Explores and visualizes bisulfite sequencing (BS-seq) data. ViewBS has several top level commands which determine the required and optimal arguments. These commands can be divided into two parts: methylation report and data visualization of functional regions. For ViewBS, the first input that users should provide is the regions of interest. These regions could be functional elements, like genes, transposable elements (TE), or differentially methylated regions (DMR).

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ViewBS classification

ViewBS specifications

Software type:
Standalone
Restrictions to use:
None
Output data:
Graph and figures
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 3.0
Version:
0.1.0
Requirements:
htslib, Perl, Perl packages (Getopt Long Subcommand, BioDB HTS Tabix, BioSeqIO), R, R package (ggplot2, pheatmap, reshape2)
Interface:
Command line interface
Input data:
Genome-wide cytosine methylation report
Output format:
PDF
Programming languages:
Perl, R
Computer skills:
Advanced
Stability:
Beta

Credits

Investigator(s)

Shaojun Xie

Developer(s)

Xiaosan Huang, Shaojun Xie

Curator(s)

Shaojun Xie

Contributor(s)

Shaojun Xie

Institution(s)

Nanjing Agricultural University Purdue University

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