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𝕀nstalling tensorqtl requires pytorch which is based on gpus but there is also a cpu based version. CRI has set up pytorch for cpus as in a conda environment and that is what I am going to use to set up tensorqtl. I will install the tensorqtl in im-lab share space for lab use. […] Create a … Read more →

𝔸 bgen file has a header block with information about the file, including number of samples, the number of variant data blocks, and flags which describe how data is stores. A variant data block contains data for a single snp, including ID, position, and alleles. bgens from UKBiobank also have a … Read more →

𝕊ome going-to-nowhere exploration on regressing out PCA Read more →

𝕥his is the header where we should describe what the analysis is about hist(rnorm(1000)) Read more →

𝕎e want to investigate whether reaction rates estimated with imat(?) are heritable. Reaction rates (binary variables) were estimated by D using GTEx gene expression data. Initially, D generated reaction rates with brain cortex expression data from ~250 individuals. Heritability of reaction rates was … Read more →

𝕙2 = read_tsv(glue::glue("{DATA}/vgvp.txt"),col_names = FALSE) ## Parsed with column specification: ## cols( ## X1 = col_character(), ## X2 = col_double(), ## X3 = col_double() ## ) h2p1 = read_tsv(glue::glue("{DATA}/vgvp_perm.txt"),col_names = FALSE) ## Parsed with column … Read more →

𝕋his is a guide to configuring a Windows system to utilize many of the tools that the Im Lab uses. […] The native command line options in Windows are not well-integrated for many bioinformatic tools, so an alternative solution is to use Windows Subsystem for Linux (WSL). This allows your … Read more →

𝕋o get access to the servers at ANL, you will need at minimum an account with Argonne’s MCS division, as well as access to specific computing groups. This process is usually handled by one of the researchers at ANL, as they need to serve as a sponsor for external users. […] Once you are … Read more →

𝕋his page is about downloading and decrypting data from NCBI dbGaP. I will split up the instructions into Downloading and Decrypting […] To download, one must be approved in the dbGaP controlled data access system, receive an email that the data is ready, and follow the given instructions. … Read more →