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micropan (version 2.1)

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

2.1

License

GPL-2

Maintainer

Lars Snipen

Last Published

July 15th, 2020

Functions in micropan (2.1)

micropan

Microbial Pan-Genome Analysis
fluidity

Computing genomic fluidity for a pan-genome
readHmmer

Reading results from a HMMER3 scan
hmmerScan

Scanning a profile Hidden Markov Model database
isOrtholog

Identifies orthologs in gene clusters
xmpl

Data sets for use in examples
readBlastSelf

Reads BLAST result files
binomixEstimate

Binomial mixture model estimates
blastpAllAll

Making BLAST search all against all genomes
xzcompress

Compressing and uncompressing text files
bClust

Clustering sequences based on pairwise distances
bDist

Computes distances between sequences
panPca

Principal component analysis of a pan-matrix
dClust

Clustering sequences based on domain sequence
chao

The Chao lower bound estimate of pan-genome size
geneWeights

Gene cluster weighting
panPrep

Preparing FASTA files for pan-genomics
getAccessions

Collecting contig accession numbers
distJaccard

Computing Jaccard distances between genomes
distManhattan

Computing Manhattan distances between genomes
heaps

Heaps law estimate
hmmerCleanOverlap

Removing overlapping hits from HMMER3 scans
entrezDownload

Downloading genome data
panMatrix

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

Rarefaction curves for a pan-genome