Files in ukaraoz/microtrait
microTrait
.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
Dockerfile_R3ondeb_kb
LICENSE
LICENSE.md
NAMESPACE
R/apply_rules.R
R/data.R
R/extern.R
R/extract_traits.R
R/fasta.R
R/hmmer.R
R/microtrait.R
R/mingentime.R
R/nucleotide.R
R/ogt.R
R/prep_hmmpackage.R
R/protein.R
R/rRNA.R
R/rule_utils.R
R/trait_conservation.R
R/trait_utils.R
R/traitanalysis_utils.R
R/utils.R
README.md
data-raw/data.R
data-raw/faprotax.R
data-raw/faprotax.txt
data-raw/faprotax_compare_results_arsenic_selenium_iron.xls
data-raw/faprotax_compare_results_carbonfixation_phototrophy_etc.xls
data-raw/faprotax_compare_results_carbonfixation_phototrophy_etc1.txt
data-raw/faprotax_compare_results_methane.xls
data-raw/faprotax_compare_results_phototrophy.xls
data-raw/faprotax_compare_results_sulfur.xls
data-raw/faprotax_hierarchical.txt
data-raw/faprotax_microtrait_comparison.xls
data-raw/faprotax_microtrait_comparison_hits_table.xls
data-raw/faprotax_taxa2ncbi_taxa.txt
data-raw/faprotax_taxa_unmatched_byspecies.xls
data-raw/faprotax_traitcheck.xls
data-raw/faprotax_traits.txt
data-raw/faprotax_traits_matchstats.xls
data-raw/hmms_fromrules_FPRvsTPRatFmax.pdf
data-raw/hmms_fromrules_Fscoredistribution.pdf
data-raw/microtrait_hmm-performance.txt
data-raw/microtrait_hmm-performance1.txt
data-raw/microtrait_hmm.txt
data-raw/microtrait_hmm_names_fromrules.txt
data-raw/microtrait_hmmsfromrules.txt
data-raw/microtrait_rule2trait.txt
data-raw/microtrait_rules.txt
data-raw/microtrait_ruleunwrapped.txt
data-raw/microtrait_substrate2rule.txt
data-raw/microtrait_traits.txt
data-raw/ogt_regression_models/README
data-raw/ogt_regression_models/allfeatures.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+ORF+protein.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+rRNA+ORF+protein.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+rRNA.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+tRNA+ORF+protein.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+tRNA+rRNA+ORF.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+tRNA+rRNA.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic+tRNA.txt
data-raw/ogt_regression_models/superkingdom-all_species-genomic.txt
data-raw/rename_addtc2hmm_commands.sh
data-raw/rename_addtc2hmm_commands1.sh
data-raw/root_tree.R
data/hmms_fromrules.rda
data/models.rda
data/rule2trait.rda
data/rules.rda
data/traits_listbygranularity.rda
guildprofiles.png
guildsize-dist.png
inst/extdata/ST8.microtrait_references.txt
inst/extdata/dbcan.selectids.txt
inst/extdata/genomic/.gitkeep
inst/extdata/genomic/100genomes/.gitkeep
inst/extdata/genomic/2503283023.fna
inst/extdata/genomic/2503283023.microtrait.rds
inst/extdata/genomic/2504136012.fna
inst/extdata/genomic/2504136012.microtrait.rds
inst/extdata/genomic/2695420375.fna
inst/extdata/genomic/2695420375.microtrait.rds
inst/extdata/genomic/2896171935.fna
inst/extdata/genomic/2896171935.microtrait.rds
inst/extdata/genomic/2896281107.fna
inst/extdata/genomic/2896281107.microtrait.rds
inst/extdata/genomic/2896293972.fna
inst/extdata/genomic/2896293972.microtrait.rds
inst/extdata/genomic/anamox1_Acidobacteria_62_5_curated.microtrait.rds
inst/extdata/hmm/arcbacribosomal/.gitkeep
inst/extdata/hmm/dbcan/.gitkeep
inst/extdata/hmm/hmmpress/.gitkeep
inst/extdata/hmm/microtrait-hmmdb/.gitkeep
inst/extdata/microtrait_genomes_retrieved.txt
inst/extdata/microtrait_species_taxonomic.txt
inst/extdata/precomputed/environmentalgenomes.metadata.rds
inst/extdata/precomputed/environmentalgenomes.microtraitresults.rds
inst/extdata/precomputed/soilgenomes_maov_results_list.rds
man/add.metadata.Rd
man/assert.rules.Rd
man/assert.rulesforgenome.Rd
man/build.taxa.model.Rd
man/calc_intergenome_variance.Rd
man/calc_mixeddist.Rd
man/cluster_traitmatrix.Rd
man/combine.results.Rd
man/compute.prevalence.Rd
man/convert_traitdatatype.Rd
man/count.traitsforgenome.Rd
man/define_guilds.Rd
man/detect.domains.fromdomtblout.Rd
man/detect.genes.fromdomtblout.Rd
man/download.arcbacribosomal.Rd
man/download.dbcan.Rd
man/download.microtrait.Rd
man/evaluate.rule.Rd
man/extract.traits.Rd
man/extract.traits.parallel.Rd
man/fetch.results.Rd
man/filter.bycoverage.domtblout.Rd
man/gp.resultsummary.Rd
man/hello.Rd
man/hmms_fromrules.Rd
man/make.genomeset.results.Rd
man/map.traits.fromdomtblout.Rd
man/melt_dist.Rd
man/nuclcheck.Rd
man/prep.hmmmodels.Rd
man/read.domtblout.Rd
man/read.tblout.Rd
man/redefine.binarytraits.Rd
man/rule2genes.Rd
man/rule2parts.Rd
man/rulename2ruleboolean.Rd
man/rules.Rd
man/run.consentrait.singletrait.Rd
man/run.hmmsearch.Rd
man/run.predictGrowth.Rd
man/run.prodigal.Rd
man/set.geneprofile.Rd
man/splitSeqsToFiles.Rd
man/trait.continuous2binary.Rd
man/trait.normalize.Rd
man/trait2trait_corr.Rd
man/unwrap.rules.Rd
man/write.genomeset.results.Rd
microtrait-hierarchy.pdf
microtrait.Rproj
microtrait.png
rename_addtc2hmm.sh
rename_addtc2hmm_commands.sh
scripts/clustering.R
scripts/compare2faprotax.R
scripts/guilds-backup.R
scripts/guilds-scratch.R
scripts/guilds.R
scripts/plot_hmm-perf-metrics.R
scripts/plot_traitconservation.R
scripts/prep-ogt-inputs.R
scripts/rp_phyloprofiler/R/hmmer.R
scripts/rp_phyloprofiler/R/rp_profiler.R
scripts/rp_phyloprofiler/R/utils.R
scripts/rp_phyloprofiler/data/udb/rplR_L18_Hugetal.udb
scripts/run_consentrait.R
scripts/run_microtrait.R
scripts/run_microtrait_backup.R
scripts/run_traitconservation.R
scripts/run_traitprevalence.R
scripts/taxonomy_summarize.R
scripts/trait_check.R
scripts/trait_check_obs.R
scripts/transportervsextracellular.R
trait2trait-correlation.png
traitmatrix.png
traitvariance.png
