micropan: Microbial Pan-Genome Analysis
Version 1.1.2

A collection of functions for computations and visualizations of microbial pan-genomes.

Browse man pages Browse package API and functions Browse package files

AuthorLars Snipen and Kristian Hovde Liland
Date of publication2017-01-17 19:41:22
MaintainerLars Snipen <lars.snipen@nmbu.no>
LicenseGPL-2
Version1.1.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("micropan")

Man pages

bClust: Clustering sequences based on pairwise distances
bDist: Computes distances between sequences based on BLAST results
binomixEstimate: Binomial mixture model estimates
blastAllAll: Making BLAST search all against all genomes
chao: The Chao lower bound estimate of pan-genome size
dClust: Clustering sequences based on domain sequence
distJaccard: Computing Jaccard distances between genomes
distManhattan: Computing Manhattan distances between genomes
entrezDownload: Downloading genome data
fluidity: Computing genomic fluidity for a pan-genome
generic.Binomix: Plot and summary of 'Binomix' objects
generic.Panmat: Plot and summary of 'Panmat' objects
generic.Panpca: Plot and summary of 'Panpca' objects
generic.Pantree: Plot and summary of 'Pantree' objects
generic.Rarefac: Plot and summary of 'Rarefac' objects
geneWeights: Gene cluster weighting
getAccessions: Collecting contig accession numbers
heaps: Heaps law estimate
hmmerCleanOverlap: Removing overlapping hits from HMMER3 scans
hmmerScan: Scanning a profile Hidden Markov Model database
isOrtholog: Identifies orthologs in gene clusters
mpneumoniae: Data sets for the _Mycoplasma pneumoniae_ casestudy
panMatrix: Computing the pan-matrix for a set of gene clusters
panpca: Principal component analysis of a pan-matrix
panPrep: Preparing FASTA files for pan-genomics
panTree: Constructing pan-genome trees
prodigalPredict: Gene predictions using Prodigal
rarefaction: Rarefaction curves for a pan-genome
readBlastTable: Reading BLAST result file
readHmmer: Reading results from a HMMER3 scan
scores.loadings: Plotting scores and loadings in a 'Panpca' object
xz: Compressing and uncompressing text files

Functions

Mpneumoniae Man page
Mpneumoniae.blast.clustering Man page
Mpneumoniae.blast.distances Man page
Mpneumoniae.blast.panmat Man page
Mpneumoniae.domain.clustering Man page
Mpneumoniae.domain.panmat Man page
Mpneumoniae.table Man page
bClust Man page Source code
bDist Man page Source code
binomixEstimate Man page Source code
binomixMachine Source code
blastAllAll Man page Source code
branchPos Source code
chao Man page Source code
clusterSignature Source code
dClust Man page Source code
distJaccard Man page Source code
distManhattan Man page Source code
entrezDownload Man page Source code
fluidity Man page Source code
geneWeights Man page Source code
getAccessions Man page Source code
heaps Man page Source code
hmmerCleanOverlap Man page Source code
hmmerScan Man page Source code
isOrtholog Man page Source code
mpneumoniae Man page
negTruncLogLike Source code
nonoverlap Source code
objectFun Source code
panColor Source code
panMatrix Man page Source code
panPrep Man page Source code
panTree Man page Source code
panpca Man page Source code
plot.Binomix Man page Source code
plot.Panmat Man page Source code
plot.Panpca Man page Source code
plot.Pantree Man page Source code
plot.Rarefac Man page Source code
plotBar Source code
plotLoadings Man page Source code
plotScores Man page Source code
prodigalPredict Man page Source code
rarefaction Man page Source code
readBlastTable Man page Source code
readHmmer Man page Source code
setLeafAttributes Source code
summary.Binomix Man page Source code
summary.Panmat Man page Source code
summary.Panpca Man page Source code
summary.Pantree Man page Source code
summary.Rarefac Man page Source code
xzcompress Man page Source code
xzuncompress Man page Source code

Files

inst
inst/extdata
inst/extdata/microfam0.hmm.h3i.xz
inst/extdata/Mpneumoniae.txt.xz
inst/extdata/GID1_vs_GID1.txt.xz
inst/extdata/GID2_vs_GID3.txt.xz
inst/extdata/GID1_vs_Pfam-A.hmm.txt.xz
inst/extdata/microfam0.hmm.h3p.xz
inst/extdata/Mpneumoniae_309_GID2.fsa.xz
inst/extdata/Mpneumoniae_M129_GID1.fsa.xz
inst/extdata/GID3_vs_GID1.txt.xz
inst/extdata/GID2_vs_GID1.txt.xz
inst/extdata/microfam0.hmm.h3m.xz
inst/extdata/GID2_vs_GID2.txt.xz
inst/extdata/GID1_vs_GID3.txt.xz
inst/extdata/microfam0.hmm.h3f.xz
inst/extdata/GID2_vs_Pfam-A.hmm.txt.xz
inst/extdata/GID3_vs_GID3.txt.xz
inst/extdata/Mpneumoniae_FH_GID3.fsa.xz
inst/extdata/GID1_vs_GID2.txt.xz
inst/extdata/GID3_vs_GID2.txt.xz
inst/extdata/Mpneumoniae_309_protein.fsa.xz
inst/extdata/GID3_vs_Pfam-A.hmm.txt.xz
inst/extdata/Mpneumoniae_309_genome.fsa.xz
inst/doc
inst/doc/vignette.Rnw
inst/doc/casestudy.pdf
inst/doc/vignette.pdf
inst/doc/vignette.R
NAMESPACE
demo
demo/casestudy.R
demo/00Index
data
data/Mpneumoniae.domain.panmat.rda
data/Mpneumoniae.blast.clustering.rda
data/Mpneumoniae.blast.distances.rda
data/Mpneumoniae.blast.panmat.rda
data/Mpneumoniae.domain.clustering.rda
data/Mpneumoniae.table.rda
R
R/rarefaction.R
R/panpca.R
R/bdist.R
R/panprep.R
R/entrez.R
R/genomedistances.R
R/powerlaw.R
R/domainclust.R
R/xz.R
R/mpneumoniae.R
R/hmmer3.R
R/bclust.R
R/prodigal.R
R/blasting.R
R/binomix.R
R/trees.R
R/panmat.R
vignettes
vignettes/vignette.Rnw
vignettes/vignette-concordance.tex
vignettes/vignette.tex
MD5
build
build/vignette.rds
DESCRIPTION
man
man/hmmerCleanOverlap.Rd
man/rarefaction.Rd
man/panPrep.Rd
man/generic.Binomix.Rd
man/generic.Pantree.Rd
man/binomixEstimate.Rd
man/panTree.Rd
man/mpneumoniae.Rd
man/bClust.Rd
man/chao.Rd
man/prodigalPredict.Rd
man/getAccessions.Rd
man/heaps.Rd
man/xz.Rd
man/bDist.Rd
man/entrezDownload.Rd
man/hmmerScan.Rd
man/fluidity.Rd
man/distJaccard.Rd
man/isOrtholog.Rd
man/panMatrix.Rd
man/readHmmer.Rd
man/blastAllAll.Rd
man/distManhattan.Rd
man/scores.loadings.Rd
man/panpca.Rd
man/geneWeights.Rd
man/generic.Panpca.Rd
man/dClust.Rd
man/readBlastTable.Rd
man/generic.Rarefac.Rd
man/generic.Panmat.Rd
micropan documentation built on May 29, 2017, 11:57 a.m.