micropan-package | Microbial Pan-Genome Analysis |
barrnap | Finding rRNA genes |
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 |
findOrfs | Finding ORFs in genomes |
fluidity | Computing genomic fluidity for a pan-genome |
geneWeights | Gene cluster weighting |
getAccessions | Collecting contig accession numbers |
gff2fasta | Retrieving sequences from genome |
gffSignature | GFF signature text |
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 |
lorfs | Longest ORF |
micropan | Microbial Pan-Genome Analysis |
Mpneumoniae | Data sets for the _Mycoplasma pneumoniae_ casestudy |
mpneumoniae | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.blast.clustering | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.blast.distances | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.blast.panmat | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.domain.clustering | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.domain.panmat | Data sets for the _Mycoplasma pneumoniae_ casestudy |
Mpneumoniae.table | Data sets for the _Mycoplasma pneumoniae_ casestudy |
orfLength | ORF lengths |
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 |
plot.Binomix | Plot and summary of 'Binomix' objects |
plot.Panmat | Plot and summary of 'Panmat' objects |
plot.Panpca | Plot and summary of 'Panpca' objects |
plot.Pantree | Plot and summary of 'Pantree' objects |
plot.Rarefac | Plot and summary of 'Rarefac' objects |
plotLoadings | Plotting scores and loadings in a 'Panpca' object |
plotScores | Plotting scores and loadings in a 'Panpca' object |
prodigal | Gene predictions using Prodigal |
rarefaction | Rarefaction curves for a pan-genome |
readBlastTable | Reading BLAST result file |
readGFF | Reading and writing GFF-tables |
readHmmer | Reading results from a HMMER3 scan |
summary.Binomix | Plot and summary of 'Binomix' objects |
summary.Panmat | Plot and summary of 'Panmat' objects |
summary.Panpca | Plot and summary of 'Panpca' objects |
summary.Pantree | Plot and summary of 'Pantree' objects |
summary.Rarefac | Plot and summary of 'Rarefac' objects |
writeGFF | Reading and writing GFF-tables |
xzcompress | Compressing and uncompressing text files |
xzuncompress | Compressing and uncompressing text files |