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Viktoria Petrova authoredViktoria Petrova authored
README.md 3.53 KiB
Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited Data | ||
| 16S sequencing data | This paper | https://www.ebi.ac.uk/ena/browser/home (Accession number: PRJEB63568) |
| Metabolomics data | This paper | https://www.metabolomicsworkbench.org/ (Study ID: ST002779) |
| Arabidopsis root spatial microarray | [https://doi.org/10.1126/science.1146265] | GEO dataset: GSE8934 ID: 200008934 |
| NIST14 Mass Spectral Library | https://www.nist.gov/srd/nist-standard-reference-database-1a-v14 | N/A |
| Arabidopsis thaliana Col-0 metabolic pathways | https://pmn.plantcyc.org/organism-summary?object=ARA | N/A |
| Software and Algorithms | ||
| iGraph | https://CRAN.R-project.org/package=igraph. | RRID:SCR_019225 |
| COBRApy | http://opencobra.sourceforge.net | RRID:SCR_012096 |
| GUROBI | https://www.gurobi.com/ | N/A |
| statsmodels | https://www.statsmodels.org/stable/index.html | RRID:SCR_016074 |
| Vegan | https://cran.r-project.org/web/packages/vegan/index.html | RRID:SCR_011950 |
| Qiime2 | https://qiime2.org/ | RRID:SCR_008249 |
| Flash2 | https://github.com/dstreett/FLASH2 | RRID:SCR_005531 |
| Dada2 | https://benjjneb.github.io/dada2 | RRID:SCR_008205 |
| Others | ||
| 16S data analyses | This work | GitHub https://github.com/duranpa/sweet_collaboration |