tjbencomo

ngs-pipeline

Pipeline for Somatic Variant Calling with WES and WGS data

survival-talk-pntlab

Best practices for survival analysis at PNT Lab

bioinfo-scripts

Assortment of bioinformatics scripts

bulk-rnaseq

Workflow to process bulk RNASeq samples using Salmon and DESeq2

cna-pipeline

Whole exome somatic copy number analysis with Sequenza and CNVKit

cs191w

rna-pipeline

RNA sequencing pipeline for Stanford's Sherlock HPC cluster

.vim

kaplan-meier-problems

Survival data simulations to evaluate statistical power of Kaplan Meier analysis

notes

Lab notes and software usage guides

pharmer

Python tool to convert UWSOM drug list info into Anki cards

check-strand

Infer strandedness of RNA-Seq data

chemistry

col11a1-manuscript

col11a1-wes-pipeline

WES Pipeline for Lee et. al paper describing neoplastic invasion caused by mutant COL11A1

cs235

cs235-final-project

docker-recipes

ecdna-cscc

FindMyForest

Matching algorithm for FindMyForest CS278 Project

github-pages-with-jekyll

nb-helper

ngs-pipeline-retired

NGS Processing Pipelines for WGS and WES data

nmsc-star

plot-test

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

scc-meta-analysis

star-rsem

TBmisc

Another R package with tools for working with biomedical data

tjbencomo.github.io

My personal website