Genomic rearrangements
| Tool | Description | URL |
|---|---|---|
| GRIDSS2 | Genomic rearrangement caller | https://github.com/PapenfussLab/gridss |
| GRIDSS1 | Genomic rearrangement caller | https://github.com/PapenfussLab/gridss |
| VirusBreakEnd | Virus presence and genome integration detection | https://github.com/PapenfussLab/gridss |
| StructuralVariantAnnotation | Generic parser for SV VCFs | https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.htm |
| CLOVE | SV classifier | https://github.com/PapenfussLab/clove |
| Socrates | Fast & sensitive split read-based SV caller | ttps://github.com/PapenfussLab/socrates |
Genomic data analysis
| KataegisBrowser | Kaetegis visualisation | https://github.com/PapenfussLab/KataegisBrowser |
| Whole genome doubling test | Branching process-based test for genome doubling | https://github.com/PapenfussLab/Genome_doubling_test |
| HaveYouSwappedYourSample | Simple methods for detecting sample swaps | https://github.com/PapenfussLab/HaveYouSwappedYourSamples |
| CNspector | Clinical copy number browser | https://github.com/PapenfussLab/CNspector |
| Canary | SNV caller | https://github.com/PapenfussLab/Canary |
Transcriptomic data analysis
| TidyHeatmap | https://cran.r-project.org/web/packages/tidyHeatmap/index.html | |
| TidySeurat | https://cran.r-project.org/web/packages/tidyseurat/index.html | |
| TidyBulk | https://bioconductor.org/packages/release/bioc/html/tidybulk.html | |
| PPCseq | https://github.com/stemangiola/ppcseq | |
| assemble_var | Framework for assembling Transcriptomics data (developed for P falciparum VAR genes) | https://github.com/PapenfussLab/assemble_var |
Pipeline frameworks
| BioNix | Robust framework for reproducible pipelines and software versioning based on the Nix build system | https://github.com/PapenfussLab/bionix |
| Bioshake | https://github.com/PapenfussLab/bioshake |
Deep Mutational Scanning
Clinical genomics
| PathOS | Clinical informatics platform | https://github.com/PapenfussLab/PathOS |