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2015

Public material for CS109

2015lab1

450k-analysis-guide

A Practical (And Opinionated) Guide To Analyzing 450K Data

aging-study

Metadata and some analysis for the T-cell repertoire aging study

alphafold

Open source code for AlphaFold.

american-gut-analyses

bnp_tutorial

bootstrap_ab_test

busseq

Batch Effect Correction with Unknown Subtypes for scRNA-seq Data

causal_inference_python_code

Python code for part 2 of the book Causal Inference, by Miguel Hernán and James Robins

causaltree

Working repository for Causal Tree and extensions

celltypes450

adjust for cell-type composition in 450K data using houseman's and other methods.

dact

Testing for mediation effects in genome-wide epigenetic studies

dasc

Detecting hidden batch factors through data adaptive adjustment for biological effects

deepmediation

depict

DEPICT code, instructions and an example

devbootcamp

porfolio repo for all Dev Bootcamp work

dmlmt

Double Machine Learning for Multiple Treatments

dnamethylation

ebmmt

erstruct

A MATLAB toolbox for inferring number of sub-populations based on genotype information

erstruct-1

The Official Python Version for Paper "An Eigenvalue Ratio Approach to Inferring Population Structure from Whole Genome Sequencing Data"

fast-lmm

Python version of Factored Spectrally Transformed Linear Mixed Models

genesis

GENetic Effect-Size distribution Inference from Summary-level data

gmpr

Calculate the normalizing factors for zeroinflated sequencing data such as microbiome sequencing data

gwas

interventional-effects

invalidiv

irls

C++ implementation of IRLS algorithm for generalized linear model

ldsc

LD Score Regression (LDSC)