Biomedical Informatics at ETH Zurich

Repositories

• spladder

  Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
  Python 30 78 31 0 Updated Jul 28, 2021

• metagraph

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

  search graph assembly metagenomics dna alignment
  C++ 4 37 2 14 Updated Jul 28, 2021

• immunopepper

  Code for the ImmunoPepper project
  Python 0 0 2 0 Updated Jul 26, 2021

• tools-project-archives

  A commandline tool to create and handle project archives
  Python MIT 0 0 5 0 Updated Jul 26, 2021

• projects-2020-Neural-SVGD

  Nonparametric variational inference by transporting samples along a dynamically learned trajectory.
  Jupyter Notebook 0 2 0 0 Updated Jul 25, 2021

• scatter

  Master thesis for hanap
  C++ 0 0 0 0 Updated Jul 19, 2021

• SVGP-VAE

  Tensorflow implementation for the SVGP-VAE model.
  Python MIT 1 9 0 0 Updated Jul 19, 2021

• Laplace

  Forked from AlexImmer/Laplace

  Laplace approximations for Deep Learning.
  Python MIT 3 0 0 0 Updated Jul 15, 2021

• HIRID-ICU-Benchmark
  Python MIT 1 3 0 0 Updated Jul 14, 2021

• ncl

  Code of the paper "Neighborhood Contrastive Learning Applied to Online Patient Monitoring"
  Python MIT 0 3 0 0 Updated Jul 6, 2021

• genome_graph_annotation

  Sparse Binary Relation Representations for Genome Graph Annotation

  de-bruijn-graphs genome-graph sparse-matrices binary-relations graph-annotation binary-matrices
  C++ 0 3 0 0 Updated Jul 4, 2021

• bnn_priors

  Code for the paper "Bayesian Neural Network Priors Revisited"
  Python MIT 3 20 0 1 Updated Jul 2, 2021

• tools-omicstools

  Collection of tools and utilities for *omics analyses
  Python MIT 0 1 0 0 Updated Jun 17, 2021

• mlschema-model-converters
  Python BSD-3-Clause 0 3 5 1 Updated Jun 11, 2021

• tools-gogo-gadget

  A tool to aggregate custom command line tools into one.
  Python MIT 1 2 0 1 Updated Jun 9, 2021

• Project2020-seq-tensor-sketching
  C++ MIT 0 2 10 2 Updated Jun 8, 2021

• scim

  Code for Universal Single-Cell Matching with Unpaired Feature Sets
  Jupyter Notebook LGPL-3.0 1 10 1 0 Updated Jun 7, 2021

• nextflow-wfpm-2
  Python MIT 0 0 0 1 Updated May 27, 2021

• projects2020-disentangled-gpvae

  Learning disentangled representations from time series.
  Python MIT 0 1 0 0 Updated May 27, 2021

• GP-VAE

  TensorFlow implementation for the GP-VAE model described in https://arxiv.org/abs/1907.04155
  Python MIT 15 58 0 2 Updated May 21, 2021

• renku-mls

  MLSchema plugin for Renku

  data-science machine-learning semantic-web knowledge-graph
  Python Apache-2.0 1 2 0 0 Updated May 21, 2021

• adaptive-stepsize-boosting-bbvi
  Python 0 1 0 0 Updated May 19, 2021

• row_diff

  RowDiff transform for sparsification of graph annotations
  Jupyter Notebook MIT 0 1 0 0 Updated May 11, 2021

• nextflow

  Forked from nextflow-io/nextflow

  A DSL for data-driven computational pipelines
  Groovy Apache-2.0 352 0 0 0 Updated Apr 30, 2021

• nextflow-wfpm-3
  0 0 0 0 Updated Apr 29, 2021

• projects2019-string-embedding
  C++ 0 0 0 3 Updated Mar 29, 2021

• sarek

  Forked from nf-core/sarek

  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  Nextflow MIT 185 0 0 0 Updated Mar 18, 2021

• tex-theses-phd-proposal-ajoudaki

  Amir's research proposal
  TeX 0 0 0 0 Updated Mar 15, 2021

• tcell_activation_dockerized

  This is the public version of the code for publication. Users can build the docker image from source and run all analyses from the paper.
  Python 0 0 0 0 Updated Mar 6, 2021

• dpsom

  Code associated with ACM-CHIL 21 paper 'T-DPSOM - An Interpretable Clustering Method for Unsupervised Learning of Patient Health States'
  Python MIT 8 38 0 0 Updated Mar 1, 2021