SGCP 1.11.1
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...10 versions - Latest release: 5 months ago - 9.65 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.4% on bioconductor.org
7 versions - Latest release: 4 months ago - 18 dependent packages - 689 thousand downloads total - 77 stars on GitHub - 1 maintainer
EBImage 4.54.0
Image processing and analysis toolbox for R7 versions - Latest release: 4 months ago - 18 dependent packages - 689 thousand downloads total - 77 stars on GitHub - 1 maintainer
orthogene 1.18.1
Gene mapping made easy9 versions - Latest release: 5 months ago - 1 dependent package - 39.5 thousand downloads total - 58 stars on GitHub - 1 maintainer
BgeeDB 2.38.1
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities...8 versions - Latest release: 4 months ago - 2 dependent packages - 33.5 thousand downloads total - 16 stars on GitHub - 4 maintainers
doubletrouble 1.12.0
Identification and classification of duplicated genes14 versions - Latest release: 6 months ago - 13.8 thousand downloads total - 37 stars on GitHub - 1 maintainer
BERT 1.8.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...5 versions - Latest release: 6 months ago - 8.69 thousand downloads total - 4 stars on GitHub - 1 maintainer
GEOfastq 1.20.0
Downloads ENA Fastqs With GEO Accessions7 versions - Latest release: 4 months ago - 12.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
NormalyzerDE 1.30.0
Evaluation of normalization methods and calculation of differential expression analysis statistics7 versions - Latest release: 5 months ago - 38.7 thousand downloads total - 26 stars on GitHub - 1 maintainer
plaid 1.0.1
PLAID ultrafast gene set enrichment scoring2 versions - Latest release: about 2 months ago - 6.41 thousand downloads total - 24 stars on GitHub - 1 maintainer
decemedip 1.0.0
hierarchical Bayesian modeling for cell type deconvolution of immunoprecipitation-based DNA methy...1 version - Latest release: 5 months ago - 6.91 thousand downloads total - 4 stars on GitHub - 1 maintainer
rBLAST 1.8.0
R Interface for the Basic Local Alignment Search Tool5 versions - Latest release: 5 months ago - 15.7 thousand downloads total - 115 stars on GitHub - 1 maintainer
HIBAG 1.48.2
HLA Genotype Imputation with Attribute Bagging10 versions - Latest release: 2 months ago - 42.6 thousand downloads total - 31 stars on GitHub - 1 maintainer
BioCor 1.36.0
Functional Similarities7 versions - Latest release: 5 months ago - 33.5 thousand downloads total - 14 stars on GitHub - 1 maintainer
CiteFuse 1.24.0
CiteFuse: multi-modal analysis of CITE-seq data7 versions - Latest release: 5 months ago - 1 dependent package - 25.6 thousand downloads total - 25 stars on GitHub - 1 maintainer
RLSeq 1.6.0 removed
RLSeq: An analysis package for R-loop mapping data3 versions - Latest release: almost 3 years ago - 2.67 thousand downloads total - 2 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.12.1
Advanced package of tensor decomposition based unsupervised feature extraction8 versions - Latest release: 5 months ago - 15.4 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 3.2% on bioconductor.org
9 versions - Latest release: 5 months ago - 11 dependent packages - 303 thousand downloads total - 116 stars on GitHub - 1 maintainer
SNPRelate 1.46.0
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data9 versions - Latest release: 5 months ago - 11 dependent packages - 303 thousand downloads total - 116 stars on GitHub - 1 maintainer
PhyloProfile 2.4.7
PhyloProfile24 versions - Latest release: 25 days ago - 25.3 thousand downloads total - 38 stars on GitHub - 1 maintainer
chromswitch 1.22.0 removed
An R package to detect chromatin state switches from epigenomic data1 version - Latest release: almost 3 years ago - 7.34 thousand downloads total - 5 stars on GitHub - 1 maintainer
POMA 1.22.0
Tools for Omics Data Analysis7 versions - Latest release: 5 months ago - 1 dependent package - 23.8 thousand downloads total - 15 stars on GitHub - 1 maintainer
rmelting 1.28.0
R Interface to MELTING 57 versions - Latest release: 5 months ago - 16.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
GraphExperiment 1.0.2
S4 Class for Quantitative Data and Associated Networks2 versions - Latest release: about 2 months ago - 3.64 thousand downloads total - 1 stars on GitHub - 1 maintainer
martini 1.32.0
GWAS Incorporating Networks7 versions - Latest release: 5 months ago - 20.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: almost 3 years ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
getDEE2 1.22.0
Programmatic access to the DEE2 RNA expression dataset8 versions - Latest release: 5 months ago - 14.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
Related Keywords
Software
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r
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bioconductor
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GeneExpression
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DataImport
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Visualization
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Network
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SingleCell
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GeneSetEnrichment
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RNASeq
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genomics
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rstats
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scrna-seq
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networks
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