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: scPipe
Pipeline for single cell multi-omic data pre-processingPapers that mentioned: 7
bioconductor: riboSeqR
Analysis of sequencing data from ribosome profiling experimentsPapers that mentioned: 7
bioconductor: hopach
Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)Papers that mentioned: 7
bioconductor: customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics searchPapers that mentioned: 7
bioconductor: DaMiRseq
Data Mining for RNA-seq data: normalization, feature selection and classificationPapers that mentioned: 7
bioconductor: SwathXtend
SWATH extended library generation and statistical data analysisPapers that mentioned: 7
bioconductor: iChip
Bayesian Modeling of ChIP-chip Data Through Hidden Ising ModelsPapers that mentioned: 7
bioconductor: CNVrd2
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.Papers that mentioned: 7
bioconductor: RDRToolbox
A package for nonlinear dimension reduction with Isomap and LLE.Papers that mentioned: 7
bioconductor: DiffLogo
DiffLogo: A comparative visualisation of biooligomer motifsPapers that mentioned: 7
bioconductor: GenomeInfoDb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming stylePapers that mentioned: 7
bioconductor: r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)Papers that mentioned: 7
bioconductor: CGHnormaliter
Normalization of array CGH data with imbalanced aberrations.Papers that mentioned: 7
bioconductor: bigmelon
Illumina methylation array analysis for large experimentsPapers that mentioned: 7
bioconductor: flowCyBar
Analyze flow cytometric data using gate informationPapers that mentioned: 7
bioconductor: ArrayExpressHTS
ArrayExpress High Throughput Sequencing Processing PipelinePapers that mentioned: 7
bioconductor: CellBench
Construct Benchmarks for Single Cell Analysis MethodsPapers that mentioned: 7
bioconductor: FGNet
Functional Gene Networks derived from biological enrichment analysesPapers that mentioned: 7
bioconductor: AlphaBeta
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plantsPapers that mentioned: 7
bioconductor: ABSSeq
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differencesPapers that mentioned: 7
bioconductor: scds
In-Silico Annotation of Doublets for Single Cell RNA Sequencing DataPapers that mentioned: 7
bioconductor: CNVPanelizer
Reliable CNV detection in targeted sequencing applicationsPapers that mentioned: 7
bioconductor: exomeCopy
Copy number variant detection from exome sequencing read depthPapers that mentioned: 7
bioconductor: CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programmingPapers that mentioned: 7
bioconductor: ExpressionAtlas
Download datasets from EMBL-EBI Expression AtlasPapers that mentioned: 7
bioconductor: SingleCellSignalR
Cell Signalling Using Single Cell RNAseq Data AnalysisPapers that mentioned: 7
bioconductor: OCplus
Operating characteristics plus sample size and local fdr for microarray experimentsPapers that mentioned: 6
bioconductor: NPARC
Non-parametric analysis of response curves for thermal proteome profiling experimentsPapers that mentioned: 6
bioconductor: DMRforPairs
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profilesPapers that mentioned: 6
bioconductor: RVS
Computes estimates of the probability of related individuals sharing a rare variantPapers that mentioned: 6
bioconductor: splatter
Simple Simulation of Single-cell RNA Sequencing DataPapers that mentioned: 6
bioconductor: IsoCorrectoR
Correction for natural isotope abundance and tracer purity in MS and MS/MS data from stable isotope labeling experimentsPapers that mentioned: 6
bioconductor: BrainStars
Papers that mentioned: 6bioconductor: INSPEcT
Modeling RNA synthesis, processing and degradation with RNA-seq dataPapers that mentioned: 6
bioconductor: DelayedArray
A unified framework for working transparently with on-disk and in-memory array-like datasetsPapers that mentioned: 6
bioconductor: InteractionSet
Base Classes for Storing Genomic Interaction DataPapers that mentioned: 6
bioconductor: autonomics
Generifying and intuifying cross-platform omics analysisPapers that mentioned: 6
bioconductor: cydar
Using Mass Cytometry for Differential Abundance AnalysesPapers that mentioned: 6
bioconductor: CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using BioconductorPapers that mentioned: 6
bioconductor: drawProteins
Package to Draw Protein Schematics from Uniprot API outputPapers that mentioned: 6
bioconductor: coRdon
Codon Usage Analysis and Prediction of Gene ExpressivityPapers that mentioned: 6
bioconductor: qPLEXanalyzer
Tools for quantitative proteomics data analysisPapers that mentioned: 6
bioconductor: crlmm
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arraysPapers that mentioned: 6
bioconductor: synergyfinder
Calculate and Visualize Synergy Scores for Drug CombinationsPapers that mentioned: 6
bioconductor: stageR
stageR: stage-wise analysis of high throughput gene expression data in RPapers that mentioned: 6
bioconductor: miRNAmeConverter
Convert miRNA Names to Different miRBase VersionsPapers that mentioned: 6
bioconductor: MEB
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq dataPapers that mentioned: 6
bioconductor: derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approachPapers that mentioned: 6
bioconductor: SIAMCAT
Statistical Inference of Associations between Microbial Communities And host phenoTypesPapers that mentioned: 6
bioconductor: flowTrans
Parameter Optimization for Flow Cytometry Data TransformationPapers that mentioned: 6
bioconductor: phenoTest
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.Papers that mentioned: 6
bioconductor: FitHiC
Confidence estimation for intra-chromosomal contact mapsPapers that mentioned: 6
bioconductor: seqTools
Analysis of nucleotide, sequence and quality content on fastq filesPapers that mentioned: 6
bioconductor: BCRANK
Predicting binding site consensus from ranked DNA sequencesPapers that mentioned: 6
bioconductor: AffyRNADegradation
Analyze and correct probe positional bias in microarray data due to RNA degradationPapers that mentioned: 6
bioconductor: countsimQC
Compare Characteristic Features of Count Data SetsPapers that mentioned: 6
bioconductor: tspair
Papers that mentioned: 6bioconductor: tradeSeq
trajectory-based differential expression analysis for sequencing dataPapers that mentioned: 6
bioconductor: TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumoursPapers that mentioned: 5
bioconductor: switchde
Switch-like differential expression across single-cell trajectoriesPapers that mentioned: 5