Niknafs

NGSTools

NGSTools

MutProfiler

Generate allelic depth table for a set of mutated genomic positions from a bam file

appliedgenomics

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

bms038_analysis

Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for manuscript https://doi.org/10.1016/j.cell.2017.09.028 See also http://www.ioexplorer.org for interactive visuallization

CancerGeneAnnotator

Tools to annotate a list of genes/mutations for causal implications of genes in cancer

cnvkit

Copy number variant detection from targeted DNA sequencing

cruk-summer-school-2017

Analysis of Cancer Genomes; 2017 edition

cruk-summer-school-2018

Summer school course materials collection

datasauRus

The Datasaurus Dozen datasets

Edward_trial

This houses some of my experiments with the Edward probabilistic programming language from http://edwardlib.org/

fishplot

Create timecourse "fish plots" that show changes in the clonal architecture of tumors

ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

IGV-snapshot-automator

Script to automatically create and run IGV snapshot batcscripts

jhu-thesis-template

JHU Thesis Template

latex-paper-template

Latex template for writing papers

niknafs.github.io

PureCN

Copy number calling and variant classification using targeted short read sequencing

rs_vv_realign

Shared code for realignment processing of Exome data

scarHRD

TMwR

Code and content for "Tidy Modeling with R"

word_cloud

A little word cloud generator in Python