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aceseqworkflow

Allele-specific copy number estimation with whole genome sequencing

alignmentandqcworkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs.

biomine

Bioinformatics data-mining

blacklist

Application for making ENCODE Blacklists

charger

Characterization of Germline variants

clinvar

This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.

cola

Unsupervised subgroup classification based on consensus clustering

compgenomr_book

coworkflowsbaseplugin

A basic Roddy plugin for computational oncology workflows

cv

My CV built using RMarkdown and the pagedown package.

deep-learning-with-r-notebooks

R notebooks for the code samples of the book "Deep Learning with R"

demo_app

docker-annotsv-cwl

Docker container for running AnnotSV

docker_flask

A demo flask app in docker

docker_test

A docker image for the ML

fashion-mnist-cnn-rkeras

updated MNIST CNN script from rKeras

germlinesmallvariantanalysis

handson-ml

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in python using Scikit-Learn and TensorFlow.

indelcallingworkflow

A Platypus-based workflow for indel calling

karpathy_nn_z2h

A tiny scalar-valued autograd engine and a neural net library on top of it with PyTorch-like API. Based on Karpathy's micrograd

kmodes

Python implementations of the k-modes and k-prototypes clustering algorithms, for clustering categorical data

learning_ml_statistics

Learning ML with different data sets

lollipops

Lollipop-style mutation diagrams for annotating genetic variations.

mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

nagacombio

nagacombio.github.io

octopus

Bayesian haplotype-based mutation calling

ph525

platypusgermlinepipeline

Platypus based small variant calling on a single or multiple samples setting.

pydata-book

Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media