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: BiocOncoTK
Bioconductor components for general cancer genomicsPapers that mentioned: 2
bioconductor: BiocParallel
Bioconductor facilities for parallel evaluationPapers that mentioned: 30
bioconductor: BiocPkgTools
Collection of simple tools for learning about Bioconductor PackagesPapers that mentioned: 1
bioconductor: BiocSingular
Singular Value Decomposition for Bioconductor PackagesPapers that mentioned: 2
bioconductor: BiocStyle
Standard styles for vignettes and other Bioconductor documentsPapers that mentioned: 1
bioconductor: BiocVersion
Set the appropriate version of Bioconductor packagesPapers that mentioned: 1
bioconductor: BiocWorkflowTools
Tools to aid the development of Bioconductor Workflow packagesPapers that mentioned: 2
bioconductor: biomvRCNS
Copy Number study and Segmentation for multivariate biological dataPapers that mentioned: 1
bioconductor: BioNet
Routines for the functional analysis of biological networksPapers that mentioned: 40
bioconductor: BioPlex
Papers that mentioned: 84bioconductor: BioQC
Detect tissue heterogeneity in expression profiles with gene setsPapers that mentioned: 7
bioconductor: biovizBase
Basic graphic utilities for visualization of genomic data.Papers that mentioned: 1
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: BitSeq
Papers that mentioned: 28bioconductor: BloodGen3Module
This R package for performing module repertoire analyses and generating fingerprint representationsPapers that mentioned: 2
bioconductor: bnbc
Bandwise normalization and batch correction of Hi-C dataPapers that mentioned: 1
bioconductor: BRAIN
Baffling Recursive Algorithm for Isotope distributioN calculationsPapers that mentioned: 10
bioconductor: BrainStars
Papers that mentioned: 6bioconductor: BridgeDbR
Code for using BridgeDb identifier mapping framework from within RPapers that mentioned: 4
bioconductor: BSgenome
Software infrastructure for efficient representation of full genomes and their SNPsPapers that mentioned: 47
bioconductor: BubbleTree
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing dataPapers that mentioned: 3
bioconductor: BufferedMatrix
A matrix data storage object held in temporary filesPapers that mentioned: 1
bioconductor: BufferedMatrixMethods
Microarray Data related methods that utlize BufferedMatrix objectsPapers that mentioned: 3
bioconductor: BUMHMM
Computational pipeline for computing probability of modification from structure probing experiment dataPapers that mentioned: 1
bioconductor: CAEN
Category encoding method for selecting feature genes for the classification of single-cell RNA-seqPapers that mentioned: 4
bioconductor: CAGEfightR
Analysis of Cap Analysis of Gene Expression (CAGE) data using BioconductorPapers that mentioned: 6
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: CAMERA
Collection of annotation related methods for mass spectrometry dataPapers that mentioned: 429
bioconductor: cancerclass
Development and validation of diagnostic tests from high-dimensional molecular dataPapers that mentioned: 1
bioconductor: CancerInSilico
An R interface for computational modeling of tumor progressionPapers that mentioned: 1
bioconductor: CancerSubtypes
Cancer subtypes identification, validation and visualization based on multiple genomic data setsPapers that mentioned: 22
bioconductor: caOmicsV
Papers that mentioned: 3bioconductor: Cardinal
A mass spectrometry imaging toolbox for statistical analysisPapers that mentioned: 19
bioconductor: CARNIVAL
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programmingPapers that mentioned: 7
bioconductor: casper
Characterization of Alternative Splicing based on Paired-End ReadsPapers that mentioned: 4
bioconductor: categoryCompare
Meta-analysis of high-throughput experiments using feature annotationsPapers that mentioned: 12
bioconductor: cBioPortalData
Exposes and makes available data from the cBioPortal web resourcesPapers that mentioned: 1
bioconductor: CellBench
Construct Benchmarks for Single Cell Analysis MethodsPapers that mentioned: 7
bioconductor: cellHTS2
Analysis of cell-based screens - revised version of cellHTSPapers that mentioned: 25
bioconductor: CellMapper
Predict genes expressed selectively in specific cell typesPapers that mentioned: 3
bioconductor: CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation dataPapers that mentioned: 25
bioconductor: cellscape
Explores single cell copy number profiles in the context of a single cell treePapers that mentioned: 1
bioconductor: CellScore
Tool for Evaluation of Cell Identity from Transcription ProfilesPapers that mentioned: 1
bioconductor: CellTrails
Reconstruction, visualization and analysis of branching trajectoriesPapers that mentioned: 1
bioconductor: cellTree
Papers that mentioned: 4bioconductor: Cepo
Cepo for the identification of differentially stable genesPapers that mentioned: 1
bioconductor: ceRNAnetsim
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)Papers that mentioned: 1
bioconductor: CeTF
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysisPapers that mentioned: 2
bioconductor: CexoR
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicatesPapers that mentioned: 1
bioconductor: CGEN
An R package for analysis of case-control studies in genetic epidemiologyPapers that mentioned: 2
bioconductor: CGHbase
CGHbase: Base functions and classes for arrayCGH data analysis.Papers that mentioned: 2
bioconductor: CGHnormaliter
Normalization of array CGH data with imbalanced aberrations.Papers that mentioned: 7
bioconductor: CGHregions
Dimension Reduction for Array CGH Data with Minimal Information Loss.Papers that mentioned: 4
bioconductor: ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPICPapers that mentioned: 208
bioconductor: ChemmineOB
R interface to a subset of OpenBabel functionalitiesPapers that mentioned: 4
bioconductor: Chicago
CHiCAGO: Capture Hi-C Analysis of Genomic OrganizationPapers that mentioned: 13
bioconductor: ChIPanalyser
ChIPanalyser: Predicting Transcription Factor Binding SitesPapers that mentioned: 1
bioconductor: ChIPComp
Quantitative comparison of multiple ChIP-seq datasetsPapers that mentioned: 3
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome rangesPapers that mentioned: 145
bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationPapers that mentioned: 161
bioconductor: ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing DataPapers that mentioned: 5