Name		Name	Last commit message	Last commit date
parent directory ..
Caprion_deCODE_UKB_PPP.sh		Caprion_deCODE_UKB_PPP.sh
README.md		README.md
ToDo.sh		ToDo.sh
coloc.R		coloc.R
coloc.sb		coloc.sb
compare.sb		compare.sb
csq.sh		csq.sh
dup-collect.sh		dup-collect.sh
dup-extract.sh		dup-extract.sh
dup-json.sh		dup-json.sh
dup-pgwas.sh		dup-pgwas.sh
dup-plot.sh		dup-plot.sh
dup-tbl.R		dup-tbl.R
eSet.sh		eSet.sh
glmnet_pense.sh		glmnet_pense.sh
impute.sb		impute.sb
inf1.sh		inf1.sh
json.sh		json.sh
peptideAssociationPlot.sh		peptideAssociationPlot.sh
pqtlGWAS.R		pqtlGWAS.R
tables.sh		tables.sh

README.md

Miscellaneous analysis

This section accommodates many largely independent tasks.

Implementation might well be generic so that both proteins and peptides are covered.

Programs and applications

These are summarised in the following table,

Program	Description
`coloc.sb`	Coloc(alisation) analysis
`csq.sh`	Consequences of variants
`Caprion_deCODE_UKB_PPP.sh`	Caprion/deCODE/UKB-PPP replication
`eSet.sh`	ExpresssionSet implementations
`glmnet_pense.sh`	glmnet/pense modeling
`impute.sb`	imputation experiments
`json.sh`	JSON file generation
`peptideAssociationPlot.sh`	protein Manhattan-peptide signal plots
`dup-pgwas.sh`	pGWAS for duplicated proteins
`dup-extract.sh`	pQTL extractions
`dup-json.sh`	LocusZoom.js plots
`dup-plot.sh`	pQTL plots
`dup-tbl.R`	pQTL table
`pqtlGWAS.R`	pQTL-GWAS lookup
`tables.sh`	`Supplementary-Tables.xlsx` generator
`ToDo.sh`	various staged experiments

NB:

coloc.sb alternatively calls coloc.R.
impute.sb employs impute_parallel() when N(isotope groups) > 500. Nevertheless, when coming to protein requantification this is an option to use the orginal intensity data.

Legacy codes

compare.sb. earlier contrast with deCODE/UKB-PPP.
inf1.sh. snapshot from SCALLOP/INF meta-analysis.

Created on 9/12/2024