📖 A collection of pure bash alternatives to external processes.

An Artificial Neural Network-based discriminator for validating clinically significant genomic variants

Python and C++ code for reading and writing genomics data.

This repository holds the companion project to Goby3, used to train and evaluate deep learning models to call variations. This repository contains the Matcha framework to help train and evaluate de…

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

RUFUS k-mer based genomic variant detection

⛔️ DEPRECATED – See https://github.com/ageron/handson-ml3 instead.

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,…

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

Fast, flexible and easy to use probabilistic modelling in Python.

Deep neural networks for predicting CpG methylation

Convolutional neural network analysis for predicting DNA sequence activity.

Python Data Science Handbook: full text in Jupyter Notebooks

📝 An awesome Data Science repository to learn and apply for real world problems.

Approximate Nearest Neighbor Search for Sparse Data in Python!

A Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Recipes for using Python's pandas library

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

Curated decibans of scientific programming resources in Python.

The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from WGS Illumina data

High throughput, pain-free big data pipelines.

bedtools - the swiss army knife for genome arithmetic

C library for high-throughput sequencing data formats

A curated list of awesome big data frameworks, ressources and other awesomeness.

Code and examples for JHU Computational Genomics class

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more