LowMACA

DOI: 10.18129/B9.bioc.LowMACA  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see LowMACA.

LowMACA - Low frequency Mutation Analysis via Consensus Alignment

Bioconductor version: 3.16

The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.

Author: Giorgio Melloni , Stefano de Pretis

Maintainer: Giorgio Melloni <melloni.giorgio at gmail.com> , Stefano de Pretis <ste.depo at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("LowMACA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("LowMACA")

 

HTML	R Script	Bioconductor style for HTML documents
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	Alignment, DataImport, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software, SomaticMutation, WholeGenome
Version	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	GPL-3
Depends	R (>= 2.10)
Imports	cBioPortalData, parallel, stringr, reshape2, data.table, RColorBrewer, methods, LowMACAAnnotation, BiocParallel, motifStack, Biostrings, httr, grid, gridBase, plyr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements	clustalo, gs, perl
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	LowMACA_1.28.0.tar.gz
Windows Binary	LowMACA_1.28.0.zip
macOS Binary (x86_64)	LowMACA_1.28.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/LowMACA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LowMACA
Bioc Package Browser	https://code.bioconductor.org/browse/LowMACA/
Package Short Url	https://bioconductor.org/packages/LowMACA/
Package Downloads Report	Download Stats