vladsaveliev
Doing bioinformatics for oncology
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Packages
| Name | Latest Version | Summary | Updated | License |
|---|
| bed_annotation | 1.1.6 | Annotate BED files | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| clearup | 1.1.3 | Sample identity validation and mix-up check | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| cpsr | 0.6.0rc | Cancer Predisposition Sequencing Reporter (CPSR) - prioritization of germline variants in cancer | Mar 25, 2025 | MIT |
| gdown | 3.8.1 | Google Drive direct download of big files. | Mar 25, 2025 | MIT |
| hail | 0.2.61 | Hail is Python-based data analysis tool for working with genomic data. | Mar 25, 2025 | MIT |
| lumpy-sv-basic | 0.3.0 | a general probabilistic framework for structural variant discovery | Mar 25, 2025 | MIT |
| lzstring | 1.0.4 | lz-string for python | Mar 25, 2025 | MIT |
| multiqc | 1.8dev | Create aggregate bioinformatics analysis reports across many samples and tools | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| multiqc-az | 1.2 | — | Mar 25, 2025 | — |
| multiqc-clarity | 0.2 | MultiQC plugin interacting with the Illumina Genologics Clarity LIMS. | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| ngs_utils | 2.8.8 | Python utilities for bioinformatics tools and pipelines | Mar 25, 2025 | GPLv3 |
| oviraptor | 1.2.0 | Oncoviral integration in cancer whole genome data | Mar 25, 2025 | GPLv3 |
| pcgr | 0.9.0rc | Personal Cancer Genome Reporter (PCGR)- variant interpretation report for precision oncology | Mar 25, 2025 | MIT |
| perl-bio-bigfile | 1.07 | Low-level interface to BigWig & BigBed files | Jun 16, 2023 | Apache v2.0 |
| r-kableextra | 0.9.0 | Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax. | Mar 25, 2025 | MIT + file LICENSE |
| reference_data | 1.0.11 | Versioning of reference data used in UMCCR pipelines, and python API to access it | Mar 25, 2025 | GPLv3 |
| snakemake | 5.2.2vlad | Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. | Mar 25, 2025 | MIT |
| spectra | 0.0.11 | Color scales and color conversion made easy for Python. | Mar 25, 2025 | MIT |
| targqc | 1.8.1 | Target capture coverage QC | Mar 25, 2025 | GNU General Public License v3 (GPLv3) |
| tsvfmt | 0.3.1 | Tab-separated file viewer for command line | Mar 25, 2025 | MIT |
| tsvtools | 0.2.0 | Utilities for operating with tab-separated files: viewing, filtering, reordering | Mar 25, 2025 | GPLv3 |
| vcf_stuff | 0.5.12 | Evaluating, filtering, comparing, and visualising variant calls | Mar 25, 2025 | GPLv3 |
| versionpy | 0.4.11 | Small utility to track and bump the version of your python tool | Mar 25, 2025 | GPLv3 |