DNAModAnnot is a R package providing a comprehensive toolkit for the genome-wide analysis and annotation of DNA modifications (Mod) (e.g. 6-methyladenine (6mA) or 5-methylcytosine (5mC)). Its modular architecture allows the analysis of Mod detection performed using Pacific Biosciences (PacBio) kineticsTools or Oxford Nanopore Technologies via DeepSignal software. DNAModAnnot also provides customized visualization functions to describe DNA modification patterns.
Functions from the following modules can be combined according to the upper diagram.
ImportPacBioCSV
or ImportDeepSignalModFrequency
can be used to import input files and convert them as GRanges-like objects.GetModReportPacBio
or DrawModLogo
will allow a global view of DNA Mod and its parameters at the genome-wide level or per contig.FiltPacBio
and FiltDeepSignal
can be used to filter respectively PacBio and DeepSignal data within R. Data can be filtered based on the contigs or FDR-associated filtering thresholds.As input, DNAModAnnot will need:
Some functions from the DNAModAnnot package will require additional input:
Additional files, such as other sequencing files, can be imported and compared with DNA modifications distribution: these files must be converted as GRanges objects after importation. This can be achieved using the Rsamtools package or the rtracklayer package: then GRanges-like objects (such as GPos, GAlignments...) must be converted as GRanges.
R (>= 4.0.0)
Packages:
Biostrings (>= 2.10.0), GenomicRanges (>= 1.38.0), BSgenome (>= 1.28.0), Biobase (> 2.1.0),
BiocGenerics (>= 0.34.0), GenomeInfoDb (>= 1.14.0), Gviz (>= 1.29.1), IRanges (>= 2.20.0),
seqLogo (>= 1.56.0), grid (>= 4.0.2),
S4Vectors (>= 0.24.0), data.table (>= 1.13.0), rtracklayer (>= 1.30.0), Rsamtools (>= 2.0.0)
First, install required packages using BiocManager:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c('Biostrings', 'BSgenome', 'Gviz', 'seqLogo'))
Next, you can directly install from GitHub using devtools package:
install.packages("devtools")
library(devtools)
install_github("AlexisHardy/DNAModAnnot")
You should then be able to load the package into your R session with:
library(DNAModAnnot)
You can also install DNAModAnnot using the tar.gz file from the GitHub repository once all required dependencies have been installed:
setwd("path/to/package/file/")
install.packages("DNAModAnnot_0.0.0.9019.tar.gz", repos = NULL, type = 'source')
You can retrieve old versions of DNAModAnnot using other branches of this repository.
The NEWS.txt file describes the changes for each version.
For detailed instructions, check the package vignette (in 'doc' directory).
Hardy, A., Matelot, M., Touzeau, A., Klopp, C., Lopez-Roques, C., Duharcourt, S., & Defrance, M. (2021). DNAModAnnot: a R toolbox for DNA modification filtering and annotation. Bioinformatics.