Microbial Pan-genome Analysis


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Documentation for package ‘micropan’ version 1.0

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micropan-package Microbial Pan-genome Analysis
bClust Clustering sequences based on pairwise distances
bDist Computes distances between sequences based on BLAST results
binomixEstimate Binomial mixture model estimates
blastAllAll Making BLAST search all against all genomes
chao The Chao lower bound estimate of pan-genome size
dClust Clustering sequences based on domain sequence
distJaccard Computing Jaccard distances between genomes
distManhattan Computing Manhattan distances between genomes
entrezDownload Downloading genome data
fluidity Computing genomic fluidity for a pan-genome
geneWeights Gene cluster weighting
getAccessions Collecting contig accession numbers
gregexpr Extended 'gregexpr' with substring retrieval
heaps Heaps law estimate
hmmerCleanOverlap Removing overlapping hits from HMMER3 scans
hmmerScan Scanning a profile Hidden Markov Model database
isOrtholog Identifies orthologs in gene clusters
micropan Microbial Pan-genome Analysis
Mpneumoniae Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.blast.clustering Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.blast.distances Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.blast.panmat Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.domain.clustering Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.domain.panmat Data sets for the _Mycoplasma pneumoniae_ casestudy
Mpneumoniae.table Data sets for the _Mycoplasma pneumoniae_ casestudy
nonoverlap Removing overlapping hits from HMMER3 scans
objectFun Heaps law estimate
panColor Plotting and printing 'Binomix' objects
panMatrix Computing the pan-matrix for a set of gene clusters
panpca Principal component analysis of a pan-matrix
panPrep Preparing FASTA files for pan-genomics
panTree Constructing pan-genome trees
plot.Binomix Plotting and printing 'Binomix' objects
plot.Fasta Plotting and printing 'Fasta' objects
plot.Panmat Plotting and printing 'Panmat' objects
plot.Panpca Plotting and printing 'Panpca' objects
plot.Pantree Plotting and printing 'Pantree' objects
plot.Rarefac Plotting and printing 'Rarefac' objects
plotLoadings Plotting scores and loadings in a 'Panpca' object
plotScores Plotting scores and loadings in a 'Panpca' object
prodigalPredict Gene predictions using Prodigal
rarefaction Rarefaction curves for a pan-genome
readBlastTable Reading BLAST result file
readFasta Read and write biological sequence files.
readHmmer Reading results from a HMMER3 scan
reverseComplement Reverse-complement of a DNA or RNA sequence
str.Binomix Plotting and printing 'Binomix' objects
str.Fasta Plotting and printing 'Fasta' objects
str.Panmat Plotting and printing 'Panmat' objects
str.Panpca Plotting and printing 'Panpca' objects
str.Pantree Plotting and printing 'Pantree' objects
str.Rarefac Plotting and printing 'Rarefac' objects
summary.Binomix Plotting and printing 'Binomix' objects
summary.Fasta Plotting and printing 'Fasta' objects
summary.Panmat Plotting and printing 'Panmat' objects
summary.Panpca Plotting and printing 'Panpca' objects
summary.Pantree Plotting and printing 'Pantree' objects
summary.Rarefac Plotting and printing 'Rarefac' objects
translate From nucleotides to proteins
writeFasta Read and write biological sequence files.
xzcompress xz (un)compress a file
xzuncompress xz (un)compress a file