Man pages for ukaraoz/microtrait
microTrait
| add.metadata | Add metadata |
| assert.rules | Apply rules to a set of detected genes |
| assert.rulesforgenome | Apply rules to a set of detected genes |
| build.taxa.model | Build lme model |
| calc_intergenome_variance | Calculate interguild variance |
| calc_mixeddist | Calculate distances between genomes. |
| cluster_traitmatrix | Genome by trait matrix heatmap. |
| combine.results | Combine microtrait results for multiple genomes |
| compute.prevalence | Count prevalence of traits, rules, or hmms |
| convert_traitdatatype | Make sure binary traits are of type logical |
| count.traitsforgenome | Apply rules to a set of detected genes |
| define_guilds | Define guild matrix. |
| detect.domains.fromdomtblout | Apply rules to a set of detected genes |
| detect.genes.fromdomtblout | Apply rules to a set of detected genes |
| download.arcbacribosomal | Prepare database for PFAM models for ribosomal proteins |
| download.dbcan | Prepare dbcan database (download and subselect) |
| download.microtrait | Prepare microtrait database (download and subselect) |
| evaluate.rule | Evaluate a boolean rule. |
| extract.traits | Apply rules to a set of detected genes |
| extract.traits.parallel | Run microtrait for genomes in parallel using mclapply |
| fetch.results | Fetch results for a single genome |
| filter.bycoverage.domtblout | Read a file created through the '–domtblout' option |
| gp.resultsummary | Fetch growthpred results for a single genome |
| hello | Hello, World! |
| hmms_fromrules | microtraithmm_fromrules. |
| make.genomeset.results | Combine microtrait outputs for multiple genomes into trait... |
| map.traits.fromdomtblout | Apply rules to a set of detected genes |
| melt_dist | Melt a square distance matrix into long format |
| nuclcheck | base =... |
| prep.hmmmodels | Prepare microtrait database |
| read.domtblout | Read a file created through the '–domtblout' option |
| read.tblout | Read a file created through the '–tblout' option |
| redefine.binarytraits | Fix traits |
| rule2genes | Get genes from rule |
| rule2parts | Return genes that are part of a rule. |
| rulename2ruleboolean | Get genes from rule |
| rules | microtraitrule_table. |
| run.consentrait.singletrait | Run consentrait script |
| run.hmmsearch | Run hmmsearch (HMMER 3) |
| run.predictGrowth | predictGrowth from codon usage bias |
| run.prodigal | Finding coding genes |
| set.geneprofile | Set gene profiles using detected genes |
| splitSeqsToFiles | Split DNA sequences in a fasta file into single sequence... |
| trait2trait_corr | Analyze trait2trait correlations. |
| trait.continuous2binary | Convert continuous traits to binary |
| trait.normalize | Normalize count traits |
| unwrap.rules | Unwraps complex rules. |
| write.genomeset.results | Add metadata |
