MitImpact
A collection of genomic, clinical and functional annotations for all nucleotide changes that cause non-synonymous substitutions in human mitochondrial protein coding genes.
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Open-source
Tools
Pyntacle
A high-performance Python package for the computational analysis of complex networks, built around non-canonical, parallelized graph metrics for large-scale biological networks.
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NetMD
A computational method for identifying consensus behaviors across multiple molecular dynamics simulations: replica trajectories are turned into networks, embedded with Graph2Vec, and ranked against a computed barycenter to surface the most representative trajectory.
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Bulk2Spot
A reproducible Snakemake workflow that takes NanoString GeoMx Digital Spatial Profiler raw counts through QC, normalization, batch correction, differential expression, pathway enrichment and cell-type deconvolution, ending in an interactive HTML report.
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MatchACell
A Snakemake toolkit for single-cell type and state annotation: automated QC and clustering resolution optimization, parallel annotation across up to eight methods, and cross-annotator consensus, for both single-cell and spatial transcriptomics data.
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STRmie-HD
An automated scanner for Huntington's disease polyQ patterns, supporting visualization and interpretation of short tandem repeat (STR) genotyping data from Huntington's disease patients.
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FastqRepair
A Nextflow pipeline that recovers corrupted FASTQ.gz files: it drops or fixes non-compliant reads, removes unpaired reads, and re-settles reads that became disordered.
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ALOA
A handy bioinformatics tool designed to transform raw data from PhenoCycler®-Fusion and inFormTM analysis into results suitable for publication, thus advancing the accessibility and utility of spatial tissue analysis in cancer research.
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Varan
A Python-based application that provides a pipeline to automatically prepare and manipulate cancer genomics data in the specific format supported by the cBioPortal.
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