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2020-genome_assembly_workshop

Explore the world of genome assembly and gain an understanding of the power and pitfalls of sequencing technologies and assembly techniques.

6.881

admixture_graph

Module for analysing admixture graphs

akt

Ancestry and Kinship Tools

asmc

Ascertained Sequentially Markovian Coalescent

awesome-cryoem

A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

bio_tools

Useful bioinformatic scripts

bite

BITE: BioInformatics tools for everyone

burchardlab_tutorials

ca-backbone-prediction

Deep Learning for Ca Backbone Prediction from High Resolution CryoEM Data

cactus

Official home of genome aligner based upon notion of Cactus graphs

canu

A single molecule sequence assembler for genomes large and small.

cms

Composite of Multiple Signals: tests for selection in meiotically recombinant populations

cnngwas

consdb

A Python tool for interfacing with large variant databases and performing consensus genome operations.

copenhagen2016tutorial

Tutorial of ngsTools and ANGSD for Copenhagen 2016 course students

cpython

The Python programming language

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

data

deep-histopath

A deep learning approach to predicting breast tumor proliferation scores for the TUPAC16 challenge

deeppath

Classification of Lung cancer slide images using deep-learning

deepslide

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

diploshic

discoal

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

dsrg

Weakly-Supervised Semantic Segmentation Network with Deep Seeded Region Growing (CVPR 2018).

dsrg-tensorflow

a tensorflow version for DSRG (Weakly-Supervised Semantic Segmentation Network with Deep Seeded Region Growing)

encurv

Tools for maintaining predefined membrane curvature in MD simulations

evoef2

a fast and accurate physical energy function extended from EvoEF for protein sequence design

filtlong

quality filtering tool for long reads

fossildating

A paper describing how to estimate fossil ages using Bayesian phylogenetic total evidence dating