micropan: Microbial Pan-Genome Analysis

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

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

View on CRAN

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

bClust Man page
bDist Man page
binomixEstimate Man page
blastAllAll Man page
chao Man page
dClust Man page
distJaccard Man page
distManhattan Man page
entrezDownload Man page
fluidity Man page
geneWeights Man page
getAccessions Man page
heaps Man page
hmmerCleanOverlap Man page
hmmerScan Man page
isOrtholog Man page
mpneumoniae Man page
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
panMatrix Man page
panpca Man page
panPrep Man page
panTree Man page
plot.Binomix Man page
plotLoadings Man page
plot.Panmat Man page
plot.Panpca Man page
plot.Pantree Man page
plot.Rarefac Man page
plotScores Man page
prodigalPredict Man page
rarefaction Man page
readBlastTable Man page
readHmmer Man page
summary.Binomix Man page
summary.Panmat Man page
summary.Panpca Man page
summary.Pantree Man page
summary.Rarefac Man page
xzcompress Man page
xzuncompress Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.