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africanelephantgenomics

bacteriaepistasissimulator

This directory contains code to simulate DNA under a neutral model of mutation and bacterial recombination, and the output of this may then be used in another simulator with multilocus epistasis.

bacteriaepistasissimulator_deprecated

bioconda-recipes

Conda recipes for the bioconda channel.

brian-arnold.github.io

💎 🐳 A super customizable Jekyll theme for personal site, team site, blog, project, documentation, etc.

calc_allelefrequency_tetraploid

Calculate allele frequencies from a VCF file of tetraploid genotypes

calculatepcovertime

Script to analyze the relationship between linkage and time

comp-pop-gen

Automatic pipeline to go from SRA to vcfs

daf_fst_faywuh

decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

dotfiles

enigma_takehome

epistasis_reanalysis

reanalyzing higher-order interactions of publically available data

git-lesson

HSPH lesson on git/github

git-lesson2

HSPH workshop on git/github

haploid_fwdpp

Using fwdpp C++ library to simulate bacterial evolution

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

intro_compbio_workflows_2024

Introduction to computational workflows in biology

intro_ml_eeb_2023

Introduction to Machine Learning for EEB

machina

Framework for Metastatic And Clonal History INtegrative Analysis

metastaticevol

Snakemake workflow combining tools developed by the Raphael lab at Princeton University

ngonorrhoeaelinkagegenomics

This repository contains a collection of Perl scripts for population genetic analysis of genomic data and C++ programs used to simulate various evolutionary scenarios.

parsevcf_2_alleletable

python script that takes VCF and BED files, outputs alleles and frequencies

pringle_lab_metabarcoding

A workflow for DNA metabarcoding

projects

metadata for ongoing or published projects

refactor_lukas_imaging_workflow

This repository is dedicated to understanding an existing calcium imaging analysis workflow through refactoring the original code.

rstudio_binder_test

Using R with Jupyter / RStudio on Binder

rstudio_binder_test2

R and RStudio via conda packages in repo2docker

shortread_variantcalling_snakemake

somaticvarcall

Snakemake workflow for calling somatic variants in tumors