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6018_2017

Repository for DBMI 6018 Course Fall 2017

691-project

Distant Authorities Project

ab-initio-protein-structure-prediction

alphafold

Open source code for AlphaFold.

alphafold2

Alphafold Api for protein Visualization

ampl

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

anatomyofmatplotlib

Anatomy of Matplotlib -- tutorial developed for the SciPy conference

arch-protein-gene

Effect of architectural proteins on gene expression regulation

artificial-intelligence-pi

Turn a Raspberry Pi into your own personal assistant - using Amazon Echo's Alexa!

azuredevday

ballgown2deseq

Python script that takes a folder of ballgown files and reformats them for DESeq2

ballgown_code

analysis code used in Ballgown paper

bamsnap

bayesian-optimization

Python code for bayesian optimization using Gaussian processes

benchm-ml

A minimal benchmark for scalability, speed and accuracy of commonly used open source implementations (R packages, Python scikit-learn, H2O, xgboost, Spark MLlib etc.) of the top machine learning algorithms for binary classification (random forests, gradient boosted trees, deep neural networks etc.).

bio.jl

Bioinformatics and Computational Biology Infrastructure for Julia

biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

biojupies-plugins

User-submitted RNA-seq data analysis tools for BioJupies.

bioservices

Access to Biological Web Services from Python.

carnd-behavioral-cloning-p3

ccbr_gatk4_exome_seq_pipeline

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

cellprofiler

An open-source application for biological image analysis

chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

chembl_multitask

blogpost notebooks

chembl_webresource_client

Official Python client for accessing ChEMBL API.

clinvar

XGBoost classifiers to predict variant classification conflict

clinvar-miner

Website to analyze conflicting assertions in ClinVar

clinvar_workflow

cmappy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

cntk

Microsoft Cognitive Toolkit (CNTK), an open source deep-learning toolkit