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from gcmp_global_disease.
Related Issues (20)
- Check in preliminary Generalized Diversity Modeling analysis
- Check in a species name mapping that harmonizes across resources
- Write script to map disease susceptibility to Huang Roy tree names HOT 1
- Add phylogenetic alpha and beta diversity metrics HOT 1
- Do phylogeny insertion with SEPP HOT 1
- Rework the make_coral_disease_graphs folder so the whole workflow coheres
- Also output the merged_disease_table.tsv in long Tidy form
- Break apart metadata sheet into constituent tables and write pandas code to merge them together
- Add a rarefaction step to the decontamination pipeline HOT 1
- Fix title of Greengenes insertion tree
- Add code to remove # from the header of the metadata before loading in PhyloSeq HOT 1
- Fix spelling of noncont tree file HOT 2
- Document difference between all.seqs.fa and GCMP_seqs.qza HOT 1
- Remove unused input files from the input of core analysis
- In core analysis incorporate Faith's PD using the results in the alpha_phylogenetic folder HOT 1
- Add differential abundance analysis
- Add cophenetic distance matrix for coral species
- Reconstruct genus level alpha diversity (with ape/ace ASR), match to Lamb et al disease data, prune the tree HOT 1
- Change 'fungid' to 'fungia' in host_scientific_name
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from gcmp_global_disease.