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: 10.1186/s13059-020-1929-3
https://doi.org/10.1186/s13059-020-1929-3
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Published: over 4 years ago
Software Mentions 21
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: 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: esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysisPapers that mentioned: 4
bioconductor: TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisPapers that mentioned: 33
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matricesPapers that mentioned: 1,283
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing readsPapers that mentioned: 1,562
pypi: PePr
Peak-calling and Prioritization pipeline for replicated ChIP-Seq dataPapers that mentioned: 18