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: infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq DataPapers that mentioned: 4
bioconductor: casper
Characterization of Alternative Splicing based on Paired-End ReadsPapers that mentioned: 4
bioconductor: cellTree
Papers that mentioned: 4bioconductor: plgem
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)Papers that mentioned: 4
bioconductor: HiCcompare
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasetsPapers that mentioned: 4
bioconductor: Pigengene
Infers biological signatures from gene expression dataPapers that mentioned: 4
bioconductor: CGHregions
Dimension Reduction for Array CGH Data with Minimal Information Loss.Papers that mentioned: 4
bioconductor: GOexpress
Visualise microarray and RNAseq data using gene ontology annotationsPapers that mentioned: 4
bioconductor: BgeeDB
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontologyPapers that mentioned: 4
bioconductor: clusterStab
Compute cluster stability scores for microarray dataPapers that mentioned: 4
bioconductor: iASeq
iASeq: integrating multiple sequencing datasets for detecting allele-specific eventsPapers that mentioned: 4
bioconductor: CytoML
A GatingML Interface for Cross Platform Cytometry Data SharingPapers that mentioned: 4
bioconductor: muscat
Multi-sample multi-group scRNA-seq data analysis toolsPapers that mentioned: 4
bioconductor: MSPrep
Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics DataPapers that mentioned: 4
bioconductor: sigFeature
sigFeature: Significant feature selection using SVM-RFE & t-statisticPapers that mentioned: 4
bioconductor: ddCt
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)Papers that mentioned: 4
bioconductor: flowUtils
Papers that mentioned: 4bioconductor: fmcsR
Mismatch Tolerant Maximum Common Substructure SearchingPapers that mentioned: 4
bioconductor: flowCL
Papers that mentioned: 4bioconductor: esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysisPapers that mentioned: 4
bioconductor: EBSeqHMM
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experimentsPapers that mentioned: 4
bioconductor: wavClusteR
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP dataPapers that mentioned: 4
bioconductor: aroma.light
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data TypesPapers that mentioned: 4
bioconductor: farms
FARMS - Factor Analysis for Robust Microarray SummarizationPapers that mentioned: 4
bioconductor: gwascat
representing and modeling data in the EMBL-EBI GWAS catalogPapers that mentioned: 4
bioconductor: CytoGLMM
Conditional Differential Analysis for Flow and Mass Cytometry ExperimentsPapers that mentioned: 4
bioconductor: ncdfFlow
ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.Papers that mentioned: 4
bioconductor: MetaboSignal
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathwaysPapers that mentioned: 4
bioconductor: NanoStringQCPro
Quality metrics and data processing methods for NanoString mRNA gene expression dataPapers that mentioned: 4
bioconductor: RareVariantVis
A suite for analysis of rare genomic variants in whole genome sequencing dataPapers that mentioned: 4
bioconductor: SPsimSeq
Semi-parametric simulation tool for bulk and single-cell RNA sequencing dataPapers that mentioned: 4
bioconductor: dStruct
Identifying differentially reactive regions from RNA structurome profiling dataPapers that mentioned: 3
bioconductor: cliqueMS
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics DataPapers that mentioned: 3
bioconductor: scRepertoire
A toolkit for single-cell immune receptor profilingPapers that mentioned: 3
bioconductor: erccdashboard
Assess Differential Gene Expression Experiments with ERCC ControlsPapers that mentioned: 3
bioconductor: heatmaps
Flexible Heatmaps for Functional Genomics and Sequence FeaturesPapers that mentioned: 3
bioconductor: doppelgangR
Identify likely duplicate samples from genomic or meta-dataPapers that mentioned: 3
bioconductor: msgbsR
msgbsR: methylation sensitive genotyping by sequencing (MS-GBS) R functionsPapers that mentioned: 3
bioconductor: CHRONOS
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysisPapers that mentioned: 3
bioconductor: oncomix
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression DataPapers that mentioned: 3
bioconductor: zFPKM
A suite of functions to facilitate zFPKM transformationsPapers that mentioned: 3
bioconductor: XVector
Foundation of external vector representation and manipulation in BioconductorPapers that mentioned: 3
bioconductor: MetaCyto
MetaCyto: A package for meta-analysis of cytometry dataPapers that mentioned: 3
bioconductor: MDTS
Detection of de novo deletion in targeted sequencing triosPapers that mentioned: 3
bioconductor: splineTimeR
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstructionPapers that mentioned: 3
bioconductor: ChIPXpress
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profilesPapers that mentioned: 3
bioconductor: ChIPComp
Quantitative comparison of multiple ChIP-seq datasetsPapers that mentioned: 3
bioconductor: INDEED
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection PackagePapers that mentioned: 3
bioconductor: MicrobiotaProcess
A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy frameworkPapers that mentioned: 3
bioconductor: quantsmooth
Quantile smoothing and genomic visualization of array dataPapers that mentioned: 3
bioconductor: ExiMiR
R functions for the normalization of Exiqon miRNA array dataPapers that mentioned: 3
bioconductor: iGC
An integrated analysis package of Gene expression and Copy number alterationPapers that mentioned: 3
bioconductor: CellMapper
Predict genes expressed selectively in specific cell typesPapers that mentioned: 3
bioconductor: tweeDEseq
RNA-seq data analysis using the Poisson-Tweedie family of distributionsPapers that mentioned: 3
bioconductor: oligoClasses
Classes for high-throughput arrays supported by oligo and crlmmPapers that mentioned: 3
bioconductor: dcanr
Differential co-expression/association network analysisPapers that mentioned: 3
bioconductor: inveRsion
Papers that mentioned: 3bioconductor: BufferedMatrixMethods
Microarray Data related methods that utlize BufferedMatrix objectsPapers that mentioned: 3
bioconductor: NTW
Predict gene network using an Ordinary Differential Equation (ODE) based methodPapers that mentioned: 3
bioconductor: mdp
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controlsPapers that mentioned: 3
bioconductor: BubbleTree
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing dataPapers that mentioned: 3