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: 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: chromDraw
chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.Papers that mentioned: 1
bioconductor: ChromSCape
Analysis of single-cell epigenomics datasets with a Shiny AppPapers that mentioned: 1
bioconductor: chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq DataPapers that mentioned: 3
bioconductor: chromswitch
An R package to detect chromatin state switches from epigenomic dataPapers that mentioned: 2
bioconductor: CHRONOS
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysisPapers that mentioned: 3
bioconductor: cicero
Predict cis-co-accessibility from single-cell chromatin accessibility dataPapers that mentioned: 2
bioconductor: circRNAprofiler
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAsPapers that mentioned: 2
bioconductor: cisPath
Visualization and management of the protein-protein interaction networks.Papers that mentioned: 1
bioconductor: ClassifyR
A framework for cross-validated classification problems, with applications to differential variability and differential distribution testingPapers that mentioned: 1
bioconductor: cleanUpdTSeq
cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending dataPapers that mentioned: 2
bioconductor: clippda
A package for the clinical proteomic profiling data analysisPapers that mentioned: 1
bioconductor: cliqueMS
Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics DataPapers that mentioned: 3
bioconductor: clonotypeR
Papers that mentioned: 1bioconductor: CluMSID
Clustering of MS2 Spectra for Metabolite IdentificationPapers that mentioned: 1
bioconductor: clusterExperiment
Compare Clusterings for Single-Cell SequencingPapers that mentioned: 8
bioconductor: ClusterJudge
Judging Quality of Clustering Methods using Mutual InformationPapers that mentioned: 1
bioconductor: clusterProfiler
A universal enrichment tool for interpreting omics dataPapers that mentioned: 2,223
bioconductor: ClusterSignificance
The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted dataPapers that mentioned: 2
bioconductor: clusterStab
Compute cluster stability scores for microarray dataPapers that mentioned: 4
bioconductor: clustifyr
Classifier for Single-cell RNA-seq Using Cell ClustersPapers that mentioned: 2
bioconductor: CNAnorm
A normalization method for Copy Number Aberration in cancer samplesPapers that mentioned: 21
bioconductor: cn.mops
cn.mops - Mixture of Poissons for CNV detection in NGS dataPapers that mentioned: 8
bioconductor: CNTools
Convert segment data into a region by sample matrix to allow for other high level computational analyses.Papers that mentioned: 21
bioconductor: CNVPanelizer
Reliable CNV detection in targeted sequencing applicationsPapers that mentioned: 7
bioconductor: CNVRanger
Summarization and expression/phenotype association of CNV rangesPapers that mentioned: 1
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: CODEX
A Normalization and Copy Number Variation Detection Method for Whole Exome SequencingPapers that mentioned: 72
bioconductor: Cogito
Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data setsPapers that mentioned: 5
bioconductor: COHCAP
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq DataPapers that mentioned: 11
bioconductor: coMET
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patternsPapers that mentioned: 18
bioconductor: compartmap
Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seqPapers that mentioned: 3
bioconductor: COMPASS
Combinatorial Polyfunctionality Analysis of Single CellsPapers that mentioned: 614
bioconductor: compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methodsPapers that mentioned: 11
bioconductor: consensus
Cross-platform consensus analysis of genomic measurements via interlaboratory testing methodPapers that mentioned: 5
bioconductor: contiBAIT
Improves Early Build Genome Assemblies using Strand-Seq DataPapers that mentioned: 2
bioconductor: conumee
Enhanced copy-number variation analysis using Illumina DNA methylation arraysPapers that mentioned: 25
bioconductor: copynumber
Segmentation of single- and multi-track copy number data by penalized least squares regression.Papers that mentioned: 13
bioconductor: CopywriteR
Copy number information from targeted sequencing using off-target readsPapers that mentioned: 28
bioconductor: coRdon
Codon Usage Analysis and Prediction of Gene ExpressivityPapers that mentioned: 6
bioconductor: CoRegNet
CoRegNet : reconstruction and integrated analysis of co-regulatory networksPapers that mentioned: 8
bioconductor: COSNet
Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelingsPapers that mentioned: 8
bioconductor: CountClust
Papers that mentioned: 5bioconductor: countsimQC
Compare Characteristic Features of Count Data SetsPapers that mentioned: 6
bioconductor: covEB
Empirical Bayes estimate of block diagonal covariance matricesPapers that mentioned: 1
bioconductor: CRImage
CRImage a package to classify cells and calculate tumour cellularityPapers that mentioned: 5
bioconductor: CRISPRseek
Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systemsPapers that mentioned: 18
bioconductor: CrispRVariants
Tools for counting and visualising mutations in a target locationPapers that mentioned: 18
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: cTRAP
Identification of candidate causal perturbations from differential gene expression dataPapers that mentioned: 1
bioconductor: cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.Papers that mentioned: 83
bioconductor: customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics searchPapers that mentioned: 7
bioconductor: cycle
Significance of periodic expression pattern in time-series dataPapers that mentioned: 2
bioconductor: cydar
Using Mass Cytometry for Differential Abundance AnalysesPapers that mentioned: 6