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@HPCBio High Performance Computing in Biology

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    90 repositories

    • workflows-nextflow

      Public
      Workflow management with Nextflow and nf-core
      Nextflow
      •
      Other
      •34•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • hpcbio-swc-shell-novice-sp2025

      Public
      Shell
      •
      Other
      •0•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • hpcbio-swc-bioc-intro

      Public
      R
      •
      Other
      •0•0•0•0•Updated Dec 24, 2024Dec 24, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •277•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • workflows-nextflow-2023

      Public
      Workflow management with Nextflow and nf-core
      HTML
      •
      Other
      •34•0•0•0•Updated Dec 4, 2024Dec 4, 2024

    • figaro

      Public
      An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
      Python
      •
      GNU General Public License v3.0
      •26•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • Mayo-Genome-Assembly

      Public
      Perl
      •0•0•2•0•Updated Jun 26, 2024Jun 26, 2024

    • Li_scATACSeq_demultiplexing_Nov23

      Public
      Shell
      •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

    • hergenrother-16S-mouse-2022Sept

      Public
      Code for the Hergenrother 2022 mouse antimicrobiall study
      R
      •1•1•1•0•Updated Apr 19, 2024Apr 19, 2024

    • Refgraph_pipeline

      Public
      H3ABioNet RefGraph assembly-based pipeline
      Shell
      •6•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • dotPlotly

      Public
      Generate an interactive dot plot from mummer or minimap alignments
      HTML
      •
      MIT License
      •56•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • caceres-16S-mosquito-2022Sept

      Public
      R
      •0•1•0•0•Updated Nov 8, 2023Nov 8, 2023

    • bishop-Shoreline-Dec2021

      Public
      0•0•0•0•Updated Oct 23, 2023Oct 23, 2023

    • spams-R

      Public
      R interface for SPAMS (SPArse Modeling Software)
      C++
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • reference_database_creator

      Public
      creating reference databases for amplicon sequencing
      Python
      •
      MIT License
      •9•0•0•0•Updated Sep 29, 2023Sep 29, 2023

    • nextflow-training

      Public
      Nextflow training material
      Nextflow
      •
      Other
      •131•0•0•0•Updated Jul 31, 2023Jul 31, 2023

    • Pangenome-Graphs-Workshop

      Public
      This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.
      HTML
      •
      GNU General Public License v2.0
      •3•0•0•0•Updated Jul 26, 2023Jul 26, 2023

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •127•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • Detect-seq

      Public
      An unbiased method for genome-wide CBE off-targets assessment
      Python
      •
      Other
      •8•0•0•0•Updated Feb 22, 2023Feb 22, 2023

    • EM-seq

      Public
      Tools and Data related to Enzymatic Methylation Sequencing
      Nextflow
      •
      GNU Affero General Public License v3.0
      •5•0•0•0•Updated Jan 25, 2023Jan 25, 2023

    • TRIDENT

      Public
      NGS variant analysis & fluctuation analysis MLE calculator
      Jupyter Notebook
      •1•0•0•0•Updated Sep 12, 2022Sep 12, 2022

    • eib-marker-design

      Public
      Workflow for designing KASP markers from resequencing data
      R
      •
      MIT License
      •2•2•0•0•Updated Aug 12, 2022Aug 12, 2022

    • methylseq-old

      Public
      Old copy of the nf-core methylseq workflow including hacked in NuGen/Tecan support
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 22, 2022Jun 22, 2022

    • NuMetRRBS

      Public
      Python
      •6•0•0•0•Updated Jun 9, 2022Jun 9, 2022

    • methylseq

      Public
      Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
      Nextflow
      •
      MIT License
      •146•0•0•0•Updated May 25, 2022May 25, 2022

    • plotly_microbiome

      Public
      R helper functions for making Plotly graphs in microbiome work
      R
      •0•0•2•0•Updated May 3, 2022May 3, 2022

    • GFF3toolkit

      Public
      Python programs for processing GFF3 files
      Python
      •
      Other
      •27•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • phyloseq-extended

      Public
      Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul
      R
      •
      GNU General Public License v3.0
      •19•0•0•1•Updated Oct 14, 2021Oct 14, 2021

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •49•0•0•0•Updated Oct 4, 2021Oct 4, 2021

    • bacterial_variant_calling

      Public
      A pipeline for variant calling on bacterial genomes created with Nextflow and singularity / docker
      Nextflow
      •
      MIT License
      •4•0•0•0•Updated Sep 22, 2021Sep 22, 2021