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.
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AWS

A. Detailed Instructions for Converting VirtualBox VMs to AWS AMIs
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Medical and Genetic Studies

1. Multifactor Clinical Study.
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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.