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@bio-datascience Biomedical Statistics and Data Science @ LMU/HMGU Munich

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    44 repositories

    • bio-datascience.github.io

      Public
      This is the repository for our group's webpage
      HTML
      •
      Other
      •4•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • BacSC

      Public
      Optimized processing of bacterial single-cell data
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Aug 19, 2024Aug 19, 2024

    • GraphReg

      Public
      GraphReg: An Extended Stability Approach to Regularization Selection in Sparse Graphical Models
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • Drug-interactions-HCS

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Apr 27, 2024Apr 27, 2024

    • Microbial-Interactions

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Apr 27, 2024Apr 27, 2024

    • ProDG

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Mar 5, 2024Mar 5, 2024

    • MetaIBS

      Public
      Meta-analysis of microbiome composition measured by 16S rRNA seq in IBS case-control studies
      Jupyter Notebook
      •2•0•0•0•Updated Jan 24, 2024Jan 24, 2024

    • asteRIa

      Public
      R
      •1•0•0•0•Updated Jan 15, 2024Jan 15, 2024

    • coda24

      Public
      Course website mini-course
      TeX
      •0•0•0•0•Updated Jan 9, 2024Jan 9, 2024

    • q2-gglasso

      Public
      QIIME 2 plugin which contains algorithms for solving General Graphical Lasso (GGLasso) problems
      Python
      •
      Other
      •1•1•0•0•Updated Dec 20, 2023Dec 20, 2023

    • tascCODA_reproducibility

      Public
      Reproductibility repository for "tascCODA: Bayesian tree-aggregated analysis of compositional amplicon and single-cell data"(Ostner, Müller, 2021))
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Apr 6, 2023Apr 6, 2023

    • viroprofiler

      Public
      A containerized bioinformatics pipeline for viral metagenomic data analysis
      Nextflow
      •
      MIT License
      •12•0•0•0•Updated Mar 29, 2023Mar 29, 2023

    • Global-rRNA-Univeral-Metabarcoding-of-Plankton

      Public
      A central repository for the GRUMP (Global rRNA Universal Metabarcoding of Plankton) dataset, containing scripts for bioinformatic processing and retrieval of associated physical / geochemical measurements from publicly available data.
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 21, 2023Mar 21, 2023

    • pertpy

      Public
      Perturbation Analysis in the scverse ecosystem.
      Jupyter Notebook
      •
      MIT License
      •21•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • lounsbery

      Public
      R
      •1•0•0•0•Updated Jan 2, 2023Jan 2, 2023

    • Bacdiving

      Public
      Bacdiving accesses the Bacterial Diversity Metadatabase BacDive and provides various visualization options.
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 23, 2022Dec 23, 2022

    • NetCoMi

      Public
      Network Comparison for Microbial Compositional Data
      R
      •
      GNU General Public License v3.0
      •28•0•0•0•Updated Dec 1, 2022Dec 1, 2022

    • overoptimism-microbiome

      Public
      R
      •1•0•0•0•Updated Oct 29, 2022Oct 29, 2022

    • atacama-soil-microbiome-tutorial

      Public
      HTML
      •
      Other
      •1•0•0•0•Updated Oct 6, 2022Oct 6, 2022

    • tascCODA

      Public
      tree-aggregated compositional analysis for high-throughput sequencing data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•8•3•0•Updated Aug 24, 2022Aug 24, 2022

    • q2-dummy

      Public
      Package for testing q2-plugin development
      Jupyter Notebook
      •1•0•0•0•Updated Jun 27, 2022Jun 27, 2022

    • SpiecEasi

      Public
      Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
      R
      •68•0•0•0•Updated Jun 27, 2022Jun 27, 2022

    • brain_challenge

      Public
      Network Analysis and Sex Prediction Based on Whole Brain Connectome
      Jupyter Notebook
      •1•0•0•0•Updated Jun 3, 2022Jun 3, 2022

    • scCODA

      Public
      A statistical test for compositional changes in scRNA
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •24•0•0•0•Updated May 31, 2022May 31, 2022

    • PDE-STRIDE

      Public
      This repository contains codes and data-sets for the PDE inference from limited spatio-temporal data
      Jupyter Notebook
      •3•0•0•0•Updated Mar 25, 2022Mar 25, 2022

    • Causal_Microbiome_Tutorial

      Public
      Causal inference framework for environment-microbiome data applied to American Gut data.
      R
      •2•6•0•0•Updated Mar 10, 2022Mar 10, 2022

    • nbfar

      Public
      C++
      •1•0•0•0•Updated Feb 22, 2022Feb 22, 2022

    • lassonet

      Public
      An implementation of LassoNet for arbitrary network architectures.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • omd

      Public
      Code for ocean mover's distance (OMD) project.
      HTML
      •3•0•0•0•Updated Nov 2, 2021Nov 2, 2021

    • comp-iv

      Public
      Collection of methods for instrumental variable settings with a compositional cause.
      Jupyter Notebook
      •1•0•0•0•Updated Sep 28, 2021Sep 28, 2021