shuang1330's repositories
450K_DataProcessing
Complete pipeline to process Illumina 450K methylation data.
aiHackCovid
Example Hackathon Submission
avocado
Avocado is a multi-scale deep tensor factorization model that learns a latent representation of the human epigenome and enables imputation of epigenomic experiments that have not yet been performed.
Beeline
BEELINE: evaluation of algorithms for gene regulatory network inference
decoupler-py
Python package to infer biological activities from omics data using a collection of methods.
easybuild-easyconfigs
A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
fertility-prediction-challenge
Fertility prediction challenge
Goodlookin
whats cookin good lookin
goshifter
GoShifter
gplvm_scrna
Scalable GPLVMs for scRNA
kafka-docker
Dockerfile for Apache Kafka
lime
Lime: Explaining the predictions of any machine learning classifier
lime-experiments
Code for all experiments.
Milo2.0Analysis_2023
Scripts and notebooks to accompany the Milo2.0 manuscript
Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
scikit-learn
scikit-learn: machine learning in Python
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
spark-cassandra-connector
DataStax Spark Cassandra Connector
systemsgenetics
Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
vimrc
The ultimate Vim configuration: vimrc