Papenfuss Lab

Walter and Eliza Hall Institute of Medical Research

Melbourne, Australia

Pinned Repositories

bionix
Functional highly reproducible bioinformatics pipelines
Language:Nix86 6 197
bioshake
Bioinformatics pipelines with Haskell and Shake
Language:Haskell55 6 47
clove
classification of higher-order structural variants from breakpoint data
Language:Java8 12 122
gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Language:Java261 22 66071
HaveYouSwappedYourSamples
This project contains simple methods to measure sample relatedness and identify potential swaps and contamination
Language:Python10 13 12
PathOS
PathOS is a clinical application for filtering, analysing and reporting on NGS variants
Language:Java28 6 118
socrates
Language:Java16 13 71
StructuralVariantAnnotation
R package designed to simplify structural variant analysis
Language:R71 5 4214
sv_benchmark
Comprehensive benchmark of structural variant callers
Language:R44 5 46
VIRUSBreakend
Viral Integration Recognition Using Single Breakends
2 3 10

Papenfuss Lab's Repositories

PapenfussLab/gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Language:Java261 22 66071
PapenfussLab/bionix
Functional highly reproducible bioinformatics pipelines
Language:Nix86 6 197
PapenfussLab/StructuralVariantAnnotation
R package designed to simplify structural variant analysis
Language:R71 5 4214
PapenfussLab/bioshake
Bioinformatics pipelines with Haskell and Shake
Language:Haskell55 6 47
PapenfussLab/sv_benchmark
Comprehensive benchmark of structural variant callers
Language:R44 5 46
PapenfussLab/PathOS
PathOS is a clinical application for filtering, analysing and reporting on NGS variants
Language:Java28 6 118
PapenfussLab/clove
classification of higher-order structural variants from breakpoint data
Language:Java8 12 122
PapenfussLab/Canary
A fast and self-contained amplicon pipeline tool.
Language:Groovy7 3 01
PapenfussLab/CNspector
Web-based copy number browser.
Language:R4 4 26
PapenfussLab/svaNUMT
Language:R3 4 70
PapenfussLab/assemble_var
A pipeline for the assembly of VAR genes from transcriptome data
Language:HTML2 17 22
PapenfussLab/nix-workshop
Language:Nix2 2 0
PapenfussLab/RothSchulze_pregnancy-gut-microbiome-T1D
Data, metadata and analyses performed in microbiome whole metagenomics sequencing data of women with and without T1D during pregnancy.
Language:HTML2 2 01
PapenfussLab/VIRUSBreakend
Viral Integration Recognition Using Single Breakends
2 3 10
PapenfussLab/dedumi
Language:Haskell1 1 0
PapenfussLab/IntroductionToGenomicsWorkshop
WEHI Masterclass Day 3: Genomics
Language:Dockerfile1 4 0
PapenfussLab/wgd.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.
Language:R1 13 03
PapenfussLab/Anomaly
Anomaly annotation web service
Language:Java0 3 00
PapenfussLab/buildcnb
Extracts copy number estimates from NGS data.
Language:R0 3 01
PapenfussLab/svaRetro
Language:R0 4 00
PapenfussLab/CascadeNeoPipe
Neoantigen analysis pipeline for CASCADE data
Language:Perl2 0
PapenfussLab/CascadePipe
Analysis pipeline for CASCADE data
Language:Perl1 0
PapenfussLab/dl_binder_design
Language:Python0 0
PapenfussLab/DMS-PLS
Using canonical Partial Least Squares (PLS) to analyse DMS and variant stability data
Language:Jupyter Notebook1 0
PapenfussLab/DMS_with_Alanine_scan
Language:Jupyter Notebook3 71
PapenfussLab/Impute_DMS
Language:Jupyter Notebook1 0
PapenfussLab/Jocelyn_tools
Short pieces of useful code
Language:R3 11
PapenfussLab/malaria-copy-numbers
Tools used to apply QDNASeq R package to our P. falciparum data, including forging a BSGenome package
Language:R1
PapenfussLab/RFdiffusion
Code for running RFdiffusion
Language:Python0 0
PapenfussLab/RothSchulze_microbiome
Language:Shell2 0