Indian gut microbiome study on fermented foods with HITChip.
This data set contains experimental data for the study by Kumaraswamy et al. (forthcoming).
Contact: Jeyaram Kumaraswamy <jeyaram.ibsd -at-here- nic.in>
License: MIT
Code used to create figures and analyses in the manuscript:
- Bimodality_densityplot (Fig. 8, Fig. S14, and Fig. S15)
- DiversityBoxplot (Fig. 1E, Fig. 5C, Fig. 5B)
- PCoA (Fig. 3)
- InteractionNetwork_plot (Fig. 4, and Fig. S16)
- Heatmap (Fig. 1B)
- Random_forest (Fig. S2, and Fig. S10)
- Wilcoxon_padjust_bonferroni (Table S2)
Some of these were done by manually selecting the necessary data from the full Excel, and then just running the script for that subset. See the code for details.
The data files in the data/ folder include:
Details on data used in the figures:
- Figures_Source Data.txt
HITChip taxonomic abundance profiles at different levels of resolution:
- Oligo_hitchip.xlsx
- Genus_hitchip.xlsx
- Phylum_hitchip.xlsx
Sample metadata:
- Metadata.xlsx
European sample data as RData file
- L2_europe.RData
Manually extracted subsets for specific analyses (see R scripts):
- Bimodality/
- MILK.csv
Other data:
- AbsoluteloadTaxaspecificqPCRdata.xlsx
- 'SCFA data-HPLC.xlsx'
- 'Fecal metabolite profile_LC-HRMS Data.xlsx'
- Longterm-diet and lifestyle.xlsx
Running R/data.R in R organizes the data into TreeSummarizedExperiment structure (file data/tse.Rds).
Other scripts include
- PCoA.R