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micropan (version 1.1.2)

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

1.1.2

License

GPL-2

Maintainer

Lars Snipen

Last Published

January 17th, 2017

Functions in micropan (1.1.2)

entrezDownload

Downloading genome data

fluidity

Computing genomic fluidity for a pan-genome

bDist

Computes distances between sequences based on BLAST results

dClust

Clustering sequences based on domain sequence

blastAllAll

Making BLAST search all against all genomes

binomixEstimate

Binomial mixture model estimates

chao

The Chao lower bound estimate of pan-genome size

bClust

Clustering sequences based on pairwise distances

distJaccard

Computing Jaccard distances between genomes

distManhattan

Computing Manhattan distances between genomes

hmmerScan

Scanning a profile Hidden Markov Model database

hmmerCleanOverlap

Removing overlapping hits from HMMER3 scans

plot.Rarefac

Plot and summary of Rarefac objects

plot.Panpca

Plot and summary of Panpca objects

getAccessions

Collecting contig accession numbers

heaps

Heaps law estimate

geneWeights

Gene cluster weighting

plot.Panmat

Plot and summary of Panmat objects

plot.Pantree

Plot and summary of Pantree objects

plot.Binomix

Plot and summary of Binomix objects

prodigalPredict

Gene predictions using Prodigal

rarefaction

Rarefaction curves for a pan-genome

isOrtholog

Identifies orthologs in gene clusters

mpneumoniae

Data sets for the Mycoplasma pneumoniae casestudy

readHmmer

Reading results from a HMMER3 scan

readBlastTable

Reading BLAST result file

panMatrix

Computing the pan-matrix for a set of gene clusters

panpca

Principal component analysis of a pan-matrix

plotScores

Plotting scores and loadings in a Panpca object

xzcompress

Compressing and uncompressing text files

panPrep

Preparing FASTA files for pan-genomics

panTree

Constructing pan-genome trees