Tag: ATAC-seq

PEPATAC v0.10.3 – Pipeline for ATAC-seq Data Processing

PEPATAC v0.10.3

:: DESCRIPTION

PEPATAC is a standardized ATAC-seq analysis pipeline designed to be modular and highly flexible.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • Python

:: DOWNLOAD

PEPATAC

:: MORE INFORMATION

Citation

Smith JP, Corces MR, Xu J, Reuter VP, Chang HY, Sheffield NC.
PEPATAC: an optimized pipeline for ATAC-seq data analysis with serial alignments.
NAR Genom Bioinform. 2021 Nov 23;3(4):lqab101. doi: 10.1093/nargab/lqab101. PMID: 34859208; PMCID: PMC8632735.

deNOPA – decoding Nucleosome Positions sensitively with Sparse ATAC-seq data

deNOPA

:: DESCRIPTION

deNOPA is a novel ATAC-seq analysis toolkit, to predict nucleosome positions.

::DEVELOPER

deNOPA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

deNOPA

:: MORE INFORMATION

Citation

Xu B, Li X, Gao X, Jia Y, Liu J, Li F, Zhang Z.
DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data.
Brief Bioinform. 2021 Dec 7:bbab469. doi: 10.1093/bib/bbab469. Epub ahead of print. PMID: 34875002.

SCATE – Single-cell ATAC-seq Signal Extraction and Enhancement

SCATE

:: DESCRIPTION

SCATE integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating individual CRE activities in single cell and rare cell subpopulations.

::DEVELOPER

Zhicheng Ji

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

SCATE

:: MORE INFORMATION

Citation

Ji Z, Zhou W, Hou W, Ji H.
Single-cell ATAC-seq signal extraction and enhancement with SCATE.
Genome Biol. 2020 Jul 3;21(1):161. doi: 10.1186/s13059-020-02075-3. PMID: 32620137; PMCID: PMC7333383.

ATACseqQC 1.14.4 – Quality Assessment of ATAC-seq data

ATACseqQC 1.14.4

:: DESCRIPTION

ATACseqQC is a Bioconductor package for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

ATACseqQC

:: MORE INFORMATION

Citation:

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ.
ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
BMC Genomics. 2018 Mar 1;19(1):169. doi: 10.1186/s12864-018-4559-3. PMID: 29490630; PMCID: PMC5831847.