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mit-deep-learning

Tutorials, assignments, and competitions for MIT Deep Learning related courses.

ml4calibrated450k

This is a companion repository for the article "Comparative analysis of machine learning classifiers and calibration algorithms for estimating class probabilities for personalized cancer diagnostics on DNA methylation microarray data"

mutation-signatures

Create mutation signatures from MAF's, and decompose them into Stratton signatures

mycnamplicon

na12878

Data and analysis for NA12878 genome on nanopore

neoantigen_calling_pipeline

Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA

neoepitopepred

Code accompanying the publication "The neoepitope landscape in pediatric cancers"

network_inference_tutorials

neural-networks-for-breast-cancer-proteins

Machine Learning for breast cancer protein screening

neutral-tumour-evolution-werner-2018

Jupyter notebook to generate figures in Werner et al 2018 Nature Genetics

neutral-tumour-evolution-williams-2018

Jupyter notebook to produce figure from "Reply to ‘Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data’ "

nextflow-tutorial

Nextflow training material for introductory tutorial

optitype

Precision HLA typing from next-generation sequencing data

pcawg-11

Code accompanying "The evolutionary history of 2,658 cancers", bioRxiv

pcawg-broad-wgs-variant-caller

pipeline

pipeline5

ppurple

Probabilistic purity ploidy estimation

prada2

prepareaa

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect.

py-webrtcvad

Python interface to the WebRTC Voice Activity Detector

pyflow-rnaseq

RNAseq pipeline based on snakemake

pymi

Python implementation of mutual information calculation using B-spline from Daub et. al.

pymutualinformation

Mutual information between continuous variables in Python

pypeliner

r-genomics

resin

REarrangement Signatures ImplemeNtation

retread

REcurrenT REArrangement Discovery

rna-seq-analysis

RNAseq analysis notes from Tommy Tang

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.