| Type: | Package |
| Title: | Gradient Boosting Algorithm for Predicting Methylation States |
| Version: | 0.1.0 |
| Author: | Dipro Sinha [aut, cre], Sunil Archak [aut], Dwijesh Chandra Mishra [aut], Tanwy Dasmandal [aut], Md Yeasin [aut] |
| Maintainer: | Dipro Sinha <diprosinha@gmail.com> |
| Description: | DNA methylation of 5-methylcytosine (5mC) is the result of a multi-step, enzyme-dependent process. Predicting these sites in-vitro is laborious, time consuming as well as costly. This ' Gb5mC-Pred ' package is an in-silico pipeline for predicting DNA sequences containing the 5mC sites. It uses a machine learning approach which uses Stochastic Gradient Boosting approach for prediction of the sequences with 5mC sites. This package has been developed by using the concept of Navarez and Roxas (2022) <doi:10.1109/TCBB.2021.3082184>. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.1 |
| Imports: | stats, devtools, tidyverse, seqinr, Biostrings, splitstackshape, entropy, party, stringr, tibble, doParallel, parallel, e1071, caret, randomForest, gbm, foreach, ftrCOOL, iterators |
| Suggests: | testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2023-07-10 17:22:06 UTC; YEASIN |
| Repository: | CRAN |
| Date/Publication: | 2023-07-11 15:40:05 UTC |
Pred5mc
Description
Prediction of sequences with 5mc sites.
Usage
Pred5mc(Fastafile)
Arguments
Fastafile |
Sequence file (.fasta format) |
Value
MethStatus: Sequences with their methylation state (methylated or non-methylated)
References
Chen, W., Lv, H., Nie, F., & Lin, H. (2019). i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome. Bioinformatics, 35(16), 2796-2800.
Examples
library(GB5mcPred)
data<-system.file("exdata/test.fasta", package = "GB5mcPred")
pred<-Pred5mc(Fastafile=data)