kcampbel

Contains accessory functions for rnaseq workflow

Pipeline for taking bamreadcount and sequenza CN/LOH through sciclone

detect known sequence read alignment breakpoints by upstream vector sequence

R scripts for HLAHAT

HLA HAT master Docker containing HISAT2, HISAT-genotype, and downstream Rscripts.

Annotate and summarize MNVs

ensembl-vep with plugins

run superfreq

RNAseq analysis methods

Run DegNorm (Degradation normalization) to assess transcript coverage by RNAseq