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atac-seq-pipeline

ENCODE ATAC-seq pipeline

autism_rnaseq

Collaboration with Chetty lab to analyze Autism RNA-seq datasets

avutils

Place to start factoring out code from av scripts

bmi210_novelgenecandidatesfordisease

Code for BMI210 final project: Finding novel gene candidates for rare diseases

bmi214

bmi217

Code for BMI217 project on colorectal cancer pathogenic variant prediction

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

codonsub

Codon substitution script

cs231n_project

mini_image_net_challenge_cs231n_project

deeplearning_inputs

deeplift

Public facing deeplift repo

download_gt3x_files_from_centrepoint_api_in_python

Python scripts to download .gt3x files from Actigraph's CentrePoint, using the CP2 API.

dragonn

Deep Neural Networks Tutorial for Regulatory Genomics

explore

Gene expression tutorial for EXPLORE course

fastqsim

Platform-Independent Data Characterization and in Silico Read Generation for NGS Datasets

gecco-rna-analysis

Pipeline for gecco RNA-seq analysis

lsgkm

mseqgen

Multi task batch generator for training deep learning models on CHIP-seq, CHIP-exo, CHIP-nexus, ATAC-seq, RNA-seq (or any other -seq)

myexamplerepo

neuralnetworkforrealtimecardiacarrhythmiadetection

source code for BMI212 Arrhythmia Busters team, Spring 2016

ngsim

Platform-Independent Data Characterization and in Silico Read Generation for NGS Datasets

nobel_lab_projects

Projects for Nobel Lab https://nobel.bme.umich.edu/

pywgcna

PyWGCNA is a Python package designed to do Weighted correlation network analysis (WGCNA)

shap

A unified approach to explain the output of any machine learning model.

sherlockstoolkit

Forensic DNA analysis pipeline that analyzes SNP/STR data and performs downstream analysis (biogeographic ancestry, kinship, replicate analysis, mixture inclusion/exclusion)

simdna

A python library for creating simulated regulatory DNA sequences

sml

synapse_mhc_scripts

tfmodisco

TF MOtif Discovery from Importance SCOres