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micropan (version 1.0)

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

240

Version

1.0

License

GPL-2

Maintainer

Lars Snipen

Last Published

September 9th, 2014

Functions in micropan (1.0)

binomixMachine

Computing engine for binomial mixture models

panTree

Constructing pan-genome trees

chao

The Chao lower bound estimate of pan-genome size

hmmerScan

Scanning a profile Hidden Markov Model database

distJaccard

Computing Jaccard distances between genomes

fluidity

Computing genomic fluidity for a pan-genome

getAccessions

Collecting contig accession numbers

geneWeights

Gene cluster weighting

entrezDownload

Downloading genome data

translate

From nucleotides to proteins

plot.Rarefac

Plotting and printing Rarefac objects

panMatrix

Computing the pan-matrix for a set of gene clusters

heaps

Heaps law estimate

gregexpr

Extended gregexpr with substring retrieval

blastAllAll

Making BLAST search all against all genomes

setLeafAttributes

Setting leaf attributes

readHmmer

Reading results from a HMMER3 scan

readFasta and writeFasta

Read and write biological sequence files.

dClust

Clustering sequences based on domain sequence

plot.Pantree

Plotting and printing Pantree objects

bDist

Computes distances between sequences based on BLAST results

rarefaction

Rarefaction curves for a pan-genome

plot.Panpca

Plotting and printing Panpca objects

hmmerCleanOverlap and nonoverlap

Removing overlapping hits from HMMER3 scans

binomixEstimate

Binomial mixture model estimates

micropan-package

Microbial Pan-genome Analysis

bClust

Clustering sequences based on pairwise distances

xzcompress

xz (un)compress a file

readBlastTable

Reading BLAST result file

panPrep

Preparing FASTA files for pan-genomics

negTruncLogLike

Negative truncated log-likelihood function

isOrtholog

Identifies orthologs in gene clusters

plot.Panmat

Plotting and printing Panmat objects

reverseComplement

Reverse-complement of a DNA or RNA sequence

distManhattan

Computing Manhattan distances between genomes

plot.Binomix

Plotting and printing Binomix objects

Mpneumoniae

Data sets for the Mycoplasma pneumoniae casestudy

plotScores

Plotting scores and loadings in a Panpca object

prodigalPredict

Gene predictions using Prodigal

panpca

Principal component analysis of a pan-matrix

plot.Fasta

Plotting and printing Fasta objects