data/README.md

In qpmnguyen/microbe_set_trait: Reproducible analyses for evaluating trait-based taxon sets

Description of data sets:

1. condensed_species_NCBI.txt: This file contains the latest database release from Madin et al.. This file is organized as a taxa-by-trait matrix with NCBI identifiers. Current timestamp:
2. gevers_biom.biom: This is the biom file for the Gevers et al. microbiome data set and can be used as inputs to picrust2.
3. gevers_dada2.rds: This is the seqtabnochim data export after running the Gevers et al. data set through dada2.
4. gevers_seq.fa: This file contains the unique amplicon sequence variants for the Gevers et al. data set that will be used as inputs to picrust2.
5. madin_proc.rds: This file contains pre-processed database from the Madin et al. comprehensive database.
6. pathabundances_3.tsv.gz, taxonomic_profiles_3.tsv.gz: This contains all the latest pathway abundances and taxonomic profiles for the integrative human microbiome project. These are results obtained from the latest biobakery version (v3).
7. weissman.csv: This is

qpmnguyen/microbe_set_trait documentation built on April 11, 2024, 6:07 p.m.