umccr
by UMCCR (Organization)
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| r-tidywigits | 0.0.7 | WiGiTS workflow tidying | Feb 26, 2026 | MIT |
| r-nemo | 0.0.3 | Tidy and explore outputs from bioinformatic pipelines | Mar 15, 2026 | MIT |
| r-rportal | 0.1.6 | UMCCR data portal R functionality | Feb 26, 2026 | MIT |
| openspliceai | 0.0.5 | Deep learning framework that decodes splicing across species | Apr 20, 2026 | MIT |
| r-ulid | 0.4.0 | Generate Universally Unique Lexicographically Sortable Identifiers | Jun 4, 2026 | MIT |
| r-gpgr | 2.3.1 | Genomics Platform Group Reporting | May 24, 2026 | MIT + file LICENSE |
| vcfanno | 0.3.5 | annotate a VCF with other VCFs/BEDs/tabixed files | Mar 25, 2025 | MIT |
| vcf_stuff | 0.6.4 | Evaluating, filtering, comparing, and visualising variant calls | Mar 25, 2025 | GPLv3 |
| r-nnlm | 0.4.4 | 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. | Mar 25, 2025 | BSD_2_clause + file LICENSE |
| r-dracarys | 0.16.0 | DRAGEN workflow post-processing | Mar 25, 2025 | MIT |
| r-rnasum | 2.0.3.9005 | RNAseq-based cancer patient reports | Jul 3, 2026 | MIT + file LICENSE |
| r-chord | 2.03 | 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. | Mar 25, 2025 | MIT |
| r-signature.tools.lib | 2.1.2 | R package with useful functions for mutational signatures analysis. | Mar 25, 2025 | see LICENCE file |
| r-sigrap | 0.3.0 | Wrappers for somatic mutation signature analysis tools | Jul 3, 2026 | MIT + file LICENSE |
| r-mutsigextractor | 1.29 | Extracts SNV, indel, DBS, and SV signatures from vcf files. | Mar 25, 2025 | GPL3 |
| reference_data | 1.0.11 | Versioning of reference data used in UMCCR pipelines, and python API to access it | Mar 25, 2025 | GPLv3 |
| ngs_utils | 2.11.0 | Python utilities for bioinformatics tools and pipelines | Mar 25, 2025 | GPLv3 |
| versionpy | 0.4.11 | Small utility to track and bump the version of your python tool | Mar 25, 2025 | GPLv3 |
| r-woofr | 0.3.3 | Helper R Functions for woof (https://github.com/pdiakumis/woof). | Mar 25, 2025 | MIT + file LICENSE |
| woof | 0.2.1 | Compare genomic data from two sources | Mar 25, 2025 | GPL |
| r-rnasum.data | 0.1.2 | Reference data for RNAsum | Jun 29, 2026 | MIT + file LICENSE |
| bed_annotation | 1.1.6 | Genome capture target coverage evaluation tool | Mar 25, 2025 | GPLv3 |
| multiqc | 1.14+umccrise.0.0.14 | Create aggregate bioinformatics analysis reports across many samples and tools | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| r-manhattanly | 0.3.0 | Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser. | Mar 25, 2025 | MIT |
| oviraptor | 1.3.2 | Oncoviral integration in cancer whole genome data | Mar 25, 2025 | GPLv3 |