Microbial Pan-Genome Analysis


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Documentation for package ‘micropan’ version 1.1.2

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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
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
Mpneumoniae Data sets for the _Mycoplasma pneumoniae_ casestudy
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
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 Plot and summary of 'Binomix' objects
plot.Panmat Plot and summary of 'Panmat' objects
plot.Panpca Plot and summary of 'Panpca' objects
plot.Pantree Plot and summary of 'Pantree' objects
plot.Rarefac Plot and summary of '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
readHmmer Reading results from a HMMER3 scan
summary.Binomix Plot and summary of 'Binomix' objects
summary.Panmat Plot and summary of 'Panmat' objects
summary.Panpca Plot and summary of 'Panpca' objects
summary.Pantree Plot and summary of 'Pantree' objects
summary.Rarefac Plot and summary of 'Rarefac' objects
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xzuncompress Compressing and uncompressing text files