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    179 repositories

    • snakemake-workshop

      Public
      Snakemake workshop
      Python
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • python-intensive

      Public
      FAS Informatics Python Workshop
      Jupyter Notebook
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • scrub-jay-genomics

      Public
      HTML
      •
      MIT License
      •0•8•4•0•Updated Aug 6, 2025Aug 6, 2025

    • informatics-website

      Public
      FAS Informatics website
      TeX
      •
      MIT License
      •1•2•1•1•Updated Aug 5, 2025Aug 5, 2025

    • AllAsia-Symbiota

      Public
      The Symbiota Virtual Flora/Fauna project is an open source software project, with central goal of developing on-line tools that aid in the generation, exploration and management of biodiversity data (collection specimens, observations, images, checklist, keys, etc.). See also: http://bdj.pensoft.net/articles.php?id=1114 and http://symbiota.org/
      JavaScript
      •
      GNU General Public License v2.0
      •98•0•0•0•Updated Aug 5, 2025Aug 5, 2025

    • snakemake-executor-plugin-cannon

      Public
      A Snakemake executor plugin for submitting jobs to the Harvard Cannon cluster
      Python
      •
      MIT License
      •36•0•3•0•Updated Jul 25, 2025Jul 25, 2025

    • Mapping-simulations

      Public
      Read mapping simulations while varying divergence levels
      Python
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • ifxvue

      Public
      Harvard FAS Informatics Vue JS components
      Vue
      •
      GNU General Public License v2.0
      •0•0•0•9•Updated Jul 22, 2025Jul 22, 2025

    • NEMO-CE2

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • NEMO-CE

      Public
      Copy of NEMO
      Python
      •
      Other
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • short-trainings

      Public
      Material for our various standalone short trainings (a potpourri, if you will)
      0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • intro-r

      Public
      The introduction to R workshop
      0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • healthy-habits

      Public
      The healthy habits for data science workshop
      0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • biotips

      Public
      The unix tips and tricks for bioinformatics workshop
      Shell
      •0•0•0•0•Updated Jul 10, 2025Jul 10, 2025

    • nextflow-run

      Public
      Workshop to teach how to run nextflow pipelines
      Dockerfile
      •
      Other
      •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • snpArcher

      Public
      Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
      Python
      •
      MIT License
      •32•80•20•0•Updated Jul 8, 2025Jul 8, 2025

    • cactus-snakemake

      Public
      Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters
      Python
      •
      MIT License
      •1•4•2•0•Updated Jul 7, 2025Jul 7, 2025

    • pacbio_hifi_assembly

      Public
      A snakemake workflow for assembly with HiFi
      Python
      •2•3•0•0•Updated Jul 1, 2025Jul 1, 2025

    • specify_rapid

      Public
      Rapid data upload tool for specify. Conversion from SVN.
      JavaScript
      •0•1•0•3•Updated Jun 27, 2025Jun 27, 2025

    • specify_web

      Public
      Conversion of HUH specify_web application to git
      PHP
      •0•3•0•0•Updated Jun 27, 2025Jun 27, 2025

    • degenotate

      Public
      Python
      •
      MIT License
      •4•50•4•1•Updated Jun 12, 2025Jun 12, 2025

    • nfcore_bulk_rnaseq

      Public
      Brief description of how to run nf-core bulk-rnaseq workflow
      Shell
      •0•0•0•0•Updated Jun 11, 2025Jun 11, 2025

    • ifxurls

      Public
      Tools for getting urls in the ifx environment
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.6k•0•0•0•Updated May 6, 2025May 6, 2025

    • hackathonSpring25_gxfProj

      Public
      Python
      •0•0•0•0•Updated May 4, 2025May 4, 2025

    • GenomeAnnotation

      Public
      Best practices and workflow for genome annotation
      Python
      •14•77•1•0•Updated Apr 14, 2025Apr 14, 2025

    • AnnotationBRAKER

      Public
      Workflows and code for generating and filtering genome annotations with BRAKER
      Python
      •0•3•0•0•Updated Apr 2, 2025Apr 2, 2025

    • AnnotationRNAseqAssembly

      Public
      Snakemake workflow for assembling transcript models from RNA-seq reads
      Python
      •0•1•0•0•Updated Mar 28, 2025Mar 28, 2025

    • AnnotationTOGA

      Public
      Guidelines for running TOGA and scripts for processing outputs
      Python
      •2•7•0•0•Updated Mar 10, 2025Mar 10, 2025

    • github-intro

      Public
      A hands-on introduction to git/github
      MIT License
      •14•1•0•2•Updated Feb 27, 2025Feb 27, 2025