Microbial Pan-Genome Analysis
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Documentation for package ‘micropan’ version 2.1
Help Pages
| 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 |