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@HTGenomeAnalysisUnit HT Genome Analysis Unit

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    50 repositories

    • TileDB-sumstat

      Public
      TileDB for storing and analyzing single-cell QTL data
      Python
      •0•1•0•3•Updated Apr 4, 2026Apr 4, 2026

    • gtf-parser

      Public
      Pure python basic parser for GTF and GFF3 files
      Python
      •
      MIT License
      •0•0•0•1•Updated Mar 19, 2026Mar 19, 2026

    • local_llm_cli

      Public
      Batch-process queries against local GGUF models or OpenAI-compatible endpoints.
      Python
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • tre-containers

      Public
      Containers recipes for G&H TRE analyses
      R
      •1•2•0•1•Updated Mar 18, 2026Mar 18, 2026

    • nf-pipeline-regenie

      Public
      GWAS and rare variants tests at high speed using regenie
      Nextflow
      •
      MIT License
      •4•16•7•1•Updated Feb 18, 2026Feb 18, 2026

    • varcall_training

      Public
      methods in genomic variant calling training course at Human Technopole
      HTML
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Feb 6, 2026Feb 6, 2026

    • nf-core-configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •356•0•0•0•Updated Jan 28, 2026Jan 28, 2026

    • nextflow-zero2hero

      Public
      Materials for the training course Nextflow - from zero to hero
      Nextflow
      •0•2•0•0•Updated Jan 28, 2026Jan 28, 2026

    • csq_selector

      Public
      Filter and select variant consequence annotations from snpEff, VEP or bcftools
      Nim
      •
      MIT License
      •0•4•0•0•Updated Dec 12, 2025Dec 12, 2025

    • projectStyleR

      Public
      utility package for R designed to enforce a consistent visual identity across all `ggplot2` plots generated for a scientific project
      HTML
      •0•1•0•0•Updated Dec 1, 2025Dec 1, 2025

    • h5ad_clean_annotate

      Public
      A small tool that help in cleaning, subsetting and annotation h5ad file efficiently.
      Python
      •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

    • eQTL_luthier

      Public
      Make nicely crafted violins to represent SNV effect of on gene expression.
      R
      •0•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • snpboost

      Public
      An algorithm to apply statistical boosting on genotype data via a batch-based approach.
      R
      •1•0•0•0•Updated Oct 15, 2025Oct 15, 2025

    • CARDINAL_styler

      Public
      Themes and palettes for plotting in the CARDINAL project
      0•1•0•0•Updated Sep 23, 2025Sep 23, 2025

    • easy_key_annotation

      Public
      Easy annotate a table from multiple sources using a key column
      Python
      •0•0•0•0•Updated Sep 17, 2025Sep 17, 2025

    • project_styler_py

      Public
      utility package for Python designed to enforce a consistent visual identity across all `matplotlib` and `seaborn` plots generated for a scientific project
      Jupyter Notebook
      •0•0•0•0•Updated Sep 5, 2025Sep 5, 2025

    • bigdata_views

      Public
      Interactive visualization for large scale single-cell data using datashader and holoviews
      Python
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • Useful_tips

      Public
      Tips for various bioinformatic tasks
      0•7•0•0•Updated Jul 7, 2025Jul 7, 2025

    • sc-scatter-shiny

      Public
      Scalable interactive view of single-cell data using jscatter and pyshiny
      Python
      •0•0•1•0•Updated Jun 19, 2025Jun 19, 2025

    • dx-snapshot_gpu

      Public
      DNANexus applet to run any snapshot container with latest NVIDIA driver
      Shell
      •0•0•0•0•Updated May 6, 2025May 6, 2025

    • dx-jupyterlab

      Public
      DNA Nexus applet to run jupyter lab from a container
      Shell
      •0•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • nf-core-modules

      Public
      fork of nf-core modules. Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •1k•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • scrnaseq

      Public
      Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
      Nextflow
      •
      MIT License
      •216•0•0•0•Updated Mar 14, 2025Mar 14, 2025

    • nf_core_configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •356•0•0•0•Updated Mar 13, 2025Mar 13, 2025

    • CellBender

      Public
      CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •85•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • dx-wdl-regenie

      Public
      A WDL workflow to run regenie on DNANexus RAP
      WDL
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • rsid_tools

      Public
      Small utilities to play with dbSNP rsID: annotate rsID for a var or get position for an rsID
      Nim
      •0•5•0•0•Updated Dec 5, 2024Dec 5, 2024

    • DIALOGUE

      Public
      DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as…
      R
      •
      Other
      •17•1•0•0•Updated Nov 7, 2024Nov 7, 2024

    • SCE-VCF

      Public
      Sample Contamination Estimate from VCF
      Nim
      •
      MIT License
      •1•20•1•0•Updated Nov 6, 2024Nov 6, 2024

    • variant-annotation-OTG

      Public
      Tools for annotating variants using OTG data
      Python
      •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024
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