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gctree
GCtree: phylogenetic inference of genotype-collapsed treessumrep
Summary statistics for repertoiresvampire
π§ Deep generative models for TCR sequences π§olmsted
B-cell repertoire and clonal family tree explorerphippery
gapml
phip-flow
A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasetsrelay
Bare-bones continuous integration using Docker Hub and Slack.hyperfreq
Bayesian tool for APOBEC hypermutation analysispt
Phylogenetic topographer.linearham
A Bayesian Phylo-HMM for B cell receptor sequence analysiscft
Clonal family treesmctc
Our fork of Adam M. Johansen's Sequential Monte Carlo Template Classbetarat
Bayesian analysis of contingency tables as the ratio of two binomially distributed random variablesvampire-analysis-1
Data analysis using the vampire models for immune cell receptor distributionstangle
Code for working with tanglegrams.ig-sw
Smith-Waterman alignment for immunoglobulinsbcr-phylo-benchmark
larch
Inference and manipulation of history DAGsalnclst
A simple UCLUST-like clustering algorithm for pre-aligned sequences with built in recenteringtransport
curvature
Ricci-Ollivier curvature of SPR and related graphs.ecgtheow
Ancestral lineage reconstruction using BEAST or RevBayessamm
Survival analysis of mutation motifssci-space-v2
phage-dms-nhp-analysis
repo for the NHP Phage DMS manuscript analysistorchdms
Analyze deep mutational scanning data with PyTorchtorchfun
Learning PyTorchpan-CoV-manuscript
This repository will contain all source code, data, and other files relevant to the pan-CoV phip-seq paper.vdjProjectComparison
Repo contains projects and script to compare projectsgoliketree
Phylogenetic likelihoods in Go via BEAGLE, just to try out the languagelibptpll
tex-template
gp-benchmark-1
gricci
SAGE implementation of Ricci-Ollivier curvature on graphs.bioboxmixcr
A biobox (http://bioboxes.org/) for Mixcr (https://github.com/milaboratory/mixcr)conda-beagle
For a Docker image containing conda and the BEAGLE phylogenetic likelihood librarybioboxpartis
This repository contains the partis project (https://github.com/psathyrella/partis) packaged into a biobox (http://bioboxes.org/).multidms
Joint modeling of multiple deep mutational scanning experimentsLove Open Source and this site? Check out how you can help us