Data

Genotype ID

• Genotype names lookup table: data/BG_genotype_names.csv

• (not needed, because the data files I provide just use the same genotype name, i.e. GX_name in the table)

• TODO: need a master file (n_MM_name = 232, n_GX_name = 277, n_overlap_with_SNP_file_geno_name = 212)

• Population structure

• PCs: data/hmp321_282_agpv4_maf005_miss03_pruned.eigenvec

Genome-sequencing data

• Whole genome sequencing data (n=271) of HapMap V3.2.1 (with imputation, AGPv4) obtained from the Panzea database https://www.panzea.org/genotypes (for more information : Bukowski et. al., 2018)
• SNP data (20 million): ``
• SNP data (50k SNPs): largedata/Zhikai/sinfo_micobiome_geno.txt

Omics data

• Microbiome (3626 ASVs): log relative abundance (largedata/Zhikai/sinfo_micobiome_geno.txt), count (largedata/Zhikai/sinfo_micobiome_geno_count.txt) (for more information : Meier et. al., 2022)
  • Sample info: data/sample_info_3626asvs.txt
  • For information about N treatment level of each ceil_id corresponding to two rows with the same genotype

Phenomics data

• UAV Phenotype: Canopy Coverage (data/ppj220030-sup-0002-tables1.csv), Vegetation Indices (data/ppj220030-sup-0003-tables2.csv)
  • (for more information: Rodene et. al., 2022)

Data Processing and Sharing:

profiling/1.A.3_yanglab_data_sharing.Rmd

Project Guideline

• To guide group members having a better sense about the project layout, here we briefly introduce the specific purposes of the dir system. The layout of dirs is based on the idea borrowed from ProjectTemplate.

• The guideline for the collaborative workflow.

• Check out progress and things to-do and throw ideas via the wiki page.

License

This is an ongoing research project. It was intended for internal lab usage. It has not been extensively tested. Use at your own risk. It is a free and open source software, licensed under GPLv3.