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: ALPS
Papers that mentioned: 18bioconductor: coMET
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patternsPapers that mentioned: 18
bioconductor: SeqGSEA
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicingPapers that mentioned: 18
bioconductor: HMMcopy
Copy number prediction with correction for GC and mappability bias for HTS dataPapers that mentioned: 18
bioconductor: RTN
RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulonsPapers that mentioned: 17
bioconductor: tilingArray
Transcript mapping with high-density oligonucleotide tiling arraysPapers that mentioned: 17
bioconductor: easyRNASeq
Count summarization and normalization for RNA-Seq dataPapers that mentioned: 17
bioconductor: DRIMSeq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seqPapers that mentioned: 17
bioconductor: genomation
Summary, annotation and visualization of genomic dataPapers that mentioned: 17
bioconductor: MotifDb
An Annotated Collection of Protein-DNA Binding Sequence MotifsPapers that mentioned: 17
bioconductor: snapCGH
Segmentation, normalisation and processing of aCGH dataPapers that mentioned: 16
bioconductor: AneuFinder
Analysis of Copy Number Variation in Single-Cell-Sequencing DataPapers that mentioned: 16
bioconductor: SLqPCR
Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbHPapers that mentioned: 16
bioconductor: scDD
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributionsPapers that mentioned: 16
bioconductor: MultiAssayExperiment
Software for the integration of multi-omics experiments in BioconductorPapers that mentioned: 16
bioconductor: IsoformSwitchAnalyzeR
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq dataPapers that mentioned: 16
bioconductor: DEsingle
DEsingle for detecting three types of differential expression in single-cell RNA-seq dataPapers that mentioned: 15
bioconductor: MetNet
Inferring metabolic networks from untargeted high-resolution mass spectrometry dataPapers that mentioned: 15
bioconductor: flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.Papers that mentioned: 15
bioconductor: RCM
Fit row-column association models with the negative binomial distribution for the microbiomePapers that mentioned: 15
bioconductor: annotatr
Annotation of Genomic Regions to Genomic AnnotationsPapers that mentioned: 15
bioconductor: VariantTools
Tools for Exploratory Analysis of Variant CallsPapers that mentioned: 15
bioconductor: trackViewer
A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics dataPapers that mentioned: 14
bioconductor: BAC
Papers that mentioned: 14bioconductor: RBM
RBM: a R package for microarray and RNA-Seq data analysisPapers that mentioned: 14
bioconductor: DropletUtils
Utilities for Handling Single-Cell Droplet DataPapers that mentioned: 14
bioconductor: puma
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)Papers that mentioned: 14
bioconductor: GlobalAncova
Global test for groups of variables via model comparisonsPapers that mentioned: 14
bioconductor: SGSeq
Splice event prediction and quantification from RNA-seq dataPapers that mentioned: 14
bioconductor: ViSEAGO
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarityPapers that mentioned: 14
bioconductor: iSeq
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising ModelsPapers that mentioned: 14
bioconductor: Chicago
CHiCAGO: Capture Hi-C Analysis of Genomic OrganizationPapers that mentioned: 13
bioconductor: PathNet
An R package for pathway analysis using topological informationPapers that mentioned: 13
bioconductor: GARS
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasetsPapers that mentioned: 13
bioconductor: miRNApath
miRNApath: Pathway Enrichment for miRNA Expression DataPapers that mentioned: 13
bioconductor: motifbreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding SitesPapers that mentioned: 13
bioconductor: copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.Papers that mentioned: 13
bioconductor: Rcpi
Molecular Informatics Toolkit for Compound-Protein Interaction in Drug DiscoveryPapers that mentioned: 13
bioconductor: SpidermiR
SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA dataPapers that mentioned: 13
bioconductor: affycomp
Graphics Toolbox for Assessment of Affymetrix Expression MeasuresPapers that mentioned: 13
bioconductor: RSVSim
RSVSim: an R/Bioconductor package for the simulation of structural variationsPapers that mentioned: 13
bioconductor: iCARE
A Tool for Individualized Coherent Absolute Risk Estimation (iCARE)Papers that mentioned: 12
bioconductor: ensembldb
Utilities to create and use Ensembl-based annotation databasesPapers that mentioned: 12
bioconductor: pRoloc
A unifying bioinformatics framework for spatial proteomicsPapers that mentioned: 12
bioconductor: EnrichmentBrowser
Seamless navigation through combined results of set-based and network-based enrichment analysisPapers that mentioned: 12
bioconductor: OLIN
Optimized local intensity-dependent normalisation of two-color microarraysPapers that mentioned: 12
bioconductor: categoryCompare
Meta-analysis of high-throughput experiments using feature annotationsPapers that mentioned: 12