Repositories list

• ifxvue

  Public
  Harvard FAS Informatics Vue JS components

  Vue

  •

  GNU General Public License v2.0

  •0•0•0•9•Updated Mar 3, 2025Mar 3, 2025

• AnnotationRNAseqAssembly

  Public
  Snakemake workflow for assembling transcript models from RNA-seq reads

  Python

  •0•1•0•0•Updated Mar 3, 2025Mar 3, 2025

• specify_web

  Public
  Conversion of HUH specify_web application to git

  PHP

  •0•3•0•0•Updated Mar 3, 2025Mar 3, 2025

• cactus-snakemake

  Public
  guidelines for running progressive CACTUS to produce a whole genome alignment required for genome annotation tools that leverage WGA

  Python

  •1•3•2•0•Updated Mar 2, 2025Mar 2, 2025

• AnnotationBRAKER

  Public
  Workflows and code for generating and filtering genome annotations with BRAKER

  Python

  •0•3•0•0•Updated Feb 28, 2025Feb 28, 2025

• informatics-website

  Public
  FAS Informatics website

  Python

  •

  MIT License

  •1•1•4•0•Updated Feb 28, 2025Feb 28, 2025

• github-intro

  Public
  A hands-on introduction to git/github

  MIT License

  •15•0•0•2•Updated Feb 27, 2025Feb 27, 2025

• NEMO-CE

  Public
  Copy of NEMO

  Python

  •

  Other

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• AnnotationTOGA

  Public
  Guidelines for running TOGA and scripts for processing outputs

  Python

  •2•6•0•0•Updated Feb 20, 2025Feb 20, 2025

• GenomeAnnotation

  Public
  Best practices and workflow for genome annotation

  Python

  •13•73•1•0•Updated Feb 19, 2025Feb 19, 2025

• scrub-jay-genomics

  Public
  HTML

  •

  MIT License

  •0•5•4•0•Updated Feb 18, 2025Feb 18, 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

  •97•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• snpArcher

  Public
  Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

  Python

  •

  MIT License

  •33•77•22•3•Updated Jan 31, 2025Jan 31, 2025

• specify_rapid

  Public
  Rapid data upload tool for specify. Conversion from SVN.

  JavaScript

  •0•1•0•3•Updated Jan 22, 2025Jan 22, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.4k•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• learning-bioinformatics-at-home

  Public
  resources for learning bioinformatics

  MIT License

  •176•984•0•0•Updated Jan 8, 2025Jan 8, 2025

• ifxurls

  Public
  Tools for getting urls in the ifx environment

  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Dec 30, 2024Dec 30, 2024

• benchmarking

  Public
  Demo repo for basic benchmarking

  Shell

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• ifxdjango

  Public
  Django project template for ifx Django REST / VueJS / Vuetify applications

  Python

  •

  GNU General Public License v2.0

  •3•3•0•2•Updated Oct 24, 2024Oct 24, 2024

• degenotate

  Public
  Python

  •

  MIT License

  •4•44•3•1•Updated Aug 7, 2024Aug 7, 2024

• IP4CI

  Public
  IP4CI: an interpretable pathway-based computational method for cross-species cell-type identification from single cell data

  R

  •0•0•0•0•Updated Jul 23, 2024Jul 23, 2024

• parse-pileup

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

• mop

  Public
  Simple tool for capturing alignment regions with sufficient quality for genotyping.

  Python

  •

  GNU General Public License v3.0

  •3•0•0•0•Updated May 30, 2024May 30, 2024

• BulkRNAseq2Counts

  Public
  A Snakemake workflow for generating expression count tables from either locally stored fastq files or NCBI-SRA accessions for bulk RNA-seq

  Python

  •

  MIT License

  •0•3•0•0•Updated May 8, 2024May 8, 2024

• pacbio_hifi_assembly

  Public
  A snakemake workflow for assembly with HiFi

  Python

  •1•2•0•0•Updated Apr 3, 2024Apr 3, 2024

• EndoriftiaTranscriptomics

  Public
  Code used in data analysis for Mitchell et al. 2024, a forthcoming paper on transcriptomic responses to environmental variation in *Candidatus Endoriftia persephone*, a bacterial symbiont of the deep sea tubeworm *Riftia pachyptila*.

  HTML

  •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

• TranscriptomeAssemblyTools

  Public
  A collection of scripts for processing fastq files in ways to improve de novo transcriptome assemblies, and for evaluating those assemblies.

  Python

  •23•48•0•0•Updated Mar 8, 2024Mar 8, 2024

• djvocab

  Public
  Vocabulary table for Django

  Python

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Jan 29, 2024Jan 29, 2024

• website

  Public
  Website markdown files

  HTML

  •5•4•0•1•Updated Oct 12, 2023Oct 12, 2023

• Mapping-simulations

  Public
  Read mapping simulations while varying divergence levels

  Python

  •0•0•0•0•Updated Oct 6, 2023Oct 6, 2023