micropan-package |
Microbial Pan-Genome Analysis |
bClust |
Clustering sequences based on pairwise distances |
bDist |
Computes distances between sequences |
binomixEstimate |
Binomial mixture model estimates |
blastpAllAll |
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 |
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 |
micropan |
Microbial Pan-Genome Analysis |
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 |
rarefaction |
Rarefaction curves for a pan-genome |
readBlastPair |
Reads BLAST result files |
readBlastSelf |
Reads BLAST result files |
readHmmer |
Reading results from a HMMER3 scan |
xmpl |
Data sets for use in examples |
xmpl.bclst |
Data sets for use in examples |
xmpl.bdist |
Data sets for use in examples |
xmpl.panmat |
Data sets for use in examples |
xzcompress |
Compressing and uncompressing text files |
xzuncompress |
Compressing and uncompressing text files |