Exploring the role of normalization and feature selection in microbiome disease classification pipelines

Code and supporting data for the article: "Exploring the role of normalization and feature selection in microbiome disease classification pipelines."

The repository contains the following folders:

1. data: contains OTU/ASV tables and class annotations for the 15 curated datasets considered.
2. src: code writen to perform the analyses from the article and the statistical tests
3. results: tables containing global nested cross validation results
4. figures

License: This project is licensed under GNU GPL 3.0 - check LICENSE file for more details.

Dataset	Samples (Cases, Controls)	Features	IR	Project ID
ART	114 (86, 28)	10733	3.07	PRJNA203810
CDI	336 (93, 243)	3456	2.61	10.1128/mbio.01021-14 (DOI)
CRC1	490 (229, 261)	6920	1.14	PRJNA290926
CRC2	102 (46, 56)	837	1.22	SRP005150
HIV	350 (293, 57)	14425	5.14	PRJNA307231
CD1	140 (78, 62)	3547	1.26	PRJNA237362
CD2	160 (68, 92)	3547	1.35	PRJNA237362
IBD1	91 (67, 24)	2742	2.79	PRJNA82109
IBD2	114 (68, 46)	1496	1.48	10.1053/j.gastro.2010.08.049 (DOI)
CIR	77 (51, 26)	3104	1.96	PRJNA174838
MHE	77 (26, 51)	3104	1.96	PRJNA174838
OB	281 (220, 61)	6386	3.61	PRJNA32089
PAR1	148 (74, 74)	10232	1.00	PRJEB4927
PAR2	333 (201, 132)	6844	1.52	PRJNA601994
PAR3	507 (323, 184)	12198	1.76	PRJNA601994

Notes:

ART: Arthritis; CDI: Clostridium difficile Infection; CRC1 and CRC2: Colorectal Cancer; HIV: Human Immunodeficiency Virus; CD1 and CD2: Crohn's Disease; IBD1 and IBD2: Inflammatory Bowel Disease; CIR: Cirrhosis; MHE: Minimal Hepatic Encephalopathy; OB: Obesity; PAR1, PAR2, and PAR3: Parkinson's Disease.
CD1 and CD2 were taken from MLRepo, PAR2 and PAR3 were retrieved from their respective article sources, and the remaining datasets were obtained from MicrobiomeHD.
Project IDs from NCBI for raw data. IBD2 data is only available via MicrobiomeHD repository, CDI raw data is available at mothur (https://mothur.org/CDI_MicrobiomeModeling/)