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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.
count DNA sequence reads in BAM files
Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.
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
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
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
Scripts for processing PacBio transcriptome (Iso-Seq) data
CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
DeconstructSigs algorithm in python.
Dirichlet Process based methods for subclonal reconstruction of tumours
Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
good tools in my data analysis incluing shell, python, R
For measuring distances between genetic programming trees, both syntactically and via operators.
For my work in lab and notes
IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
Code and data for García-Mulero S et al, Journal for Immunotherapy of Cancer
Analysis pipeline for genomic study of Mongolian hepatocellular carcinoma
Mutational Signature Comprehensive Analysis Toolkit
An R package to time somatic mutations
Remove lambda phage reads from a fastq file
Scripts for the preprint "The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution".
A Nextflow Genome-Wide Association Study (GWAS) Pipeline
Code for mutational timing of gains and signatures analysis
Structural Variants Pipeline for Long Reads
DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.