Papenfuss Lab

Repositories

• gridss

  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  Java 26 110 22 0 Updated Aug 12, 2020

• bionix

  Functional highly reproducible bioinformatics pipelines
  Nix BSD-3-Clause 0 5 2 0 Updated Aug 9, 2020

• StructuralVariantAnnotation

  R package designed to simplify structural variant analysis
  R GPL-3.0 13 36 3 0 Updated Jul 10, 2020

• PathOS

  PathOS is a clinical application for filtering, analysing and reporting on NGS variants
  Java GPL-3.0 7 20 5 6 Updated Jun 7, 2020

• RothSchulze_pregnancy-gut-microbiome-T1D

  Data, metadata and analyses performed in microbiome 16s rRNA amplicon sequencing data and whole metagenomics sequencing data of women with and without T1D during pregnancy.
  HTML 0 1 0 0 Updated Mar 9, 2020

• Jocelyn_tools

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

• CascadePipe

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

• Genome_doubling_test

  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 1 0 0 0 Updated Nov 28, 2019

• Anomaly

  Anomaly annotation web service
  Java GPL-3.0 0 0 0 0 Updated Nov 11, 2019

• bioshake

  Bioinformatics pipelines with Haskell and Shake
  Haskell ISC 7 43 3 0 Updated Aug 13, 2019

• sv_benchmark

  Comprehensive benchmark of structural variant callers
  R GPL-3.0 6 18 0 0 Updated Jul 1, 2019

• nix-workshop
  Nix 0 1 0 0 Updated Jun 19, 2019

• CNspector

  Web-based copy number browser.
  R GPL-3.0 3 4 0 0 Updated Jun 1, 2019

• assemble_var

  A pipeline for the assembly of VAR genes from transcriptome data

  var transcriptome-assembly
  HTML 1 1 2 0 Updated Dec 16, 2018

• clove

  classification of higher-order structural variants from breakpoint data
  Java GPL-2.0 2 3 7 0 Updated Jan 8, 2018

• buildcnb

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

• Canary

  A fast and self-contained amplicon pipeline tool.
  Groovy GPL-3.0 0 4 0 0 Updated Nov 28, 2017

• RothSchulze_microbiome
  Shell GPL-3.0 0 0 0 0 Updated Nov 23, 2017

• malaria-copy-numbers

  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, 2017

• endiaQC

  Code for ENDIA microbiome QC paper
  HTML 0 0 0 0 Updated Sep 19, 2017

• svqsc

  Structural Variation Quality Score Calculator
  R GPL-3.0 1 1 0 0 Updated Feb 3, 2017

• sv_tools

  A few tools for plotting and reasoning about genomic structural variants.
  Python MIT 3 2 2 0 Updated Feb 1, 2017

• socrates
  Java 2 14 4 0 Updated Dec 19, 2016

• Mungo

  Python library for munging biological sequence and annotation data
  Python Artistic-2.0 1 1 0 0 Updated Jun 12, 2016

• reads_to_domains

  allocates NGS reads to VAR domain models
  Python 0 0 0 0 Updated Feb 17, 2016

• HaveYouSwappedYourSamples

  This project contains simple methods to measure sample relatedness and identify potential swaps and contamination
  Python 2 9 1 0 Updated Jan 8, 2016

• MHC-clogs

  MHC Class I Gene Search tool
  Python Artistic-2.0 0 0 0 0 Updated Aug 20, 2015

• Srtools

  Short read tools - a small python package with some convenience modules for dealing with short read data
  Python Artistic-2.0 0 0 0 0 Updated Aug 20, 2015