Man pages for iferres/pewit
Microbial Pan-Genomics in R

alignMultiple alignment with mafft.
assignOrphansAssign Orphan Clusters to other clusters.
buildPanMatrixBuild the pan-matrix
checkIfParaloguesCheck if cluster contains paralogues
clusterOrphansCluster 'orphan' sequences (i.e. without Pfam-A domains of...
compComplements a nucleic acid sequence
coreAlignAlign Core-Genes
determineOverlapDetermine which Pfam domains overlaps.
domainSearchCompute All Pfam Related Functions
extractGffTableExtract the gff3 table and make it 'R'eadable.
extractSeqsFromGff3Extract Sequences from Gff3 file
getClusterGenesExtract the genes of a set of clusters
getCoreClustersExtract core cluster names
getFfnFaaExtract CDS gene (DNA) and protein (AA) sequences
getSeqOfTypeGet sequences (nucleotidic or aminoacidic)
groupingSplit hmmscan output by query.
hmmBuildhmmBuild
hmmPresshmmPress
maxTrueOGsMaximum subtrees which contains only true orthologues
outhmmsearchProcess hmmsearch output to make it 'R'eadable.
outphmmerProcess phmmer output to make ir 'R'eadable.
pangenomeCompute the pangenome of a set of related organisms.
pdist.aaCalculate p distance from a multiple alignment
plot.pangenomePlot a 'pangenome' object.
plotRarefactionPlot Pangenome Rarefaction Curves
print.pangenomePrint Generic for Pangenome Objects
processHmmsearchMain hmmsearch output processing function
processPfam_A_DatProcess Pfam-A.dat file
readTbloutRead tblout Formated Files
realocateSingletonsRefining Singletons
rm_overlaping_clansRemoves same-clan overlapping domains
rmvRecentParaloguesRemove recent paralogues
runHmmsearchRun Hmmsearch (HMMER 3)
runMCLRun MCL
runOnExitRemoves everything if an error occur
setClusterNamesSet cluster names
splitAndWriteFastasSplit sequences to distribute among threads
splitClustersSplit clusters
splitPreClustersSplit Pre Clusters
summary.pangenomeSummarizing pangenome object
translateTranslate
whichNodeHaveRecentParaloguesWhich nodes have recent paralogues
whichSubtreesAreTrueOrthologuesWhich subtrees are true orthologues
writeClustersWrite Clusters
writeFastaClustersWrite Cluster Sequences in Fasta Format
writeParaloguesWrite Paralogues
iferres/pewit documentation built on Oct. 18, 2017, 1:03 a.m.