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Papers: 10.1038/s41598-020-66998-4

https://doi.org/10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data

Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Published: about 5 years ago

Software Mentions 9

bioconductor: DESeq2
Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583
Very Likely Science (100)
bioconductor: DiffBind
Differential Binding Analysis of ChIP-Seq Peak Data
Papers that mentioned: 217
Very Likely Science (100)
bioconductor: edgeR
Empirical Analysis of Digital Gene Expression Data in R
Papers that mentioned: 6,568
Very Likely Science (100)
bioconductor: limma
Linear Models for Microarray Data
Papers that mentioned: 7,776
Very Likely Science (78)
bioconductor: RUVSeq
Remove Unwanted Variation from RNA-Seq Data
Papers that mentioned: 91
Very Likely Science (100)
cran: ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
Papers that mentioned: 11,441
Very Likely Science (100)
cran: STAR
Spike Train Analysis with R
Papers that mentioned: 5,759
Very Likely Science (100)
pypi: cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Papers that mentioned: 1,562
Very Likely Science (100)
pypi: MACS2
Model Based Analysis for ChIP-Seq data
Papers that mentioned: 1,203
Very Likely Science (100)