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abs_maf_clustering_vis

This workflow can be used to visualize the data from an *ABS_MAF.txt absolute file output. Both detection power and genomic locus are plotted for all SNPs, along with clustering information based on cancer cell fraction.

arm_level_alteration

bam-readcount

count DNA sequence reads in BAM files

bioinfscripts

Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.

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

call_cna_from_absolute

Given gene annotated segtab files from ABSOLUTE generate arm and band level annotations and calls for amplifications, LOH, and deletions based on process from Brastianos, Carter et al Cancer Discovery 2015

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

cdna_primer

Scripts for processing PacBio transcriptome (Iso-Seq) data

comut

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

deconstruct_sigs_py

DeconstructSigs algorithm in python.

dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours

fastclone_guanlab

freec

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

good-tools

good tools in my data analysis incluing shell, python, R

gpdistance

For measuring distances between genetic programming trees, both syntactically and via operators.

gsk-spring-semester-rotation-and-class-notes

For my work in lab and notes

isoseq3

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

lopez_etal_2019_wgd-cancer

lungdevelopment

mets-immunecluster

Code and data for García-Mulero S et al, Journal for Immunotherapy of Cancer

mongolianhcc

Analysis pipeline for genomic study of Mongolian hepatocellular carcinoma

musicatk

Mutational Signature Comprehensive Analysis Toolkit

mutationtimer

An R package to time somatic mutations

nanolyse

Remove lambda phage reads from a fastq file

neoantigen-landscape-msi

Scripts for the preprint "The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution".

nf-gwas-pipeline

A Nextflow Genome-Wide Association Study (GWAS) Pipeline

pcawg11-timing_and_signatures

Code for mutational timing of gains and signatures analysis

phylogicndt

picky

Structural Variants Pipeline for Long Reads

pvac-seq

DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools