Papers: 10.1186/s13059-020-1929-3
https://doi.org/10.1186/s13059-020-1929-3
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Published: over 5 years ago
Software Mentions 21
Very Likely Science (100)
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
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bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and VisualizationPapers that mentioned: 161
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bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distributionPapers that mentioned: 9,583
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bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak DataPapers that mentioned: 217
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bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in RPapers that mentioned: 6,568
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bioconductor: esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysisPapers that mentioned: 4
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bioconductor: TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) AnalysisPapers that mentioned: 33
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cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matricesPapers that mentioned: 1,283
Very Likely Science (75)
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing readsPapers that mentioned: 1,562
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pypi: PePr
Peak-calling and Prioritization pipeline for replicated ChIP-Seq dataPapers that mentioned: 18
Very Likely Science (100)