RNASeq Sample Attribute Processing

I'm adding some of my RNA-Seq Data Analysis to this page.

1. RNA-Seq FASTQ processing pipeline using Hisat2, StringTie, Samtools and Salmon.
2. Determining Important Sample Attributes in Genomic Data Commons
3. Cleaning Up RNASeq and Sample Attribute Dataframes

Machine Learning on RNA-Seq Data

1. Using Lasso-Regularized Logistic Regression to Predict Breast Cancer. ComBat-corrected structured data.
2. Using Lasso-Regularized Logistic Regression to Predict Breast Cancer. Non-batch corrected with structured data.

AWS

A. Detailed Instructions for Converting VirtualBox VMs to AWS AMIs

Medical and Genetic Studies

1. Multifactor Clinical Study.

Python

1. Query cBioPortal with HUGO gene name, and determine all mutations in that gene across cBioPortal, along with the number of unique samples containing each mutation.