Matt Jones's Projects
Neural Net to predict the outcomes for ABC's The Bachelor.
Sorting Algs written in Python
Clustering Protein Sequences
10x Genomics Single Cell 3' Gene Expression and VDJ Assembly
Scripts for Analyzing Mutational Bias in Coding Regions of the Human Genome
An interactive map for representing projected savings per County
contributing a lineage tracing chapter to the extended-single-best-practices textbook
Dimensionality reduction for single cell RNA-seq data
An interactive map for representing projected savings per HRR
An interactive map for representing projected savings per HSA
C library for high-throughput sequencing data formats
Code & utilities for the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
Local Sequence Alignment using Smith-Waterman, implemented in Julia.
Scripts & Notebooks for the analysis of dynamic lineage tracing of lung cancer metastasis.
R implementation of MULTI-seq sample classification workflow
website for Northern California Computational Biology group
Basic 3 Layer Neural Nets for Classifying Transcription Factor Binding Sequences
PEPPER-Margin-DeepVariant
Pod5: a high performance file format for nanopore reads.
A small module for computing dihedral angles between molecules in a protein, and generating Ramachandran plots from the results.
A tutorial on how to make your first R package.
Single-Cell Analysis in Python. Scales to >1M cells.
R package for analyzing single-cell RNA-seq data
Deep generative modeling for single-cell transcriptomics
Simple simulation of single-cell RNA sequencing data
RNA-seq aligner
An introduction to using Tensorflow for the Center for Computational Biology Skills Seminar
Tools for handling Unique Molecular Identifiers in NGS data sets