Discover ratschlab/pmvae Open Source project

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

629

SOM-VAE

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

186

GP-VAE

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

120

spladder

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

101

metagraph

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

dpsom

Code for the paper "Bayesian Neural Network Priors Revisited"

bnn_priors

circEWS

circEWS public code

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

Tensorflow implementation for the SVGP-VAE model.

SVGP-VAE

Code for Universal Single-Cell Matching with Unpaired Feature Sets

scim

Repo for our paper "Repulsive deep ensembles are Bayesian"

repulsive_ensembles

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

uRNN

Code accompanying the publication for compressed graph annotation

graph_annotation

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

tensor-sketch-alignment

boosting-bbvi

dgp-vae

Project2020-seq-tensor-sketching

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

secedo

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

counting_dbg

Lossless Indexing with Counting de Bruijn Graphs

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

tls

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

clinical-embeddings

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

Library of common Python code used across various projects

ratschlab-common

adaptive-stepsize-boosting-bbvi

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

mmugl

projects2017-kG

The RNA-seq transcript predictor for multiple samples

MiTie

mla

Scripts and data for reproducing the results of MetaGraph-MLA

The master Oqtans repository with submodules

oqtans

Shell

SNBNMF-mutsig-public

Supervised Negative Binomial NMF for Mutational Signature Discovery

Accurate splice form prediction based on discriminative learning

mSplicer

A tool to aggregate custom command line tools into one.

tools-gogo-gadget

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

immunopepper

Code for the ImmunoPepper project

embedding sequence using a convolutional network

seqCNN

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

metagraph_paper_resources

RowDiff transform for sparsification of graph annotations

row_diff

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