LowMACA: LowMACA - Low frequency Mutation Analysis via Consensus Alignment

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
Stefano de Pretis , Giorgio Melloni
Date of publication
None
Maintainer
Stefano de Pretis <ste.depo@gmail.com>, Giorgio Melloni <melloni.giorgio@gmail.com>
License
GPL-3
Version
1.6.0

View on Bioconductor

Man pages

alignSequences
Align sequences via clustalo
allPfamAnalysis
Global analysis of a repository of mutations
BLOSUM62
BLOSUM62 matrix
bpAll
Draw a mutation barplot
entropy
Calculate LowMACA statistics
getMutations
Retrieve mutation data for a LowMACA object
lfm
Show significant clusters of mutations
lfmSingleSequence
Show significant clusters of mutations of every gene in a...
lmAlignment
Show Alignment Results from a LowMACA object
lmEntropy
Show Entropy Information Contained in a LowMACA object
lmMutations
Show Mutation Data Contained in a LowMACA object
lmObj
Example of a LowMACA object
lmParams
Show and set parameters
lmPlot
Draw a comprehensive LowMACA plot
lmPlotSingleSequence
Draw a LowMACA comprehensive plot of a specified gene within...
LowMACA_AML
Example of a LowMACA object
LowMACA-class
Class '"LowMACA"'
LowMACA-package
LowMACA : Low frequency Mutations Analysis via Consensus...
mapMutations
Map mutations on consensus sequence
newLowMACA
Construct a LowMACA object
nullProfile
Draw a mutational profile plot
parallelize
Show and set parallelization options
protter
Draw a Protter plot
setup
Setup of a LowMACA object
showTumorType
List of tumor types

Files in this package

LowMACA/DESCRIPTION
LowMACA/NAMESPACE
LowMACA/R
LowMACA/R/allPfamAnalysis.R
LowMACA/R/class_and_methods.R
LowMACA/R/genericFunctions.R
LowMACA/R/zzz.R
LowMACA/README
LowMACA/build
LowMACA/build/vignette.rds
LowMACA/data
LowMACA/data/BLOSUM62.RData
LowMACA/data/LowMACA_AML.RData
LowMACA/data/lmObj.RData
LowMACA/inst
LowMACA/inst/CITATION
LowMACA/inst/NEWS
LowMACA/inst/clustalo_lwp.pl
LowMACA/inst/doc
LowMACA/inst/doc/LowMACA.R
LowMACA/inst/doc/LowMACA.Rnw
LowMACA/inst/doc/LowMACA.pdf
LowMACA/man
LowMACA/man/BLOSUM62.Rd
LowMACA/man/LowMACA-class.Rd
LowMACA/man/LowMACA-package.Rd
LowMACA/man/LowMACA_AML.Rd
LowMACA/man/alignSequences.Rd
LowMACA/man/allPfamAnalysis.Rd
LowMACA/man/bpAll.Rd
LowMACA/man/entropy.Rd
LowMACA/man/getMutations.Rd
LowMACA/man/lfm.Rd
LowMACA/man/lfmSingleSequence.Rd
LowMACA/man/lmAlignment.Rd
LowMACA/man/lmEntropy.Rd
LowMACA/man/lmMutations.Rd
LowMACA/man/lmObj.Rd
LowMACA/man/lmParams.Rd
LowMACA/man/lmPlot.Rd
LowMACA/man/lmPlotSingleSequence.Rd
LowMACA/man/mapMutations.Rd
LowMACA/man/newLowMACA.Rd
LowMACA/man/nullProfile.Rd
LowMACA/man/parallelize.Rd
LowMACA/man/protter.Rd
LowMACA/man/setup.Rd
LowMACA/man/showTumorType.Rd
LowMACA/vignettes
LowMACA/vignettes/LowMACA.Rnw