Explore @ratschlab Open Source projects

Biomedical Informatics at ETH Zurich (@ratschlab)

ratschlab

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Location 🇨🇭 Switzerland
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RGAN

Recurrent (conditional) generative adversarial networks for generating real-valued time series data.

SOM-VAE

TensorFlow implementation of the SOM-VAE model as described in https://arxiv.org/abs/1806.02199

GP-VAE

TensorFlow implementation for the GP-VAE model described in https://arxiv.org/abs/1907.04155

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.

dpsom

Code associated with ACM-CHIL 21 paper 'T-DPSOM - An Interpretable Clustering Method for Unsupervised Learning of Patient Health States'

circEWS

circEWS public code

bnn_priors

Code for the paper "Bayesian Neural Network Priors Revisited"

HIRID-ICU-Benchmark

Repository for the HiRID ICU Benchmark (HiB) project

pancanatlas_code_public

Public repository containing research code for the TCGA PanCanAtlas Splicing project

mmr

A tool for Read Multi-Mapper Resolution

RiboDiff

RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data

ncl

Code of the paper "Neighborhood Contrastive Learning Applied to Online Patient Monitoring"

scim

Code for Universal Single-Cell Matching with Unpaired Feature Sets

Jupyter Notebook

SVGP-VAE

Tensorflow implementation for the SVGP-VAE model.

repulsive_ensembles

Repo for our paper "Repulsive deep ensembles are Bayesian"

Jupyter Notebook

uRNN

Code for "Learning Unitary Operators with Help From u(n)", AAAI-17. (https://arxiv.org/abs/1607.04903)

graph_annotation

Code accompanying the publication for compressed graph annotation

pmvae

Code for pmVAE model, seen in ICML CompBio '21

Jupyter Notebook

tensor-sketch-alignment

Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.

aestetik

AESTETIK: AutoEncoder for Spatial Transcriptomics Expression with Topology and Image Knowledge

boosting-bbvi

dgp-vae

Disentangled GP-VAE

Project2020-seq-tensor-sketching

secedo

Clustering tumor cells based on SNVs from single-cell sequencing data

mmugl

Code repository for MMUGL: Multi-modal Graph Learning over UMLS Knowledge Graphs

mlhc-seminar

Materials for a reading group on machine learning for healthcare and medicine.

oqtans_tools

Oqtans repository

rDiff

Tests for Differential RNA Isoform Expression

clinical-embeddings

Repository for the Paper: „On the Importance of Step-wise Embeddings for Heterogeneous Clinical Time-Series“

counting_dbg

Lossless Indexing with Counting de Bruijn Graphs

Jupyter Notebook

tls

Code for paper Temporal Label Smoothing for Early Event Prediction (ICML 2023)

easysvm

The EasySVM Toolbox based on Shogun

genome_graph_annotation

Sparse Binary Relation Representations for Genome Graph Annotation

sim_read_until

Simulator of an ONT device with ReadUntil gRPC support

Jupyter Notebook

HMSVMToolbox

The Hidden Markov SVM Toolbox

PBWT-sec

C++ implementation of PBWT-seq

projects-2020-Neural-SVGD

Nonparametric variational inference by transporting samples along a dynamically learned trajectory.

Jupyter Notebook

SNBNMF-mutsig-public

Supervised Negative Binomial NMF for Mutational Signature Discovery

oqtans

The master Oqtans repository with submodules

immunopepper

Code for the ImmunoPepper project

adaptive-stepsize-boosting-bbvi

ratschlab-common

Library of common Python code used across various projects

Jupyter Notebook

MiTie

The RNA-seq transcript predictor for multiple samples

mla

Scripts and data for reproducing the results of MetaGraph-MLA

Jupyter Notebook

projects2017-kG

row_diff

RowDiff transform for sparsification of graph annotations

Jupyter Notebook

genomic-gnn

Repository for the paper "Learning Genomic Sequence Representations using Graph Neural Networks over De Bruijn Graph"

mSplicer

Accurate splice form prediction based on discriminative learning

tools-gogo-gadget

A tool to aggregate custom command line tools into one.

path-fa

Code for "Probabilistic pathway based multimodal factor analysis"

Jupyter Notebook

simulate_spatial_transcriptomics_tool

Simulate spatial transcriptomics data

Jupyter Notebook

projects2020-disentangled-gpvae

Learning disentangled representations from time series.

rQuant

The RNA-seq transcript quantifier with Bias Correction

AdaBoost

Adaboost-Reg and RBF-Network code

seqCNN

embedding sequence using a convolutional network

Jupyter Notebook

metagraph_paper_resources

This repository contains resources related to the manuscript describing the MetaGraph framework

Jupyter Notebook

hif_splicing_code_public

public repo for the code used in "Characterisation of HIF-dependent alternative isoforms in pancreatic cancer"

gromics

Collection of tools and utilities for *omics analyses

ASP

Accurate Splice Site Predictions

palmapper

The accurate RNA-seq mapper

metannot

Multithreaded wavelet trie construction library

tools-cwl-workflow-experiments

Very simple workflows to experiment with containers and cwl

st-rep

Code of the paper "Representation learning for multi-modal spatially resolved transcriptomics data"

Jupyter Notebook