micropan: Microbial Pan-Genome Analysis

Share:

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

Author
Lars Snipen and Kristian Hovde Liland
Date of publication
2016-12-06 23:43:56
Maintainer
Lars Snipen <lars.snipen@nmbu.no>
License
GPL-2
Version
1.1

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/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