https://github.com/sgibb/cleaver

Cleavage of polypeptide sequences
https://github.com/sgibb/cleaver

bioc cleavage digest peptides r

Last synced: 2 months ago
JSON representation

Cleavage of polypeptide sequences

• Host: GitHub
• URL: https://github.com/sgibb/cleaver
• Owner: sgibb
• Created: 2013-04-07T17:27:23.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2024-04-24T08:18:09.000Z (8 months ago)
• Last Synced: 2024-09-30T03:55:19.641Z (3 months ago)
• Topics: bioc, cleavage, digest, peptides, r
• Language: R
• Homepage: http://sgibb.github.io/cleaver/
• Size: 354 KB
• Stars: 12
• Watchers: 3
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# cleaver

[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![build status](https://github.com/sgibb/cleaver/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sgibb/cleaver/actions)

[![codecov.io](https://img.shields.io/codecov/c/github/sgibb/cleaver.svg?branch=master)](https://codecov.io/github/sgibb/cleaver/?branch=master)

[![license](https://img.shields.io/badge/license-GPL%20%28%3E=%203%29-brightgreen.svg?style=flat)](https://www.gnu.org/licenses/gpl-3.0.html)

[![years in bioc](https://bioconductor.org/shields/years-in-bioc/cleaver.svg)](https://bioconductor.org/packages/release/bioc/html/cleaver.html)

[![Ranking by downloads](http://bioconductor.org/shields/downloads/release/cleaver.svg)](https://bioconductor.org/packages/stats/bioc/cleaver/)

Release: [![build release](https://bioconductor.org/shields/build/release/bioc/cleaver.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/cleaver/)

Devel: [![build devel](https://bioconductor.org/shields/build/devel/bioc/cleaver.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/cleaver/)

## Description

This package cleaves polypeptide sequences. The

cleavage rules are taken from:

https://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html

cleaver is part of [Bioconductor](https://bioconductor.org/packages/release/bioc/html/cleaver.html).

## Install development version (not recommended)

```r

install.packages("devtools")

library("devtools")

install_github("sgibb/cleaver")

```

## Usage

```r

## load library

library("cleaver")

## Gastric juice peptide 1 (UniProtKB/Swiss-Prot: GAJU_HUMAN/P01358)

gaju <- "LAAGKVEDSD"

cleave(gaju, "trypsin")

# $LAAGKVEDSD

# [1] "LAAGK" "VEDSD"

cleave(gaju, "trypsin", missedCleavages=1)

# $LAAGKVEDSD

# [1] "LAAGKVEDSD"

cleave(gaju, "trypsin", missedCleavages=0:1)

# $LAAGKVEDSD

# [1] "LAAGK" "VEDSD" "LAAGKVEDSD"

cleave(gaju, "pepsin")

# $LAAGKVEDSD

# [1] "LAAGKVEDSD"

# (no cleavage)

```