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: TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisPapers that mentioned: 33
bioconductor: Rgraphviz
Provides plotting capabilities for R graph objectsPapers that mentioned: 33
bioconductor: iClusterPlus
Integrative clustering of multi-type genomic dataPapers that mentioned: 32
bioconductor: MutationalPatterns
Comprehensive genome-wide analysis of mutational processesPapers that mentioned: 32
bioconductor: aCGH
Classes and functions for Array Comparative Genomic Hybridization dataPapers that mentioned: 32
bioconductor: treeio
Base Classes and Functions for Phylogenetic Tree Input and OutputPapers that mentioned: 32
bioconductor: QDNAseq
Quantitative DNA Sequencing for Chromosomal AberrationsPapers that mentioned: 31
bioconductor: graphite
GRAPH Interaction from pathway Topological EnvironmentPapers that mentioned: 30
bioconductor: BiocParallel
Bioconductor facilities for parallel evaluationPapers that mentioned: 30
bioconductor: globaltest
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set TestingPapers that mentioned: 30
bioconductor: regioneR
Association analysis of genomic regions based on permutation testsPapers that mentioned: 30
bioconductor: BitSeq
Papers that mentioned: 28bioconductor: MethylAid
Visual and interactive quality control of large Illumina DNA Methylation array data setsPapers that mentioned: 28
bioconductor: MODA
MODA: MOdule Differential Analysis for weighted gene co-expression networkPapers that mentioned: 28
bioconductor: CopywriteR
Copy number information from targeted sequencing using off-target readsPapers that mentioned: 28
bioconductor: systemPipeR
systemPipeR: workflow management and report generation environmentPapers that mentioned: 27
bioconductor: ENmix
Quality control and analysis tools for Illumina DNA methylation BeadChipPapers that mentioned: 27
bioconductor: HEM
Heterogeneous error model for identification of differentially expressed genes under multiple conditionsPapers that mentioned: 27
bioconductor: CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome miningPapers that mentioned: 27
bioconductor: QUBIC
An R package for qualitative biclustering in support of gene co-expression analysesPapers that mentioned: 26
bioconductor: EBarrays
Unified Approach for Simultaneous Gene Clustering and Differential Expression IdentificationPapers that mentioned: 26
bioconductor: pcaExplorer
Interactive Visualization of RNA-seq Data Using a Principal Components ApproachPapers that mentioned: 26
bioconductor: deepSNV
Detection of subclonal SNVs in deep sequencing data.Papers that mentioned: 26
bioconductor: CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation dataPapers that mentioned: 25
bioconductor: cellHTS2
Analysis of cell-based screens - revised version of cellHTSPapers that mentioned: 25
bioconductor: conumee
Enhanced copy-number variation analysis using Illumina DNA methylation arraysPapers that mentioned: 25
bioconductor: variancePartition
Quantify and interpret drivers of variation in multilevel gene expression experimentsPapers that mentioned: 25
bioconductor: MSnbase
Base Functions and Classes for Mass Spectrometry and ProteomicsPapers that mentioned: 24
bioconductor: gdsfmt
R Interface to CoreArray Genomic Data Structure (GDS) FilesPapers that mentioned: 23
bioconductor: dupRadar
Assessment of duplication rates in RNA-Seq datasetsPapers that mentioned: 23
bioconductor: DeconRNASeq
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq dataPapers that mentioned: 23
bioconductor: NanoStringDiff
Differential Expression Analysis of NanoString nCounter DataPapers that mentioned: 22
bioconductor: rbsurv
Robust likelihood-based survival modeling with microarray dataPapers that mentioned: 22
bioconductor: SISPA
SISPA: Method for Sample Integrated Set Profile AnalysisPapers that mentioned: 22
bioconductor: CancerSubtypes
Cancer subtypes identification, validation and visualization based on multiple genomic data setsPapers that mentioned: 22
bioconductor: ballgown
Flexible, isoform-level differential expression analysisPapers that mentioned: 21
bioconductor: M3Drop
Michaelis-Menten Modelling of Dropouts in single-cell RNASeqPapers that mentioned: 21
bioconductor: Pi
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway LevelPapers that mentioned: 21
bioconductor: RedeR
Interactive visualization and manipulation of nested networksPapers that mentioned: 21
bioconductor: HiTC
High Throughput Chromosome Conformation Capture analysisPapers that mentioned: 21
bioconductor: CNAnorm
A normalization method for Copy Number Aberration in cancer samplesPapers that mentioned: 21
bioconductor: CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses.Papers that mentioned: 21
bioconductor: IPO
Automated Optimization of XCMS Data Processing parametersPapers that mentioned: 20
bioconductor: MassSpecWavelet
Peak Detection for Mass Spectrometry data using wavelet-based algorithmsPapers that mentioned: 19
bioconductor: ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer MethylomesPapers that mentioned: 19
bioconductor: flowStats
Statistical methods for the analysis of flow cytometry dataPapers that mentioned: 19
bioconductor: Cardinal
A mass spectrometry imaging toolbox for statistical analysisPapers that mentioned: 19
bioconductor: PADOG
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)Papers that mentioned: 19
bioconductor: RPA
RPA: Robust Probabilistic Averaging for probe-level analysisPapers that mentioned: 19
bioconductor: Sushi
Papers that mentioned: 18bioconductor: CrispRVariants
Tools for counting and visualising mutations in a target locationPapers that mentioned: 18
bioconductor: CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systemsPapers that mentioned: 18
bioconductor: diffcyt
Differential discovery in high-dimensional cytometry via high-resolution clusteringPapers that mentioned: 18
bioconductor: shinyMethyl
Interactive visualization for Illumina methylation arraysPapers that mentioned: 18