| Package Name | Access | Summary | Updated |
|---|---|---|---|
| multiqc | public | Create aggregate bioinformatics analysis reports across many samples and tools | 2025-03-25 |
| woof-nf | public | No Summary | 2025-03-25 |
| tsvtools | public | Utilities for operating with tab-separated files: viewing, filtering, reordering | 2025-03-25 |
| ngs_utils | public | Python utilities for bioinformatics tools and pipelines | 2025-03-25 |
| oviraptor | public | Oncoviral integration in cancer whole genome data | 2025-03-25 |
| r-chord | public | CHORD is a random forest model that uses the relative counts of somatic mutation contexts to predict homologous recombination deficiency (HRD). The primary contexts used by CHORD are deletions with flanking microhomology and 1-100kb structural duplications. Additionally, 1-100kb structural duplications are used to distinguish BRCA1-type HRD from BRCA2-type HRD. | 2025-03-25 |
| r-nnlm | public | This is a package for Non-Negative Linear Models (NNLM). It implements fast sequential coordinate descent algorithms for non-negative linear regression and non-negative matrix factorization (NMF). It supports mean square error and Kullback-Leibler divergence loss. Many other features are also implemented, including missing value imputation, domain knowledge integration, designable W and H matrices and multiple forms of regularizations. | 2025-03-25 |
| r-pebbles | public | Contains cancer genomics datasets for running tests and examples in the rock R package (https://github.com/pdiakumis/rock). | 2025-03-25 |
| versionpy | public | Small utility to track and bump the version of your python tool | 2025-03-25 |
| r-rock | public | Contains visualisation functions for bioinformatics work at UMCCR. | 2025-03-25 |
| r-signature.tools.lib | public | R package with useful functions for mutational signatures analysis. | 2025-03-25 |
| tsvfmt | public | Tab-separated file viewer for command line | 2025-03-25 |
| reference_data | public | Versioning of reference data used in UMCCR pipelines, and python API to access it | 2025-03-25 |
| r-woofr | public | Helper R Functions for woof (https://github.com/pdiakumis/woof). | 2025-03-25 |
| bed_annotation | public | Genome capture target coverage evaluation tool | 2025-03-25 |
| r-mutsigextractor | public | Extracts SNV, indel, DBS, and SV signatures from vcf files. | 2025-03-25 |
| vcf_stuff | public | Evaluating, filtering, comparing, and visualising variant calls | 2025-03-25 |
