shuang1330's repositories

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450K_DataProcessing

Complete pipeline to process Illumina 450K methylation data.

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aiHackCovid

Example Hackathon Submission

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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.

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Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

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decoupler-py

Python package to infer biological activities from omics data using a collection of methods.

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easybuild-easyconfigs

A collection of easyconfig files that describe which software to build using which build options with EasyBuild.

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fertility-prediction-challenge

Fertility prediction challenge

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Goodlookin

whats cookin good lookin

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goshifter

GoShifter

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gplvm_scrna

Scalable GPLVMs for scRNA

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kafka-docker

Dockerfile for Apache Kafka

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lime

Lime: Explaining the predictions of any machine learning classifier

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lime-experiments

Code for all experiments.

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Milo2.0Analysis_2023

Scripts and notebooks to accompany the Milo2.0 manuscript

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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 ;)

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scikit-learn

scikit-learn: machine learning in Python

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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"

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spark-cassandra-connector

DataStax Spark Cassandra Connector

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systemsgenetics

Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool

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vimrc

The ultimate Vim configuration: vimrc

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