R/python/unix scripts for 5-ASA analysis
READ ME FOR FILES --> see folder 12.20.22 for code resubmitted after the revision, now with basic annotations (2.24.23) ##### --> contact rmehta2@mgh.harvard.edu or raajmehta@gmail.com with questions.
#Data processing:
- metadata_create.R
- hmp2omics_preprocessingbb3.R
- uniref_proptable_dnabb3.R
- uniref_proptable_rnabb3.R
- PRISM/prismprocessing.R
#Overview (results, section 1):
- table1_v3.R
- icons come from shutterstock (free)
#Metabolomics analysis (results, section 2):
- metabPCOA_clean.R --> Fig2A
- DA_test_species.R --> supp table 3
- ROCmetabs_newclean.R --> Fig2B, Supp Fig 1, Ext Fig 2, 3c/3d, Supp table 2
- hallabb3.py --> ext fig 3b (done on FAS bc software is installed there)
- biotransf_clean.R --> Fig2C , Ext Fig 3
- prismmetab_reviewed.R --> Fig 2C , Supp Fig 2
- metabs_newuserextra.R --> this is info for text about new steroid and new biologic users #NB: chemdraw was used to make the structures
#Gene discovery (results, section 3):
- DA_test_uniref_clean.R --> fig 3a, 3c
- sen_spec_clean --> Fig 3b
- jalview.txt --> Fig 3d
- proteobacteriaplot.R --> ext fig 4
- proteoheatmap.R --> ext fig 4
- graphlanprep_revision2.R --> ext fig 4
#Biochemistry (results, section 4):
- genecontext.R
- proteindomains.R
- chimerascript8.txt --> Fig 4c,d,e
- chemdraw was used to make structures
- jared made panels 4a,b, ext fig 6,7
#Clinical (results, section 5):
- clinical_clean.R --> Fig 5a, 5c
- sparcvalidation_final.R --> Fig 5b