Skip to content

@PapenfussLab Papenfuss Lab

Change the repository type filter

All

    Repositories list

    39 repositories

    • bionix

      Public
      Functional highly reproducible bioinformatics pipelines
      Nix
      •
      BSD 3-Clause "New" or "Revised" License
      •7•78•2•0•Updated Nov 12, 2024Nov 12, 2024

    • dl_binder_design

      Public
      Python
      •
      MIT License
      •58•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • RFdiffusion

      Public
      Code for running RFdiffusion
      Python
      •
      Other
      •344•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • dedumi

      Public
      Haskell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated May 21, 2024May 21, 2024

    • gridss

      Public
      GRIDSS: the Genomic Rearrangement IDentification Software Suite
      Java
      •
      Other
      •71•257•78•8•Updated Jan 10, 2024Jan 10, 2024

    • Impute_DMS

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 10, 2023Oct 10, 2023

    • DMS-PLS

      Public
      Using canonical Partial Least Squares (PLS) to analyse DMS and variant stability data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2023Sep 25, 2023

    • DMS_with_Alanine_scan

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•1•0•Updated Aug 4, 2023Aug 4, 2023

    • svaRetro

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 14, 2022Jun 14, 2022

    • svaNUMT

      Public
      R
      •
      GNU General Public License v3.0
      •0•3•2•0•Updated Jun 14, 2022Jun 14, 2022

    • StructuralVariantAnnotation

      Public
      R package designed to simplify structural variant analysis
      R
      •
      GNU General Public License v3.0
      •14•70•10•0•Updated Dec 22, 2021Dec 22, 2021

    • IntroductionToGenomicsWorkshop

      Public
      WEHI Masterclass Day 3: Genomics
      Dockerfile
      •
      Other
      •0•1•0•0•Updated Aug 26, 2021Aug 26, 2021

    • wgd.test

      Public
      By modelling aneuploidy with interleaving branching processes we can make a decision about whether or not genome doubling occurred. We can also label each event as being pre or post GD.
      R
      •3•1•0•0•Updated Aug 3, 2021Aug 3, 2021

    • RothSchulze_pregnancy-gut-microbiome-T1D

      Public
      Data, metadata and analyses performed in microbiome whole metagenomics sequencing data of women with and without T1D during pregnancy.
      HTML
      •1•2•0•0•Updated May 18, 2021May 18, 2021

    • PathOS

      Public
      PathOS is a clinical application for filtering, analysing and reporting on NGS variants
      Java
      •
      GNU General Public License v3.0
      •8•28•5•0•Updated Mar 30, 2021Mar 30, 2021

    • VIRUSBreakend

      Public
      Viral Integration Recognition Using Single Breakends
      0•2•0•0•Updated Feb 8, 2021Feb 8, 2021

    • sv_benchmark

      Public
      Comprehensive benchmark of structural variant callers
      R
      •
      GNU General Public License v3.0
      •6•43•0•0•Updated Feb 4, 2021Feb 4, 2021

    • CascadeNeoPipe

      Public
      Neoantigen analysis pipeline for CASCADE data
      Perl
      •0•0•0•0•Updated Nov 16, 2020Nov 16, 2020

    • Jocelyn_tools

      Public
      Short pieces of useful code
      R
      •1•0•0•0•Updated Mar 2, 2020Mar 2, 2020

    • CascadePipe

      Public
      Analysis pipeline for CASCADE data
      Perl
      •0•0•0•0•Updated Dec 20, 2019Dec 20, 2019

    • Anomaly

      Public
      Anomaly annotation web service
      Java
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 11, 2019Nov 11, 2019

    • bioshake

      Public
      Bioinformatics pipelines with Haskell and Shake
      Haskell
      •
      ISC License
      •7•55•3•0•Updated Aug 13, 2019Aug 13, 2019

    • nix-workshop

      Public
      Nix
      •0•2•0•0•Updated Jun 19, 2019Jun 19, 2019

    • CNspector

      Public
      Web-based copy number browser.
      R
      •
      GNU General Public License v3.0
      •6•4•1•0•Updated Jun 1, 2019Jun 1, 2019

    • assemble_var

      Public
      A pipeline for the assembly of VAR genes from transcriptome data
      vartranscriptome-assembly
      HTML
      •2•2•2•0•Updated Dec 16, 2018Dec 16, 2018

    • clove

      Public
      classification of higher-order structural variants from breakpoint data
      Java
      •
      GNU General Public License v2.0
      •2•7•8•0•Updated Jan 8, 2018Jan 8, 2018

    • buildcnb

      Public
      Extracts copy number estimates from NGS data.
      R
      •1•0•0•0•Updated Nov 30, 2017Nov 30, 2017

    • Canary

      Public
      A fast and self-contained amplicon pipeline tool.
      Groovy
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Nov 28, 2017Nov 28, 2017

    • RothSchulze_microbiome

      Public
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 23, 2017Nov 23, 2017

    • malaria-copy-numbers

      Public
      Tools used to apply QDNASeq R package to our P. falciparum data, including forging a BSGenome package
      R
      •1•0•0•0•Updated Nov 7, 2017Nov 7, 2017