Files in sawers-rellan-labs/grassGEA
Sorghum and Corn Genome Environment analysis
.Rbuildignore
.gitignore
DESCRIPTION
INSTALL.md
NAMESPACE
R/IO.R
R/Models.R
R/config.R
R/log.R
README.md
grassGEA.Rproj
hpc_pipeline.md
inst/extdata/base_config.yaml
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c1.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c10.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c2.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c3.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c4.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c5.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c6.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c7.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c8.imp.hmp.txt
inst/extdata/batch_test/sb_snpsDryad_sept2013_filter.c9.imp.hmp.txt
inst/extdata/config.yaml
inst/extdata/hayu_config.yaml
inst/extdata/hpc_config.yaml
inst/extdata/script_value_config.yaml
inst/scripts/GIS/Correlations.R
inst/scripts/GIS/MC_Dowell_observed_predicted correlation.R
inst/scripts/GIS/change_raster_resolution.R
inst/scripts/GIS/covstack_to_raster.R
inst/scripts/GIS/get_Batjes2019_pvars.sh
inst/scripts/GIS/make_landcover_table.R
inst/scripts/GIS/predict_Pvariable.R .R
inst/scripts/GIS/q_phos_predict.sh
inst/scripts/batch/get_config.sh
inst/scripts/batch/info_gemma.md
inst/scripts/batch/make_kinship_matrix.sh
inst/scripts/batch/q_make_kinship_matrix.sh
inst/scripts/batch/q_run_chr_GLM.sh
inst/scripts/batch/q_run_chr_MLM.sh
inst/scripts/batch/run_chr10_GLM.sh
inst/scripts/batch/run_chr_GLM.sh
inst/scripts/batch/run_chr_MLM.sh
inst/scripts/make_kinship_matrix.R
inst/scripts/plot_manhattan.R
inst/scripts/preprocessing/Genotype_filter.R
inst/scripts/preprocessing/batch/fix_hapmap.sh
inst/scripts/preprocessing/batch/get_help.sh
inst/scripts/preprocessing/batch/make_phenotype_table.sh
inst/scripts/preprocessing/batch/q_fix_hapmap.sh
inst/scripts/preprocessing/batch/q_get_help.sh
inst/scripts/preprocessing/batch/q_make_hapmap_geo_loc.sh
inst/scripts/preprocessing/batch/q_make_phenotype_table.sh
inst/scripts/preprocessing/batch/q_test_loop.sh
inst/scripts/preprocessing/batch/test_loop.sh
inst/scripts/preprocessing/combine_VP.LongLat.R
inst/scripts/preprocessing/export_diploid_hmp.sh
inst/scripts/preprocessing/extract_var.R
inst/scripts/preprocessing/filter_hapmap_AF_001.sh
inst/scripts/preprocessing/haploid2diploid.R
inst/scripts/preprocessing/kinship_matrix.sh
inst/scripts/preprocessing/make_hapmap_geo_loc.R
inst/scripts/preprocessing/make_loco_sample.sh
inst/scripts/preprocessing/make_phenotype_table.R
inst/scripts/preprocessing/merge_ids.R
inst/scripts/preprocessing/sample_kinship_snps.sh
inst/scripts/preprocessing/sorghum_phenotype.R
inst/scripts/preprocessing/split_hapmap_ids.sh
inst/scripts/run_GLM.R
inst/scripts/run_GWAS.R
inst/scripts/run_MLM.R
man/no_match_append.Rd
