Biomedical Informatics at ETH Zurich (@ratschlab)
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ratschlab

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Top repositories

1

RGAN

Recurrent (conditional) generative adversarial networks for generating real-valued time series data.
Python
625
star
2

SOM-VAE

TensorFlow implementation of the SOM-VAE model as described in https://arxiv.org/abs/1806.02199
Python
186
star
3

GP-VAE

TensorFlow implementation for the GP-VAE model described in https://arxiv.org/abs/1907.04155
Python
120
star
4

spladder

Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
Python
101
star
5

metagraph

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
C++
86
star
6

dpsom

Code associated with ACM-CHIL 21 paper 'T-DPSOM - An Interpretable Clustering Method for Unsupervised Learning of Patient Health States'
Python
64
star
7

bnn_priors

Code for the paper "Bayesian Neural Network Priors Revisited"
Python
53
star
8

circEWS

circEWS public code
Python
52
star
9

HIRID-ICU-Benchmark

Repository for the HiRID ICU Benchmark (HiB) project
Python
48
star
10

pancanatlas_code_public

Public repository containing research code for the TCGA PanCanAtlas Splicing project
Python
40
star
11

mmr

A tool for Read Multi-Mapper Resolution
C++
24
star
12

RiboDiff

RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data
Python
21
star
13

ncl

Code of the paper "Neighborhood Contrastive Learning Applied to Online Patient Monitoring"
Python
20
star
14

SVGP-VAE

Tensorflow implementation for the SVGP-VAE model.
Python
18
star
15

scim

Code for Universal Single-Cell Matching with Unpaired Feature Sets
Jupyter Notebook
17
star
16

repulsive_ensembles

Repo for our paper "Repulsive deep ensembles are Bayesian"
Jupyter Notebook
16
star
17

uRNN

Code for "Learning Unitary Operators with Help From u(n)", AAAI-17. (https://arxiv.org/abs/1607.04903)
Python
15
star
18

graph_annotation

Code accompanying the publication for compressed graph annotation
C++
13
star
19

pmvae

Jupyter Notebook
12
star
20

tensor-sketch-alignment

Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.
C++
12
star
21

boosting-bbvi

Python
7
star
22

dgp-vae

Disentangled GP-VAE
Python
7
star
23

Project2020-seq-tensor-sketching

C++
7
star
24

secedo

Clustering tumor cells based on SNVs from single-cell sequencing data
C++
6
star
25

mlhc-seminar

Materials for a reading group on machine learning for healthcare and medicine.
5
star
26

oqtans_tools

Oqtans repository
C++
5
star
27

rDiff

Tests for Differential RNA Isoform Expression
C
5
star
28

counting_dbg

Lossless Indexing with Counting de Bruijn Graphs
Jupyter Notebook
5
star
29

tls

Code for paper Temporal Label Smoothing for Early Event Prediction (ICML 2023)
Python
5
star
30

clinical-embeddings

Repository for the Paper: โ€žOn the Importance of Step-wise Embeddings for Heterogeneous Clinical Time-Seriesโ€œ
Python
5
star
31

easysvm

The EasySVM Toolbox based on Shogun
Python
5
star
32

genome_graph_annotation

Sparse Binary Relation Representations for Genome Graph Annotation
C++
4
star
33

sim_read_until

Simulator of an ONT device with ReadUntil gRPC support
Jupyter Notebook
3
star
34

HMSVMToolbox

The Hidden Markov SVM Toolbox
MATLAB
3
star
35

PBWT-sec

C++ implementation of PBWT-seq
C++
3
star
36

projects-2020-Neural-SVGD

Nonparametric variational inference by transporting samples along a dynamically learned trajectory.
Jupyter Notebook
3
star
37

ratschlab-common

Library of common Python code used across various projects
Jupyter Notebook
2
star
38

adaptive-stepsize-boosting-bbvi

Python
2
star
39

mmugl

Code repository for MMUGL: Multi-modal Graph Learning over UMLS Knowledge Graphs
Python
2
star
40

projects2017-kG

Python
2
star
41

MiTie

The RNA-seq transcript predictor for multiple samples
C
2
star
42

mla

Scripts and data for reproducing the results of MetaGraph-MLA
Python
2
star
43

oqtans

The master Oqtans repository with submodules
Shell
2
star
44

SNBNMF-mutsig-public

Supervised Negative Binomial NMF for Mutational Signature Discovery
Python
2
star
45

mSplicer

Accurate splice form prediction based on discriminative learning
C++
2
star
46

tools-gogo-gadget

A tool to aggregate custom command line tools into one.
Python
2
star
47

projects2020-disentangled-gpvae

Learning disentangled representations from time series.
Python
1
star
48

rQuant

The RNA-seq transcript quantifier with Bias Correction
MATLAB
1
star
49

AdaBoost

Adaboost-Reg and RBF-Network code
C
1
star
50

immunopepper

Code for the ImmunoPepper project
Python
1
star
51

seqCNN

embedding sequence using a convolutional network
Jupyter Notebook
1
star
52

metagraph_paper_resources

This repository contains resources related to the manuscript describing the MetaGraph framework
Jupyter Notebook
1
star
53

row_diff

RowDiff transform for sparsification of graph annotations
Jupyter Notebook
1
star
54

hif_splicing_code_public

public repo for the code used in "Characterisation of HIF-dependent alternative isoforms in pancreatic cancer"
R
1
star
55

gromics

Collection of tools and utilities for *omics analyses
Python
1
star
56

ASP

Accurate Splice Site Predictions
C++
1
star
57

palmapper

The accurate RNA-seq mapper
C++
1
star
58

metannot

Multithreaded wavelet trie construction library
C++
1
star
59

tools-cwl-workflow-experiments

Very simple workflows to experiment with containers and cwl
Python
1
star