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.
Papers: 10.3389/fonc.2020.00423
https://doi.org/10.3389/fonc.2020.00423
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Published: about 4 years ago
Software Mentions 46
bioconductor: AMARETTO
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized RegressionPapers that mentioned: 5
bioconductor: CancerSubtypes
Cancer subtypes identification, validation and visualization based on multiple genomic data setsPapers that mentioned: 22
bioconductor: CODEX
A Normalization and Copy Number Variation Detection Method for Whole Exome SequencingPapers that mentioned: 72
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataPapers that mentioned: 217
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
bioconductor: epigenomix
Epigenetic and gene transcription data normalization and integration with mixture modelsPapers that mentioned: 1
bioconductor: esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysisPapers that mentioned: 4
bioconductor: GEM
GEM: fast association study for the interplay of Gene, Environment and MethylationPapers that mentioned: 317
bioconductor: GenomicInteractions
Utilities for handling genomic interaction dataPapers that mentioned: 10
bioconductor: Gviz
Plotting data and annotation information along genomic coordinatesPapers that mentioned: 134
bioconductor: iClusterPlus
Integrative clustering of multi-type genomic dataPapers that mentioned: 32
bioconductor: MultiAssayExperiment
Software for the integration of multi-omics experiments in BioconductorPapers that mentioned: 16
bioconductor: omicRexposome
Exposome and omic data associatin and integration analysisPapers that mentioned: 2
bioconductor: OMICsPCA
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samplesPapers that mentioned: 1
bioconductor: pathview
a tool set for pathway based data integration and visualizationPapers that mentioned: 144
bioconductor: pathwayPCA
Integrative Pathway Analysis with Modern PCA Methodology and Gene SelectionPapers that mentioned: 4
bioconductor: ropls
PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics dataPapers that mentioned: 81
bioconductor: STATegRa
Classes and methods for multi-omics data integrationPapers that mentioned: 7
pypi: PePr
Peak-calling and Prioritization pipeline for replicated ChIP-Seq dataPapers that mentioned: 18
pypi: SICER2
SICER2, a redesigned and improved ChIP-seq broad peak calling toolPapers that mentioned: 4