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codedefectai

Code Defect AI

coding-guidelines

Coding guidelines and best practices for developers @uniport @embl-ebi

compchem

Computational Chemistry stuff

cookbook

cs-video-courses

List of Computer Science courses with video lectures.

csb

Material for Computing Skills for Biologists

dash

Interactive, reactive web apps in pure python :level_slider: :bar_chart:

data-science-ipython-notebooks

Data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe, Keras), scikit-learn, Kaggle, big data (Spark, Hadoop MapReduce, HDFS), matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines.

datasciencepython

common data analysis and machine learning tasks using python

datascienceresources

Open Source Data Science Resources.

dcell

DCell browser and gene deletion simulator

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deepcut

A Thai word tokenization library using Deep Neural Network

deepsea

Similarity Ensemble Approach with deep learning substance fingerprints

detectdesign

toolkit for finding likely cas9 off-target binding and effect on gene expression, designing sgRNAs and pairs of sgRNAs with minimal off-target effect on gene-expression

dimpyplot

A Python frontend to the LigPlot+ program, allowing batch processing of Protein Data Bank (PDB) files through the DIMPLOT algorithm.

djiastats

Wikipedia page views plotted against stock metrics.

dlaicourse

Notebooks for learning deep learning

docker-dock6

Docker container for DOCK6 molecular docking software

docking-scripts

Scripts used for virtual screening of small molecule inhibitors from ZINC database using Autodock Vina

drugsetlibrary

e3fp

3D molecular fingerprints

ehr-phenolyzer

A pipeline that takes clinical notes from EHRs and generate phenotype terms, then generate ranked gene list

emr_visualization

examples

GPT

explore-uniprotkb-with-amazon-neptune

In this example, we will demonstrate the step-by-step process to create and use your own protein knowledge base using UniProt RDF data. We will show how to ingest a subset of UniProtKB data into your own Amazon Neptune database directly from the Registry of Open Data on AWS. We will then show how to query the data with SPARQL, create new relationships in the data and visualise the data as a graph.

fastq_compression_comparison

Creating a simple Docker image to help perform comparisons for FASTQ compression

galaxy-tool-temp-2019

Repo to test adjusted tools for the newest galaxy

gatk_pipeline

Pipeline for processing raw fastq files through SNP calling with GATK and subsequent filtering

gdynet

Unsupervised learning of atomic scale dynamics from molecular dynamics.