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