ratschlab repositories

148 repositories

tools-project-archives
Public
A commandline tool to create and handle project archives
Python
•
MIT License
•1•2•5•1•Updated Oct 6, 2026Oct 6, 2026
metagraph
Public
Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
search rna-seq genomics
search rna-seq genomics graph assembly metagenomics indexing dna alignment amino-acids
C++
•
GNU General Public License v3.0
•26•229•4•17•Updated Oct 6, 2026Oct 6, 2026
DeepSpot
Public
DeepSpot: Deep learning model for predicting spatial transcriptomics from H&E histopathology images. Supports spot-level (Visium) and single-cell (Xenium) resol…
machine-learning bioinformatics deep-learning
machine-learning bioinformatics deep-learning gene-expression pytorch single-cell cancer-research digital-pathology pathology computational-pathology
Jupyter Notebook
•
MIT License
•21•101•0•0•Updated Oct 5, 2026Oct 5, 2026
DeepSpot2Cell
Public
DeepSpot2Cell: Predicting virtual single-cell spatial transcriptomics from H&E images using spot-level supervision
bioinformatics deep-learning gene-expression
bioinformatics deep-learning gene-expression pytorch single-cell deconvolution cell-segmentation digital-pathology computational-pathology spatial-transcriptomics
Python
•
MIT License
•4•21•0•0•Updated Oct 5, 2026Oct 5, 2026
winn
Public
R package for metabolomics data correction using a multi-step pipeline
HTML
•1•1•0•0•Updated Sep 16, 2026Sep 16, 2026
NASExperiments
Public
Selective Sequencing Experiments
Python
•1•0•0•0•Updated Sep 15, 2026Sep 15, 2026
ReadBouncer
Public
Fast and scalable nanopore adaptive sampling
C++
•
GNU General Public License v3.0
•3•0•0•0•Updated Sep 10, 2026Sep 10, 2026
DeepSpotM
Public
Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.
bioinformatics deep-learning cancer
bioinformatics deep-learning cancer gene-expression pytorch medical-imaging transcriptomics histology digital-pathology oncology
Python
•
Other
•10•58•2•0•Updated Sep 4, 2026Sep 4, 2026
vision-guided-transcriptomics-fm-2026
Public
Python
•0•0•0•0•Updated Sep 1, 2026Sep 1, 2026
immunopepper_analysis
Public
Analyses for ImmunoPepper paper
Jupyter Notebook
•
Other
•0•0•0•0•Updated Aug 21, 2026Aug 21, 2026
aestetik
Public
AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data
machine-learning bioinformatics deep-learning
machine-learning bioinformatics deep-learning pytorch autoencoder representation-learning single-cell digital-pathology computational-pathology multimodal
Jupyter Notebook
•
MIT License
•4•28•0•0•Updated Aug 18, 2026Aug 18, 2026
mla
Public
Scripts and data for reproducing the results of MetaGraph-MLA
Jupyter Notebook
•
GNU General Public License v3.0
•0•3•0•0•Updated Jul 27, 2026Jul 27, 2026
WiNN-for-technical-correction
Public
Repository accompanying the WiNN paper, containing reproducible analysis notebooks for the simulation benchmark and public multi-batch dataset, together with co…
R
•
MIT License
•0•0•0•0•Updated Jul 26, 2026Jul 26, 2026
collinearity
Public
C++
•0•0•0•0•Updated Jul 26, 2026Jul 26, 2026
sigmoni
Public
Nanopore signal-based classification using compressed indexing and matching statistics
Python
•
GNU General Public License v3.0
•3•0•0•0•Updated Jul 7, 2026Jul 7, 2026
spumoni
Public
Pan-Genomic Matching Statistics
C++
•
GNU General Public License v3.0
•9•0•0•0•Updated Jul 2, 2026Jul 2, 2026
RawHash
Public
RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genomes) in real-time without…
C
•
GNU General Public License v3.0
•12•1•0•0•Updated Jun 24, 2026Jun 24, 2026
MinknoApiSimulator
Public
Python
•0•0•0•0•Updated Jun 11, 2026Jun 11, 2026
seq2squiggle
Public
End-to-end simulation of nanopore sequencing signals with feed-forward transformers
Python
•
MIT License
•4•0•0•0•Updated Jun 3, 2026Jun 3, 2026
multi-slide-aestetik-2026-analysis
Public
cross-patient multi-modal integration using aestetik
Jupyter Notebook
•0•0•0•0•Updated May 29, 2026May 29, 2026
he2st
Public
Code of the paper "DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images"
machine-learning reproducible-research pathology
machine-learning reproducible-research pathology spatial-transcriptomics
Jupyter Notebook
•
MIT License
•1•15•0•0•Updated May 12, 2026May 12, 2026
stmdit
Public
Python
•
Apache License 2.0
•0•1•0•0•Updated Apr 28, 2026Apr 28, 2026
spladder
Public
Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
Python
•
Other
•35•115•33•1•Updated Apr 13, 2026Apr 13, 2026
icarefm
Public
Root repository for ICareFM: "A Foundation Model for Intensive Care Unlocking Generalization across Tasks and Domains at Scale"
0•25•4•1•Updated Apr 4, 2026Apr 4, 2026
Megatron-LM
Public
Ongoing research training transformer models at scale
Python
•
Other
•4.6k•0•0•0•Updated Apr 3, 2026Apr 3, 2026
apertus-finetuning-recipes
Public
Python
•
Apache License 2.0
•17•0•0•0•Updated Mar 28, 2026Mar 28, 2026
metagraphRF
Public
Python
•0•0•0•0•Updated Mar 24, 2026Mar 24, 2026
sshash
Public
A compressed, associative, exact, and weighted dictionary for k-mers.
C++
•
MIT License
•20•0•0•0•Updated Mar 7, 2026Mar 7, 2026
pthash
Public
✈️ PTHash is a fast and compact minimal perfect hash function.
C++
•
MIT License
•37•0•0•0•Updated Mar 7, 2026Mar 7, 2026
bits
Public
🛠 Succinct utilities to handle bits.
C++
•
MIT License
•8•0•0•0•Updated Mar 6, 2026Mar 6, 2026

ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.

Navigation Menu

Biomedical Informatics at ETH Zurich

All

148 repositories

tools-project-archives

metagraph

DeepSpot

DeepSpot2Cell

winn

NASExperiments

ReadBouncer

DeepSpotM

vision-guided-transcriptomics-fm-2026

immunopepper_analysis

aestetik

mla

WiNN-for-technical-correction

collinearity

sigmoni

spumoni

RawHash

MinknoApiSimulator

seq2squiggle

multi-slide-aestetik-2026-analysis

he2st

stmdit

spladder

icarefm

Megatron-LM

apertus-finetuning-recipes

metagraphRF

sshash

pthash

bits

Repositories list

148 repositories