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

Files in this package

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.