Discover ratschlab/uRNN Open Source project

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

639

SOM-VAE

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

190

GP-VAE

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

124

metagraph

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

110

spladder

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

103

dpsom

circEWS

circEWS public code

Code for the paper "Bayesian Neural Network Priors Revisited"

bnn_priors

Repository for the HiRID ICU Benchmark (HiB) project

HIRID-ICU-Benchmark

Public repository containing research code for the TCGA PanCanAtlas Splicing project

pancanatlas_code_public

A tool for Read Multi-Mapper Resolution

mmr

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

RiboDiff

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

ncl

Code for Universal Single-Cell Matching with Unpaired Feature Sets

scim

Tensorflow implementation for the SVGP-VAE model.

SVGP-VAE

Repo for our paper "Repulsive deep ensembles are Bayesian"

repulsive_ensembles

Code accompanying the publication for compressed graph annotation

graph_annotation

Code for pmVAE model, seen in ICML CompBio '21

pmvae

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

tensor-sketch-alignment

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

aestetik

boosting-bbvi

dgp-vae

Project2020-seq-tensor-sketching

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

secedo

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

mmugl

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

mlhc-seminar

oqtans_tools

Oqtans repository

Tests for Differential RNA Isoform Expression

rDiff

clinical-embeddings

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

Lossless Indexing with Counting de Bruijn Graphs

counting_dbg

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

tls

The EasySVM Toolbox based on Shogun

easysvm

Sparse Binary Relation Representations for Genome Graph Annotation

genome_graph_annotation

Simulator of an ONT device with ReadUntil gRPC support

sim_read_until

The Hidden Markov SVM Toolbox

HMSVMToolbox

MATLAB

PBWT-sec

C++ implementation of PBWT-seq

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

projects-2020-Neural-SVGD

Supervised Negative Binomial NMF for Mutational Signature Discovery

SNBNMF-mutsig-public

The master Oqtans repository with submodules

oqtans

Shell

immunopepper

Code for the ImmunoPepper project

adaptive-stepsize-boosting-bbvi

Library of common Python code used across various projects

ratschlab-common

The RNA-seq transcript predictor for multiple samples

MiTie

mla

Scripts and data for reproducing the results of MetaGraph-MLA

projects2017-kG

RowDiff transform for sparsification of graph annotations

row_diff

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

genomic-gnn

Accurate splice form prediction based on discriminative learning

mSplicer

A tool to aggregate custom command line tools into one.

tools-gogo-gadget

Code for "Probabilistic pathway based multimodal factor analysis"

path-fa

Simulate spatial transcriptomics data

simulate_spatial_transcriptomics_tool

Learning disentangled representations from time series.

projects2020-disentangled-gpvae

The RNA-seq transcript quantifier with Bias Correction

rQuant

MATLAB

AdaBoost

Adaboost-Reg and RBF-Network code

seqCNN

embedding sequence using a convolutional network

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

metagraph_paper_resources

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

hif_splicing_code_public

gromics

Collection of tools and utilities for *omics analyses

Accurate Splice Site Predictions

ASP

The accurate RNA-seq mapper

palmapper

Multithreaded wavelet trie construction library

metannot

Very simple workflows to experiment with containers and cwl

tools-cwl-workflow-experiments

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

st-rep