Matsen Group

Fred Hutchinson Cancer Research Center, Seattle, WA

Pinned Repositories

gapml
Language:Python11 9 193
gctree
GCtree: phylogenetic inference of genotype-collapsed trees
Language:Python16 12 752
hyperfreq
Bayesian tool for APOBEC hypermutation analysis
Language:Python10 7 232
olmsted
B-cell repertoire and clonal family tree explorer
Language:JavaScript15 3 1464
phip-flow
A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
Language:Python9 5 406
phippery
Language:Python13 5 952
pt
Phylogenetic topographer.
Language:C++7 9 122
relay
Bare-bones continuous integration using Docker Hub and Slack.
Language:Python10 5 27
sumrep
Summary statistics for repertoires
Language:R16 11 416
vampire
🧛 Deep generative models for TCR sequences 🧛
Language:Python16 9 724

Matsen Group's Repositories

matsengrp/gctree
GCtree: phylogenetic inference of genotype-collapsed trees
Language:Python16 12 752
matsengrp/sumrep
Summary statistics for repertoires
Language:R16 11 416
matsengrp/olmsted
B-cell repertoire and clonal family tree explorer
Language:JavaScript15 3 1464
matsengrp/phippery
Language:Python13 5 952
matsengrp/phip-flow
A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
Language:Python9 5 406
matsengrp/linearham
A Bayesian Phylo-HMM for B cell receptor sequence analysis
Language:C++6 10 624
matsengrp/bcr-phylo-benchmark
Language:Jupyter Notebook3 4 48
matsengrp/phip-viz
Language:Python3 4 13
matsengrp/gp-benchmark-1
Language:Python2 2 01
matsengrp/larch
Inference and manipulation of history DAGs
Language:C++2 6 312
matsengrp/tex-template
Language:TeX2 3 1
matsengrp/antigen
Simulating virus evolution and epidemiology
Language:Mathematica1 3 160
matsengrp/multidms
Joint modeling of multiple deep mutational scanning experiments
Language:Jupyter Notebook1 4 960
matsengrp/phylostability
Language:Python1 4 1
matsengrp/SARS-CoV-2_spike_multidms
Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2
Language:Jupyter Notebook1 5 0
matsengrp/gp-benchmark-1-environment
Code to explore to what extent GP composite likelihoods and their derivatives correspond to more well-understood quantities
Language:Python0 3 100
matsengrp/CYP-multidms
a repository for the analysis of C9 and C19 dms data
Language:Jupyter Notebook5 0
matsengrp/dmsa-pred
A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.
Language:Python5 1
matsengrp/dnsm-json-database
Language:Python4 0
matsengrp/hdag-benchmark
Language:Python4 4
matsengrp/historydag
Language:Python3 231
matsengrp/infection-timing
Language:R2 0
matsengrp/lassa-dmsa
Nextstrain build for Lassa virus
Language:Python1 0
matsengrp/LASV-manuscript-nextstrain-dmsa
This repository holds the build code for generating a nextstrain tree with escape score predictions.
Language:Python4 0
matsengrp/LK-SARS-CoV-2
Repository for Linda Kizazi SARS-CoV-2 manuscript Analysis
Language:Jupyter Notebook5 0
matsengrp/SARS-CoV-2-S2-Abs
Repository for Antibody Responses to SARS-CoV-2 S2 manuscript
Language:Jupyter Notebook5 0
matsengrp/sdag-nni-experiments
Language:Jupyter Notebook
matsengrp/seasonal-flu-dmsa
Fork of seasonal-flu nextstrain build to include phenotype predictions informed by dms data.
Language:Python1 0
matsengrp/usher
Ultrafast Sample Placement on Existing Trees
Language:C++3 11
matsengrp/zika-dmsa
Nextstrain build for Zika virus with dms model phenotype predictions
Language:Python1 0