Pinned Repositories
ALE
Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
ASTRAL
Accurate Species TRee ALgorithm
aws-scripts
BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
bpp
Bayesian analysis of genomic sequence data under the multispecies coalescent model
coalhmm
CoalHMM
compbio
Python libraries and utilities for computational biology
compbioftw
Essential introductory materials to get into computational biology.
eeiyowei's Repositories
eeiyowei/ALE
Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
eeiyowei/An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
eeiyowei/ASTRAL
Accurate Species TRee ALgorithm
eeiyowei/aws-scripts
eeiyowei/BactDating
Bayesian inference of ancestral dates on bacterial phylogenetic trees
eeiyowei/bpp
Bayesian analysis of genomic sequence data under the multispecies coalescent model
eeiyowei/compbioftw
Essential introductory materials to get into computational biology.
eeiyowei/competititiveRooting
comparing various rooting algorithms for phylogenetic language trees
eeiyowei/Complete-Python-3-Bootcamp
Course Files for Complete Python 3 Bootcamp Course on Udemy
eeiyowei/CppCoreGuidelines
The C++ Core Guidelines are a set of tried-and-true guidelines, rules, and best practices about coding in C++
eeiyowei/deep-learning-genomics-primer
Contains files for the deep learning in genomics primer.
eeiyowei/dgrp-rna-seq
Codes for the DGRP RNA-Seq analyses
eeiyowei/EQG
Arnold & Felsenstein's Evolutionary Quantitative Genetics course
eeiyowei/fucking-algorithm
手把手撕LeetCode题目，扒各种算法套路的裤子。English version supported! Crack LeetCode, not only how, but also why.
eeiyowei/graphsage-simple
Simple reference implementation of GraphSAGE.
eeiyowei/HyDe
Hybridization detection using phylogenetic invariants
eeiyowei/ipcoal
Simulation package for getting gene tree distributions and loci / SNPs from input tree topologies and migration / Ne scenarios. Wraps around msprime.
eeiyowei/MrBayes
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
eeiyowei/NRLPapers
Must-read papers on network representation learning (NRL) / network embedding (NE)
eeiyowei/OnJava8
《On Java 8》中文版，又名《Java编程**》 第5版
eeiyowei/phylomad
eeiyowei/PhyloNetworks.jl
A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks
eeiyowei/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
eeiyowei/pytorch-template
PyTorch deep learning projects made easy.
eeiyowei/RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
eeiyowei/seurat
R toolkit for single cell genomics
eeiyowei/Taming-the-BEAST-2019-Sydney-Lectures
Repository for lectures held at the 2019 TTB workshop at the University of Sydney.
eeiyowei/tutorials
Tutorials on phylogenetic and phylogenomic inference
eeiyowei/USTC-Course
:heart:**科学技术大学课程资源
eeiyowei/variational-smc
Reference implementation of variational sequential Monte Carlo proposed by Naesseth et al. "Variational Sequential Monte Carlo" (2018)