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    67 repositories

    • MANTIS

      Public
      Multimodal Alignment of Normalized Tissue Sections
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • aigen2026

      Public
      workshop page
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 28, 2026Jul 28, 2026

    • HistologyMultiInstanceLearning

      Public
      Nextflow pipeline to evaluate MIL architectures in concordance with histology foundational models.
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jul 27, 2026Jul 27, 2026

    • HistoMILTrainer

      Public
      Python library to train Multi Instance Learning algorithms in histology for custom tasks.
      machine-learningdeep-learningpytorch
      machine-learningdeep-learningpytorchhistologymulti-instance-learning
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Jul 27, 2026Jul 27, 2026

    • HistologyEvaluateMIL

      Public
      Nextflow pipeline to evaluate Multi Instance Learning approaches using IHC slides as ground truth.
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Jul 23, 2026Jul 23, 2026

    • rfhap_ms

      Public
      Figures and analysis for RFHAP manuscript
      HTML
      •
      MIT License
      •0•0•0•0•Updated Jul 7, 2026Jul 7, 2026

    • LEMUR

      Public
      Local ancestry & Epigenetic Methylation for differential Regions
      C++
      •
      MIT License
      •0•0•0•0•Updated Jul 4, 2026Jul 4, 2026

    • Pipelines

      Public
      Repository to organize pipelines and repositories of DiGenomaLab.
      MIT License
      •0•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • HistologyFeatureExtraction

      Public
      Nextflow pipeline to extract features in histology WSIs.
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jul 1, 2026Jul 1, 2026

    • HistologyPyramidConvert

      Public
      Pipeline that converts a standard tiff WSI into a pyramid file.
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • covid_genomics

      Public
      Repository holding analysis of 100 covid chilean genomes
      HTML
      •
      MIT License
      •0•0•0•0•Updated May 30, 2026May 30, 2026

    • alndv

      Public
      call variants with deepvariant
      Nextflow
      •
      MIT License
      •0•4•0•0•Updated Apr 23, 2026Apr 23, 2026

    • HistologyLinearProbing

      Public
      Executes a linear probing to evaluate some foundational models in histopathology cases.
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 17, 2026Apr 17, 2026

    • facets-nf

      Public
      Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing
      Nextflow
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • nf-ssvsr

      Public
      Somatic sv calling from short-reads
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Mar 11, 2026Mar 11, 2026

    • Eval-RF-hap

      Public
      Nextflow pipeline to evaluate RFhap results
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • FastKM

      Public
      ultra-fast matching of kmers using rolling and perfect hashing
      C++
      •
      MIT License
      •0•4•0•0•Updated Jan 28, 2026Jan 28, 2026

    • rfhap

      Public
      Random Forest for the Classification of Paternal and Maternal Haplotypes from Long-Read Sequencing Data.
      Python
      •
      MIT License
      •1•8•1•0•Updated Jan 28, 2026Jan 28, 2026

    • biomining_metagenomes

      Public
      Repository that holds data, scripts and figures regarding to the mining MAGs (Cauquenes tailing) article
      HTML
      •
      MIT License
      •2•1•0•0•Updated Dec 9, 2025Dec 9, 2025

    • alnsl

      Public
      Nextflow pipeline for short-read alignment
      nextflowmappingillumina
      nextflowmappingilluminamgishort-reads
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated May 22, 2025May 22, 2025

    • snps_mags

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 2, 2025May 2, 2025

    • BRCA12_ms

      Public
      Code for figure and analysis of BRCA12 ms
      R
      •
      MIT License
      •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

    • ppilon

      Public
      Nextflow pipeline for polising a large genome using pilon
      Roff
      •
      MIT License
      •2•0•0•0•Updated Apr 17, 2025Apr 17, 2025

    • minibusco-nf

      Public
      Nextflow
      •0•0•0•0•Updated Apr 13, 2025Apr 13, 2025

    • hic-scaffolding-nf

      Public
      Nextflow pipeline for scaffolding genome assemblies with Hi-C reads
      Nextflow
      •
      MIT License
      •5•0•0•0•Updated Apr 5, 2025Apr 5, 2025

    • Summer_Course_ML

      Public
      Material for the CMM summer course
      Jupyter Notebook
      •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

    • BRCA

      Public
      Nexflow pipeline for processing target BRCA data
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Oct 22, 2024Oct 22, 2024

    • prok-annotate

      Public
      Annotation pipeline for prokaryotic genomes
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • nf-mag-depths

      Public
      A nextflow pipeline to calculate depth of coverage from a metagenomic set of bins
      coveragebioinformaticsmetagenomics
      coveragebioinformaticsmetagenomicsshort-reads
      Nextflow
      •
      MIT License
      •1•1•0•0•Updated Jul 11, 2024Jul 11, 2024

    • somatic_point_mutations

      Public
      call somatic point mutations from tumor/normal pairs
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated May 21, 2024May 21, 2024
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