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: consensus
Cross-platform consensus analysis of genomic measurements via interlaboratory testing methodPapers that mentioned: 5
bioconductor: switchde
Switch-like differential expression across single-cell trajectoriesPapers that mentioned: 5
bioconductor: MetID
Network-based prioritization of putative metabolite IDsPapers that mentioned: 5
bioconductor: MethPed
A DNA methylation classifier tool for the identification of pediatric brain tumor subtypesPapers that mentioned: 5
bioconductor: LOBSTAHS
Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy SequencesPapers that mentioned: 5
bioconductor: Cogito
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data setsPapers that mentioned: 5
bioconductor: BiRewire
High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)Papers that mentioned: 5
bioconductor: GRridge
Better prediction by use of co-data: Adaptive group-regularized ridge regressionPapers that mentioned: 5
bioconductor: networkBMA
Papers that mentioned: 5bioconductor: ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing DataPapers that mentioned: 5
bioconductor: MSstatsTMT
Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labelingPapers that mentioned: 5
bioconductor: SpacePAC
Identification of Mutational Clusters in 3D Protein Space via Simulation.Papers that mentioned: 5
bioconductor: annmap
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.Papers that mentioned: 5
bioconductor: iCheck
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression DataPapers that mentioned: 5
bioconductor: EMDomics
Earth Mover's Distance for Differential Analysis of Genomics DataPapers that mentioned: 5
bioconductor: SpectralTAD
SpectralTAD: Hierarchical TAD detection using spectral clusteringPapers that mentioned: 5
bioconductor: RITAN
Rapid Integration of Term Annotation and Network resourcesPapers that mentioned: 5
bioconductor: funtooNorm
Normalization Procedure for Infinium HumanMethylation450 BeadChip KitPapers that mentioned: 5
bioconductor: pwrEWAS
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)Papers that mentioned: 5
bioconductor: TargetScore
TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence informationPapers that mentioned: 5
bioconductor: AMARETTO
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized RegressionPapers that mentioned: 5
bioconductor: rGREAT
GREAT Analysis - Functional Enrichment on Genomic RegionsPapers that mentioned: 5
bioconductor: pRolocGUI
Interactive visualisation of spatial proteomics dataPapers that mentioned: 5
bioconductor: altcdfenvs
alternative CDF environments (aka probeset mappings)Papers that mentioned: 5
bioconductor: segmentSeq
Methods for identifying small RNA loci from high-throughput sequencing dataPapers that mentioned: 5
bioconductor: GraphPAC
Identification of Mutational Clusters in Proteins via a Graph Theoretical Approach.Papers that mentioned: 5
bioconductor: EBcoexpress
EBcoexpress for Differential Co-Expression AnalysisPapers that mentioned: 5
bioconductor: DAPAR
Tools for the Differential Analysis of Proteins Abundance with RPapers that mentioned: 5
bioconductor: CRImage
CRImage a package to classify cells and calculate tumour cellularityPapers that mentioned: 5
bioconductor: sangeranalyseR
sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in RPapers that mentioned: 5
bioconductor: DeMixT
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platformsPapers that mentioned: 5
bioconductor: MAGeCKFlute
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic ScreensPapers that mentioned: 5
bioconductor: TitanCNA
Subclonal copy number and LOH prediction from whole genome sequencing of tumoursPapers that mentioned: 5
bioconductor: EventPointer
An effective identification of alternative splicing events using junction arrays and RNA-Seq dataPapers that mentioned: 5
bioconductor: iCOBRA
Comparison and Visualization of Ranking and Assignment MethodsPapers that mentioned: 5
bioconductor: UNDO
Unsupervised Deconvolution of Tumor-Stromal Mixed ExpressionsPapers that mentioned: 5
bioconductor: trio
Testing of SNPs and SNP Interactions in Case-Parent Trio StudiesPapers that mentioned: 4
bioconductor: TADCompare
TADCompare: Identification and characterization of differential TADsPapers that mentioned: 4
bioconductor: scAlign
Papers that mentioned: 4bioconductor: BridgeDbR
Code for using BridgeDb identifier mapping framework from within RPapers that mentioned: 4
bioconductor: timecourse
Statistical Analysis for Developmental Microarray Time Course DataPapers that mentioned: 4
bioconductor: SCATE
SCATE: Single-cell ATAC-seq Signal Extraction and EnhancementPapers that mentioned: 4
bioconductor: rTRM
Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction NetworksPapers that mentioned: 4
bioconductor: ChemmineOB
R interface to a subset of OpenBabel functionalitiesPapers that mentioned: 4
bioconductor: ABarray
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.Papers that mentioned: 4
bioconductor: XDE
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expressionPapers that mentioned: 4
bioconductor: ReactomeGSA
Client for the Reactome Analysis Service for comparative multi-omics gene set analysisPapers that mentioned: 4
bioconductor: RandomWalkRestartMH
Random walk with restart on multiplex and heterogeneous NetworksPapers that mentioned: 4
bioconductor: Melissa
Bayesian clustering and imputationa of single cell methylomesPapers that mentioned: 4
bioconductor: bacon
Controlling bias and inflation in association studies using the empirical null distributionPapers that mentioned: 4
bioconductor: BADER
Bayesian Analysis of Differential Expression in RNA Sequencing DataPapers that mentioned: 4
bioconductor: miRmine
Data package with miRNA-seq datasets from miRmine database as RangedSummarizedExperimentPapers that mentioned: 4
bioconductor: philr
Phylogenetic partitioning based ILR transform for metagenomics dataPapers that mentioned: 4
bioconductor: BiGGR
Constraint based modeling in R using metabolic reconstruction databasesPapers that mentioned: 4
bioconductor: pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene SelectionPapers that mentioned: 4
bioconductor: mBPCR
Bayesian Piecewise Constant Regression for DNA copy number estimationPapers that mentioned: 4
bioconductor: isobar
Analysis and quantitation of isobarically tagged MSMS proteomics dataPapers that mentioned: 4
bioconductor: CAEN
Category encoding method for selecting feature genes for the classification of single-cell RNA-seqPapers that mentioned: 4