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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.

decoupler_visualization

dotfiles

paul's shell, git, etc config files. also homebrew, migration setup. good stuff.

easybuild-easyconfigs

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

eqtm

eurocat

experiments_for_fun

fertility-prediction-challenge

Fertility prediction challenge

gaspacho

gavin

Gene specific calibrations for CADD scores based on ClinVar, ExAC and SnpEff

goodlookin

whats cookin good lookin

goshifter

GoShifter

gplvm_scrna

Scalable GPLVMs for scRNA

intermediatepython

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

mvid

ontology_test

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 ;)

project_scyfer

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"

single_cell

spark-cassandra-connector

DataStax Spark Cassandra Connector