bioconductor projects 1,374
bioconductor: wateRmelon
Illumina 450 and EPIC methylation array normalization and metricsPapers that mentioned: 108
Very Likely Science (98)
bioconductor: rtracklayer
R interface to genome annotation files and the UCSC genome browserPapers that mentioned: 107
Very Likely Science (90)
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bioconductor: iPath
iPath pipeline for detecting perturbed pathways at individual levelPapers that mentioned: 95
Very Likely Science (100)
bioconductor: beadarray
Quality assessment and low-level analysis for Illumina BeadArray dataPapers that mentioned: 94
Very Likely Science (100)
Very Likely Science (100)
bioconductor: vsn
Variance stabilization and calibration for microarray dataPapers that mentioned: 91
Very Likely Science (100)
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Very Likely Science (90)
bioconductor: BioPlex
Papers that mentioned: 84
Unlikely Science (0)
bioconductor: cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.Papers that mentioned: 83
Very Likely Science (83)
bioconductor: SIMD
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG sitePapers that mentioned: 83
Very Likely Science (100)
bioconductor: STRINGdb
STRINGdb - Protein-Protein Interaction Networks and Functional Enrichment AnalysisPapers that mentioned: 82
Very Likely Science (100)
Very Likely Science (100)
bioconductor: ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataPapers that mentioned: 81
Very Likely Science (100)
Very Likely Science (100)
Very Likely Science (83)
Very Likely Science (100)
bioconductor: scater
Single-Cell Analysis Toolkit for Gene Expression Data in RPapers that mentioned: 79
Very Likely Science (100)
bioconductor: Heatplus
Heatmaps with row and/or column covariates and colored clustersPapers that mentioned: 77
Very Likely Science (90)
bioconductor: AIMS
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular SubtypePapers that mentioned: 77
Very Likely Science (100)
bioconductor: decontam
Identify Contaminants in Marker-gene and Metagenomics Sequencing DataPapers that mentioned: 76
Very Likely Science (100)
bioconductor: KEGGREST
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)Papers that mentioned: 75
Very Likely Science (90)
bioconductor: PSICQUIC
Papers that mentioned: 75
Unlikely Science (0)
Very Likely Science (100)
bioconductor: AnnotationDbi
Manipulation of SQLite-based annotations in BioconductorPapers that mentioned: 73
Very Likely Science (90)
Very Likely Science (90)
bioconductor: siggenes
Multiple Testing using SAM and Efron's Empirical Bayes ApproachesPapers that mentioned: 72
Very Likely Science (90)
bioconductor: CODEX
A Normalization and Copy Number Variation Detection Method for Whole Exome SequencingPapers that mentioned: 72
Very Likely Science (93)
bioconductor: ASSET
An R package for subset-based association analysis of heterogeneous traits and subtypesPapers that mentioned: 72
Very Likely Science (100)
Very Likely Science (100)
Very Likely Science (100)
bioconductor: TCC
TCC: Differential expression analysis for tag count data with robust normalization strategiesPapers that mentioned: 67
Very Likely Science (100)
bioconductor: ACME
Algorithms for Calculating Microarray Enrichment (ACME)Papers that mentioned: 63
Very Likely Science (100)
Very Likely Science (75)
Very Likely Science (100)
bioconductor: IRanges
Foundation of integer range manipulation in BioconductorPapers that mentioned: 62
Very Likely Science (75)
bioconductor: marray
Exploratory analysis for two-color spotted microarray dataPapers that mentioned: 62
Very Likely Science (100)
bioconductor: EDASeq
Exploratory Data Analysis and Normalization for RNA-SeqPapers that mentioned: 61
Very Likely Science (100)
bioconductor: monocle
Clustering, differential expression, and trajectory analysis for single- cell RNA-SeqPapers that mentioned: 60
Very Likely Science (100)
bioconductor: SMAP
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number ProfilingPapers that mentioned: 58
Very Likely Science (90)
Very Likely Science (100)
bioconductor: LOLA
Locus overlap analysis for enrichment of genomic rangesPapers that mentioned: 56
Very Likely Science (100)
bioconductor: SCOPE
A normalization and copy number estimation method for single-cell DNA sequencingPapers that mentioned: 56
