𝕋his is a workflow to show how to open jupyter notebook on CRI or RCC. There are some detailed instructions here, CRI’s instructions and More general instructions […] https://rcc.uchicago.edu/docs/software/environments/python/index.html#running-jupyter-notebooks […] log into … Read more →

𝕋o keep track of traffic to blogdown (hugo-based) webpages in google analytics, follow the steps below See Google’s instructions here. Briefly […] Copy the global site tag, which is several lines of code that you need to paste into each webpage you want to measure. Below is the code for … Read more →

𝕋o get a list of SNPs and the corresponding weights to predict expression levels (or splicing) of a given gene, you will first need to download the databases where the prediction models are stored. For example, you can download them from here more specifically from this tar file On CRI they are … Read more →

𝕐anyu’s notes on uploading to zenodo Read more →

ℙrediXcan and TWAS methods in general correlate genetically predicted levels of gene expression traits with complex traits to understand the mechanism behind GWAS loci. A key component is the training of gene expression traits. A tutorial on how to generate elastic net models can be found in this … Read more →

𝕋o publish an analysis note in the notebook, you need to have blogdown and hugo installed on your computer. […] When running analysis, data should be placed in Box not under the githup repo. Add block as shown in the next block, which will automatically create a folder with the same name in … Read more →

𝕋his is the readme of the codes here. This module extract HapMap 3 SNPs for downstream use. Download data from https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3_r3/plink_format/ The workflow is based on snakemake and it contains the following steps: […] If one wants to do liftover, then … Read more →

ℕote: A shortcut to login your tarbell account, please follow the following instruction: How-to-set-up-SSH-keys-and-configure-custom-connection-options-for-your-SSH-Client […] Please follow the instructions to access /gpfs/data/im-lab/ from the University of Chicago’s Network: … Read more →

ℙredictDB databases are stored in simple sqlite files. You can programmatically query them via python, R, perl, etc (using appropriate libraries). Below is an example on how to query the database in R. Each has two tables the extra and the weights tables. - extra table contains the list of available … Read more →

ℍost bionimbus HostName bionimbus-pdc.opensciencedatacloud.org User username IdentityFile ~/.ssh/id_rsa ForwardAgent yes Host bionimbusvm HostName instanceIPaddress User ubuntu IdentityFile ~/.ssh/id_rsa ProxyCommand ssh -q -A bionimbus -W %h:%p ForwardAgent yes Load your key into the ssh-agent by … Read more →