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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
Version
2.1
2.0.1
2.0
1.2
1.1.2
1.1.1
1.1
1.0
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)
Search all functions
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