lifebit-ai gwas issues - Githubissues

lifebit-ai / gwas

GWAS pipeline using SAIGE

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Replace plinkFile variable name with more descriptive

#33 cgpu closed 4 years ago
0
For review of changes only [DO NOT MERGE]

#32 cgpu closed 4 years ago
0
Implement cohort_name variable with 2 allowed values: covid, 100k

#31 cgpu opened 4 years ago
0
Adds formatR::tidy_dir() suggestions

#30 cgpu closed 4 years ago
1
Issue with CB: All the PCs are listed, no way to find the one associated with the platekey from the aggr

#29 cgpu opened 4 years ago
0
Install locuszoom

#28 kousathanas opened 4 years ago
1
Adds parameterisation to helper r scripts [create_report]

#27 cgpu closed 4 years ago
0
Verify what is the preferred strategy for handling multiple entries for phenotypes based on type (continuous, categorical)

#26 cgpu opened 4 years ago
0
Verify that IID are needed in the pheno file instead of platekeys

#25 cgpu closed 4 years ago
2
Verify that covid cohort aggregate vcfs consist of both cases and controls

#24 cgpu opened 4 years ago
0
Replace GWAS catalogue with SAIGE summary stats table

#23 cgpu opened 4 years ago
0
Add p_value_cutoff param

#22 cgpu opened 4 years ago
0
Shebangs must strictly be the 1st line, delete new line

#21 cgpu opened 4 years ago
0
Consider adding optional create_cohort before gwas_filtering

#20 cgpu opened 4 years ago
0
Add -T, --targets-file FILE flag to bcftools view for user's to subset sites

#19 cgpu opened 4 years ago
0
Add -S flag to bcftools view and use phenoFile's 1st column (IID column)

#18 cgpu opened 4 years ago
0
Check if files are staged in master node or workers

#17 cgpu opened 4 years ago
0
Run realistic GENOMICC gwas with 1500 participants and sites with MAF > 0.005

#16 cgpu opened 4 years ago
0
Create index for final filtered vcf

#15 cgpu closed 4 years ago
0
Reduce featurespace: Omit filter and start analysis from subsetted with keep snps MAF > 0.005

#14 cgpu opened 4 years ago
0
address (nil), cause 'memory not mapped' [rmarkdown issue]

#13 cgpu closed 4 years ago
1
Adds GH actions for linting and library listing

#12 cgpu closed 4 years ago
0
Test realistic gwas with v1.0

#11 cgpu opened 4 years ago
0
Convert accesion to url in DTable

#10 cgpu opened 4 years ago
0
Adds r scripts gh actions

#9 cgpu closed 4 years ago
0
Adds more filtering steps to (pre)gwas_filtering

#8 Vlad-Dembrovskyi closed 4 years ago
3
Enables git diff to inspect additions during reportathon

#7 cgpu closed 4 years ago
0
UX and data related issues that arise from development

#6 cgpu opened 4 years ago
0
Adds report and R code quality GH actions

#5 cgpu closed 4 years ago
0
Adds parameterised R plot scripts and gh actions

#4 cgpu closed 4 years ago
0
RData allowed to be saved?

#3 cgpu opened 4 years ago
0
Create process(es) for manhattan and qqplot

#2 cgpu opened 4 years ago
0
Add additional commands for filtering in the plink process

#1 cgpu closed 4 years ago
0