Mickaël Canouil’s Analysis Scripts Templates
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Script templates to work with omics datasets.
R
R/functions
- tar-biomart.R
- tar-clean_sample_sheet.R
- tar-crossmap.R
- tar-ewas.R
- tar-gwas.R
- tar-manhattan.R
- tar-meqtl.R
- tar-plink2.R
- tar-pval_trans.R
- tar-qc_idats.R
- tar-qc_plink.R
- tar-sub_chunk.R
- tar-twas.R
- tar-vep.R
R/scripts
- 01-design.R
- 02-qc_idats_snps.Rmd
- 02-qc_idats.Rmd
- 03-qc_plink.Rmd
- 04-qc_impute.Rmd
- 05-ethnicity.R
- 06-omni_to_hg38.R
- 07-save_outputs.R
- 08-vep_vcf_docker.R
- 09-gwas.R
- 10-ewas.R
- 11-twas.R
- 12-ora.R
- 13-gsea.R
- 14-meqtl.R
- 15-eqtl.R
- 16-eqtm_estimated_time.R
- 16-eqtm.R
R/targets
- tar_crossmap.R
- tar_ewas.R
- tar_genotype.R
- tar_gsea.R
- tar_gwas.R
- tar_meqtl.R
- tar_methylation.R
- tar_ora.R
- tar_twas.R
- tar_vep.R
Rmarkdown
Note: assets directory from
github.com/umr1283/xaringan-template
is required!