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micropan (version 1.2)

Microbial Pan-Genome Analysis

Description

A collection of functions for computations and visualizations of microbial pan-genomes.

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Version

Install

install.packages('micropan')

Monthly Downloads

284

Version

1.2

License

GPL-2

Maintainer

Lars Snipen

Last Published

February 15th, 2018

Functions in micropan (1.2)

hmmerCleanOverlap

Removing overlapping hits from HMMER3 scans
readGFF

Reading and writing GFF-tables
mpneumoniae

Data sets for the Mycoplasma pneumoniae casestudy
plot.Pantree

Plot and summary of Pantree objects
readHmmer

Reading results from a HMMER3 scan
micropan

Microbial Pan-Genome Analysis
isOrtholog

Identifies orthologs in gene clusters
prodigal

Gene predictions using Prodigal
plot.Rarefac

Plot and summary of Rarefac objects
panpca

Principal component analysis of a pan-matrix
barrnap

Finding rRNA genes
lorfs

Longest ORF
binomixEstimate

Binomial mixture model estimates
plot.Panmat

Plot and summary of Panmat objects
hmmerScan

Scanning a profile Hidden Markov Model database
panMatrix

Computing the pan-matrix for a set of gene clusters
orfLength

ORF lengths
plot.Panpca

Plot and summary of Panpca objects
xzcompress

Compressing and uncompressing text files
plotScores

Plotting scores and loadings in a Panpca object
rarefaction

Rarefaction curves for a pan-genome
readBlastTable

Reading BLAST result file
entrezDownload

Downloading genome data
blastAllAll

Making BLAST search all against all genomes
bClust

Clustering sequences based on pairwise distances
dClust

Clustering sequences based on domain sequence
distManhattan

Computing Manhattan distances between genomes
chao

The Chao lower bound estimate of pan-genome size
bDist

Computes distances between sequences based on BLAST results
findOrfs

Finding ORFs in genomes
fluidity

Computing genomic fluidity for a pan-genome
getAccessions

Collecting contig accession numbers
heaps

Heaps law estimate
panPrep

Preparing FASTA files for pan-genomics
distJaccard

Computing Jaccard distances between genomes
geneWeights

Gene cluster weighting
gffSignature

GFF signature text
panTree

Constructing pan-genome trees
gff2fasta

Retrieving sequences from genome
plot.Binomix

Plot and summary of Binomix objects