Very Likely Science (100)
bioconductor: RcisTarget
RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regionsPapers that mentioned: 55
Very Likely Science (90)
Very Likely Science (100)
Very Likely Science (100)
bioconductor: missMethyl
Analysing Illumina HumanMethylation BeadChip DataPapers that mentioned: 54
Very Likely Science (98)
Very Likely Science (100)
bioconductor: ASSIGN
Adaptive Signature Selection and InteGratioN (ASSIGN)Papers that mentioned: 54
Very Likely Science (100)
bioconductor: MethylMix
MethylMix: Identifying methylation driven cancer genesPapers that mentioned: 53
Very Likely Science (90)
Very Likely Science (100)
Very Likely Science (100)
Very Likely Science (98)
bioconductor: karyoploteR
Plot customizable linear genomes displaying arbitrary dataPapers that mentioned: 50
Very Likely Science (100)
Very Likely Science (75)
Very Likely Science (90)
bioconductor: IVAS
Identification of genetic Variants affecting Alternative SplicingPapers that mentioned: 49
Very Likely Science (100)
Very Likely Science (100)
bioconductor: GDCRNATools
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDCPapers that mentioned: 48
Very Likely Science (100)
Very Likely Science (100)
bioconductor: BSgenome
Software infrastructure for efficient representation of full genomes and their SNPsPapers that mentioned: 47
Very Likely Science (90)
Very Likely Science (100)
Very Likely Science (65)
bioconductor: gage
Generally Applicable Gene-set Enrichment for Pathway AnalysisPapers that mentioned: 45
Very Likely Science (100)
bioconductor: AUCell
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)Papers that mentioned: 45
Very Likely Science (100)
Very Likely Science (90)
bioconductor: multiMiR
Integration of multiple microRNA-target databases with their disease and drug associationsPapers that mentioned: 43
Very Likely Science (100)
bioconductor: genefu
Computation of Gene Expression-Based Signatures in Breast CancerPapers that mentioned: 42
Very Likely Science (100)
bioconductor: GOSim
Computation of functional similarities between GO terms and gene products; GO enrichment analysisPapers that mentioned: 41
Very Likely Science (100)
bioconductor: DriverNet
Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancerPapers that mentioned: 41
Very Likely Science (100)
bioconductor: apeglm
Approximate posterior estimation for GLM coefficientsPapers that mentioned: 41
Very Likely Science (98)
Very Likely Science (100)
bioconductor: OmicCircos
High-quality circular visualization of omics dataPapers that mentioned: 40
Very Likely Science (100)
bioconductor: SIMLR
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)Papers that mentioned: 40
Very Likely Science (65)
bioconductor: BioNet
Routines for the functional analysis of biological networksPapers that mentioned: 40
Very Likely Science (100)
Very Likely Science (95)
Very Likely Science (85)
Very Likely Science (100)
bioconductor: KEGGgraph
KEGGgraph: A graph approach to KEGG PATHWAY in R and BioconductorPapers that mentioned: 39
Very Likely Science (100)
Very Likely Science (100)
Very Likely Science (100)
Very Likely Science (100)
bioconductor: AgiMicroRna
Processing and Differential Expression Analysis of Agilent microRNA chipsPapers that mentioned: 37
Very Likely Science (100)
Very Likely Science (90)
Very Likely Science (100)
bioconductor: affycoretools
Functions useful for those doing repetitive analyses with Affymetrix GeneChipsPapers that mentioned: 36
Very Likely Science (98)
Very Likely Science (100)
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Very Likely Science (75)
Very Likely Science (100)
bioconductor: PING
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read DataPapers that mentioned: 36
Very Likely Science (90)
Very Likely Science (100)
bioconductor: HTSFilter
Filter replicated high-throughput transcriptome sequencing dataPapers that mentioned: 35
Very Likely Science (75)
bioconductor: TargetSearch
A package for the analysis of GC-MS metabolite profiling dataPapers that mentioned: 34
Very Likely Science (100)
bioconductor: scmap
A tool for unsupervised projection of single cell RNA-seq dataPapers that mentioned: 34
Very Likely Science (100)
bioconductor: GeneAnswers
Papers that mentioned: 33
Unlikely Science (0)