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r-tinc
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public |
TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses.
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2025-06-02 |
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longtrack
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public |
Track FMT strains using long-read metagenomic assemblies.
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2025-06-02 |
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freebayes
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public |
Bayesian haplotype-based polymorphism discovery and genotyping.
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2025-06-02 |
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diatracer
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public |
A diaPASEF spectrum-centric analysis tool
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2025-06-02 |
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fgsmk
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public |
Supporting functions for running Snakemake workflows.
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2025-06-02 |
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pytwobit
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public |
A fast reader for local or remote UCSC twobit sequence files.
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2025-06-02 |
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pdbx
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public |
A parser module in python for structures of the protein data bank in the mmcif format
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2025-06-02 |
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vafator
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public |
VAFator annotates the variants in a VCF file with technical annotations extracted from one or more BAM alignment files. We implement a set of basic coverage annotations and also more sophisticated published annotations used to assess the quality of every variant call.
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2025-06-02 |
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mmcif
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public |
mmCIF Core Access Library
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2025-06-02 |
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bioconductor-dirichletmultinomial
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public |
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
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2025-06-02 |
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vcfx
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public |
VCFX: A Comprehensive VCF Manipulation Toolkit
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2025-06-02 |
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corgi
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public |
Classifier for ORganelle Genomes Inter alia
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2025-06-02 |
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nda-tools
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public |
Python package for interacting with NDA web services.
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2025-06-02 |
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bandage_ng
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public |
Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily.
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2025-06-02 |
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r-peakpick
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public |
Peak Picking Methods Inspired by Biological Data
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2025-06-02 |
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r-cnaqc
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public |
Copy number quality control
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2025-06-02 |
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ezfastq
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public |
Organize FASTQs by sample for analysis
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2025-05-30 |
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hmftools-teal
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public |
Characterises telomeres in tumor and normal samples from WGS data.
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2025-05-30 |
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prokbert
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public |
ProkBERT is a genomic language model specifically designed for microbiome applications. It leverages the power of machine learning to decipher complex microbial interactions, predict functionalities, and uncover novel patterns in extensive datasets. The ProkBERT model family, built on transfer learning and self-supervised methodologies, capitalizes on the abundant genomic data available.
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2025-05-30 |
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piranha-polio
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public |
Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis
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2025-05-30 |
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targetdb
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public |
Package with an application to generate report on potential drug targets.
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2025-05-30 |
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regenie
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public |
Regenie is a C++ program for whole genome regression modelling of large genome-wide association studies (GWAS).
|
2025-05-29 |
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msfragger
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public |
Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics
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2025-05-29 |
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bioconductor-decipher
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public |
Tools for curating, analyzing, and manipulating biological sequences
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2025-05-29 |
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hamronization
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public |
Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
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2025-05-29 |
