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LowMACA

This package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see LowMACA.

LowMACA - Low frequency Mutation Analysis via Consensus Alignment


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("LowMACA")):

Installation

To install this package, start R (version "4.3") 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

Reference Manual PDF

Details

biocViews Alignment, DataImport, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software, SomaticMutation, WholeGenome
Version 1.31.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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
System Requirements clustalo, gs, perl
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64) LowMACA_1.31.0.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/
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