Table 1 Comparison of ggcoverage to other visualization tools
From: ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
ggcoverage | ggbio | Gviz | GenVisR | karyoploteR | UCSC | IGV | |
|---|---|---|---|---|---|---|---|
Platform | R | R | R | R | R | Web | Application |
Data transmission | ✓ | ✓ | |||||
Input file formats | |||||||
BAM | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
BigWig | ✓ | ✓ | ✓ | ✓ | ✓ | ||
BedGraph | ✓ | ✓ | ✓ | ✓ | |||
TSV/Excel | ✓ | ✓ | |||||
Sample group | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Preprocessing | |||||||
Normalize reads | ✓ | ||||||
Consensus peak | ✓ | ||||||
Track loading (region subset) | ✓ | ✓ | ✓ | ✓ | |||
Protein coverage | ✓ | ||||||
Annotations | |||||||
GC content | ✓ | ✓ | ✓ | ✓ | ✓ | * | |
Base | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Base frequency | ✓ | ✓ | ✓ | ||||
Amino acid | ✓ | ✓ | ✓ | ||||
CNV | ✓ | ✓ | |||||
Gene | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Transcript | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ |
Peak | ✓ | ✓ | ✓ | ✓ | |||
Ideogram | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | |
Contact map | ✓ | ||||||
Link | ✓ | ✓ | |||||
Feature | ✓ | ||||||
Superimpose annotations (‘+’) | ✓ | ✓ | |||||
Customize figure (ggplot2) | ✓ | ✓ | |||||