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

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: almost 5 years ago

Software Mentions 21

bioconductor: ATACseqQC
ATAC-seq Quality Control
Papers that mentioned: 14
bioconductor: ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Papers that mentioned: 145
bioconductor: ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Papers that mentioned: 161
bioconductor: chromVAR
Chromatin Variation Across Regions
Papers that mentioned: 46
bioconductor: csaw
ChIP-Seq Analysis with Windows
Papers that mentioned: 29
bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
bioconductor: esATAC
An Easy-to-use Systematic pipeline for ATACseq data analysis
Papers that mentioned: 4
bioconductor: MAST
Model-based Analysis of Single Cell Transcriptomics
Papers that mentioned: 668
bioconductor: motifmatchr
Fast Motif Matching in R
Papers that mentioned: 5
bioconductor: PICS
Probabilistic inference of ChIP-seq
Papers that mentioned: 73
bioconductor: TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
Papers that mentioned: 33
cran: JASPAR
R modules for JASPAR databases: a collection of transcription factor DNA-binding preferences, modeled as matrices
Papers that mentioned: 1,283
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
pypi: DAStk
Differential ATAC-seq toolkit
Papers that mentioned: 4
pypi: DeFCoM
A supervised learning genomic footprinter
Papers that mentioned: 3
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203
pypi: MAST
MAterials Simulation Toolkit
Papers that mentioned: 668
pypi: NucleoATAC
python package for calling nucleosomes with ATAC-Seq
Papers that mentioned: 17
pypi: PePr
Peak-calling and Prioritization pipeline for replicated ChIP-Seq data
Papers that mentioned: 18