# Microbial Pan-Genome Analysis

## Documentation for package ‘micropan’ version 1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

micropan-package | Microbial Pan-Genome Analysis
barrnap | Finding rRNA genes
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
findOrfs | Finding ORFs in genomes
fluidity | Computing genomic fluidity for a pan-genome
geneWeights | Gene cluster weighting
getAccessions | Collecting contig accession numbers
gff2fasta | Retrieving sequences from genome
gffSignature | GFF signature text
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
lorfs | Longest ORF
micropan | Microbial Pan-Genome Analysis
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
orfLength | ORF lengths
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
prodigal | Gene predictions using Prodigal
rarefaction | Rarefaction curves for a pan-genome
readBlastTable | Reading BLAST result file
readGFF | Reading and writing GFF-tables
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
writeGFF | Reading and writing GFF-tables
xzcompress | Compressing and uncompressing text files
xzuncompress | Compressing and uncompressing text files