bioinfo-dirty-jobs Goto Github PK

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100-days-of-ml-code

100 Days of ML Coding

2016-adv-begin-shell-genomics

Workshop content for http://dib-training.readthedocs.org/en/pub/2016-01-13-adv-beg-shell.html

3d-deep-learning

3D Deep Learning works

3d-resnets-pytorch

3D ResNets for Action Recognition (CVPR 2018)

alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

ants

Advanced Normalization Tools (ANTs)

attention-gated-networks

Use of Attention Gates in a Convolutional Neural Network / Medical Image Classification and Segmentation

awesome-cancer-variant-databases

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

awk-lesson

an introduction to awk

balzac-for-jekyll

Your favorite AnchorCMS theme, now for Jekyll!

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio_validation_workflows

A community menagarie of automated variant validations using bcbio and the Common Workflow Language

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bioinformatics

Tools for bioinformatics

brain-tumor-detection-and-segmentation-using-deep-learning

This repo includes Glioma Segmentation with Mask R-CNN and U-Net.

brainstools

A suite of tools for medical image processing focused on brain analysis

callings-nf

GATK RNA-Seq Variant Calling in Nextflow

cdgnet

Repository for code related to the CDGnet tool for prioritizing targeted cancer therapies

chance

Download binary executables and sample data here:

chimerascan-vrl

A fork of chimerascan that supports variable read lengths

chipseq

ChIPSeQ Analysis Protocol

cipher-workflow-platform

A data processing platform for ChIP-seq, RNA-seq, MNase-seq, DNase-seq, ATAC-seq and GRO-seq datasets. Please ignore information on cipher.readthedocs.io, it is currently out of date. Follow information in README.

conda_vcf2maf

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

custom_errors

This is mostly for me to keep my ErrorDocuments straight. I have a few galaxies that benefit from having 503 catch pages!

darcsign

DNA repair classification signatures: Using XGBoost models to classify DNA repair defects from liquid biopsy sequencing.

data

data-augmentation-and-segmentation-with-gans-for-medical-images

Generating randomized brain MRI images from random noise using a GAN. Additionally translating from one image domain to another with a conditional GAN (pix2pix): Segmenting brain anatomy - Generating brain MRI from the segmentation - Augmenting the translation of image modalities in a limited dataset to perform ischemic stroke segmentation.

deepmedic

Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans