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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
2.1
2.0.1
2.0
1.2
1.1.2
1.1.1
1.1
1.0
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Install
install.packages('micropan')
Monthly Downloads
265
Version
2.1
License
GPL-2
Maintainer
Lars Snipen
Last Published
July 15th, 2020
Functions in micropan (2.1)
Search functions
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