how_to

Downloading and Decrypting dbGaP Data

2020-07-30
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 →

Downloading Data from Biobank Japan

2020-07-30
𝕋he same info can be found at this page, https://www.ddbj.nig.ac.jp/jga/download-e.html, but the steps may be slightly different because we applied for Biobank Japan data before they integrated with the D-way system. Register a user account: […] Download Data: […] -[ ] ADD HOW TO … Read more →

How to Configure Custom SSH Connection

2020-07-30
𝕋his wiki will show you how to set up SSH keys and configure custom connection options for accessing uchicago tarbell. After successful configuration, you can login your tarbell much more simply by running the following command: ssh tarbell […] Reference: Read more →

How to Prepare a Post Implementation Report?

2020-07-30
𝕋his is a guide on how to prepare a Post-Implementation Report for cloud credits, for future reference. This guide is based on the one prepared for the deadline of February 28th 2019. A Post-Implementation Report (PIR) provides data to compare the Cloud Credits model to traditional mechanisms of … Read more →

How to Submit to Zenodo

2020-07-30
ℍow to submit data to Zenodo Read more →

How to Use AWS

2020-07-30
𝕊top/start your EC2 instances programatically through AWS Command Line Interface (CLI). […] Stop your EC2 instances to avoid incurring charges when not in use. […] Your secret key must be kept very secret. Please store it in a very safe place and don’t include it in your code. … Read more →

How to Use RCC Cluster

2020-07-30
ℙlease follow the instruction to request your RCC account: General RCC User Account Request PI Account Name: pi-haky Rcc Software: R, RStudio, Python, Python Rcc Research: My main research goal is to perform biomedical big data analysis and develop computation tools to address a wide range of … Read more →

How to Use Workflowr

2020-07-30
#Open RStudio #Type the following: nameproject = “PNPO-Alcohol-Epilepsy” githubuser = “hakyimlab” library(workflowr) setwd("~/Github") wflow_git_config(user.name = “Your Name”, user.email = “email@domain”) wflow_start(nameproject) … Read more →

Molecular data available in GDC

2020-07-30
𝕋he NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including … Read more →

Querying BigQuery

2020-07-30
𝕗ind examples here https://hakyimlab.github.io/bigquery-covid19/query-phenomexcan.html […] worflowr code https://github.com/hakyimlab/bigquery-covid19 Read more →