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: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics dataPapers that mentioned: 2,223
bioconductor: ArrayExpress
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSetPapers that mentioned: 1,962
bioconductor: phyloseq
Handling and analysis of high-throughput microbiome census dataPapers that mentioned: 1,702
bioconductor: GSVA
Gene Set Variation Analysis for microarray and RNA-seq dataPapers that mentioned: 893
bioconductor: DEGseq
Identify Differentially Expressed Genes from RNA-seq dataPapers that mentioned: 697
bioconductor: COMPASS
Combinatorial Polyfunctionality Analysis of Single CellsPapers that mentioned: 614
bioconductor: RTCA
Open-source toolkit to analyse data from xCELLigence System (RTCA)Papers that mentioned: 516
bioconductor: ACE
Absolute Copy Number Estimation from Low-coverage Whole Genome SequencingPapers that mentioned: 478
bioconductor: ggtree
an R package for visualization of tree and annotation dataPapers that mentioned: 474
bioconductor: CAMERA
Collection of annotation related methods for mass spectrometry dataPapers that mentioned: 429
bioconductor: DECIPHER
Tools for curating, analyzing, and manipulating biological sequencesPapers that mentioned: 415
bioconductor: tximport
Import and summarize transcript-level estimates for transcript- and gene-level analysisPapers that mentioned: 367
bioconductor: Rsubread
Mapping, quantification and variant analysis of sequencing dataPapers that mentioned: 331
bioconductor: GenomicRanges
Representation and manipulation of genomic intervalsPapers that mentioned: 323
bioconductor: NOISeq
Exploratory analysis and differential expression for RNA-seq dataPapers that mentioned: 321
bioconductor: GEM
GEM: fast association study for the interplay of Gene, Environment and MethylationPapers that mentioned: 317
bioconductor: TCGAbiolinks
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC dataPapers that mentioned: 276
bioconductor: dada2
Accurate, high-resolution sample inference from amplicon sequencing dataPapers that mentioned: 274
bioconductor: EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq dataPapers that mentioned: 261
bioconductor: GPA
GPA (Genetic analysis incorporating Pleiotropy and Annotation)Papers that mentioned: 260
bioconductor: GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatednessPapers that mentioned: 243
bioconductor: lumi
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysPapers that mentioned: 238
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataPapers that mentioned: 217
bioconductor: RankProd
Rank Product method for identifying differentially expressed genes with application in meta-analysisPapers that mentioned: 213
bioconductor: ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICPapers that mentioned: 208
bioconductor: SNPRelate
Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP DataPapers that mentioned: 204
bioconductor: arrayQualityMetrics
Quality metrics report for microarray data setsPapers that mentioned: 190
bioconductor: DART
Denoising Algorithm based on Relevance network TopologyPapers that mentioned: 182
bioconductor: FlowSOM
Using self-organizing maps for visualization and interpretation of cytometry dataPapers that mentioned: 177
bioconductor: metagenomeSeq
Statistical analysis for sparse high-throughput sequencingPapers that mentioned: 169
bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationPapers that mentioned: 161
bioconductor: SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbationsPapers that mentioned: 155
bioconductor: methylKit
DNA methylation analysis from high-throughput bisulfite sequencing resultsPapers that mentioned: 154
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesPapers that mentioned: 145
bioconductor: pathview
a tool set for pathway based data integration and visualizationPapers that mentioned: 144
bioconductor: genefilter
genefilter: methods for filtering genes from high-throughput experimentsPapers that mentioned: 142
bioconductor: baySeq
Empirical Bayesian analysis of patterns of differential expression in count dataPapers that mentioned: 139
bioconductor: LEA
LEA: an R package for Landscape and Ecological Association StudiesPapers that mentioned: 139
bioconductor: Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file importPapers that mentioned: 138
bioconductor: ALDEx2
Analysis Of Differential Abundance Taking Sample and Scale Variation Into AccountPapers that mentioned: 136
bioconductor: Gviz
Plotting data and annotation information along genomic coordinatesPapers that mentioned: 134
bioconductor: GenomicAlignments
Representation and manipulation of short genomic alignmentsPapers that mentioned: 134
bioconductor: DMRcate
Methylation array and sequencing spatial analysis methodsPapers that mentioned: 132
bioconductor: goseq
Gene Ontology analyser for RNA-seq and other length biased dataPapers that mentioned: 132
bioconductor: EnhancedVolcano
Publication-ready volcano plots with enhanced colouring and labelingPapers that mentioned: 123
bioconductor: maSigPro
Significant Gene Expression Profile Differences in Time Course Gene Expression DataPapers that mentioned: 119
bioconductor: survcomp
Performance Assessment and Comparison for Survival AnalysisPapers that mentioned: 117
bioconductor: MSstats
Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics ExperimentsPapers that mentioned: 115
bioconductor: PROMISE
PRojection Onto the Most Interesting Statistical EvidencePapers that mentioned: 111
bioconductor: flowCore
flowCore: Basic structures for flow cytometry dataPapers that mentioned: 109