softbear

pytorch-seq2seq

Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText.

qstrader

QuantStart.com - QSTrader backtesting simulation engine.

course-content

NMA Computational Neuroscience course

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

in-silico-labeling

Code for In silico labeling: Predicting fluorescent labels in unlabeled images

Palantir

Single cell trajectory detection

DL4MolecularGraph

Literature of deep learning for graphs in Chemistry and Biology

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

PoincareMaps

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

memote

memote – the genome-scale metabolic model test suite

Cerebro

Visualization of scRNA-seq data.

kmer-db

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

ntJoin

🔗Genome assembly scaffolder using minimizer graphs

hsm

Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."

GGN

Gumbel Graph Network (GGN) : A General Deep Learning Framework for Network Reconstruction

APPLS

Applied Python Programming for Life Scientists

ARNI

Algorithm for Revealing Network Interactions (ARNI) from nonlinear collective dynamics

homefarm

Tools for deploying and managing a BOINC compute farm

MoonlightR

RCK

RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes

MLSummerSchool_CCA19

Materials for the Mini Summer School in Machine Learning x Astro taught at CCA in Summer '19

fqsqueezer

FQSqueezer - FASTQ compressor based on k-mer statistics

quarantineAtHome

quarantine@Home

sfa

A simulation framework to analyze signal flows in complex networks

rescue

Bootstrap imputation for scRNAseq data

ivado-mila-dl-school-2019-vancouver

training

GISA

C code and more for the GISA algorithm

NGNC

Neural Gene Network Constructor: A Neural Based Model for Reconstructing Gene Regulatory Network

MVIAm