Joshua Levy's repositories
Joshua-Levy-Synteny-Analysis
Integrated Analysis of Synteny (Multiple Synteny Comparison for Multiple Alignment, Circos Outputs, Allmaps Genome Reconstructions), Find Ghost Genes, Identify and Analyze CNS Elements from Multiple Alignment Files and More!
ScaffolderPipeline
Highly parallelized scaffolder, turns scaffold level genomes into chromosomes via synteny
PolyCRACKER-Unofficial-Mirror
A robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5828-5
CircosDropper
Automated visualization of pairwise synteny
JoshuaTree
Using pairwise synteny for high throughput genomics, multiple sequence alignment, population genetics, and phylogeny
JoshuaTree2
High throughput scaffolding and phylogenetic inference pipeline from syntenic blocks.
PyMethylProcess
Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
gae-pytorch
Graph Auto-Encoder in PyTorch
LearningScripts
Scripts I wrote when I first learned python
pytorch_cluster
PyTorch Extension Library of Optimized Graph Cluster Algorithms
pytorch_geometric
Geometric Deep Learning Extension Library for PyTorch
pytorch_practice
Some practice scripts from earlier this year
SimpleHTTPAuthServer
Python SSL server using Basic auth and SimpleHTTP. extended and imported from gist: https://gist.github.com/fxsjy/5465353
util
Utility modules for Python