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    29 repositories

    • vizgen_data_transfer

      Public
      Vizgen Data Transfer
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 16, 2026Mar 16, 2026

    • Pre_meet-annotation-workshop-2026

      Public
      EI Annotation Workshop 2026 (Pre-meet)
      MIT License
      •0•0•0•0•Updated Feb 5, 2026Feb 5, 2026

    • mikado

      Public
      Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models i…
      Python
      •
      GNU Lesser General Public License v3.0
      •19•112•19•2•Updated Jan 30, 2026Jan 30, 2026

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.9k•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • LiftClean

      Public
      Lifton/Liftoff transcript filtering and comparison pipeline
      Python
      •
      MIT License
      •0•1•1•0•Updated Jan 28, 2026Jan 28, 2026

    • annooddities

      Public
      AnnoOddities detects, identifies, and characterises oddities in genome annotations
      Python
      •
      MIT License
      •0•2•0•0•Updated Jan 28, 2026Jan 28, 2026

    • ENA_validation

      Public
      Script to pre-screen gff3 for validation
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 15, 2025Apr 15, 2025

    • FusariumPanAnno

      Public
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

    • reat

      Public
      Robust Eukaryotic Annotation Toolkit
      bioinformaticssingularityworkflows
      bioinformaticssingularityworkflowscromwell
      Python
      •
      MIT License
      •3•17•5•1•Updated Feb 28, 2025Feb 28, 2025

    • eirepeat

      Public
      eirepeat - EI Repeat Identification pipeline
      Python
      •
      GNU General Public License v3.0
      •2•7•1•0•Updated Feb 28, 2025Feb 28, 2025

    • eifunannot

      Public
      eifunannot - EI AHRD functional annotation pipeline
      Python
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Feb 28, 2025Feb 28, 2025

    • singlecellQC

      Public
      R
      •
      MIT License
      •1•0•1•1•Updated Sep 16, 2024Sep 16, 2024

    • CoassemblyPipeline

      Public
      Snakemake pipeline for genome coassembly
      Python
      •
      MIT License
      •0•0•2•0•Updated Aug 21, 2024Aug 21, 2024

    • Pre_meet-annotation-workshop-2024

      Public
      EI Annotation Workshop 2024 (Pre-meet)
      MIT License
      •0•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • annotation-workshop-2024

      Public
      EI Annotation Workshop 2024
      MIT License
      •0•1•0•0•Updated Apr 22, 2024Apr 22, 2024

    • SkimSeqQC

      Public
      Snakemake pipeline for QC of low-coverage skim-sequencing of G&T seq data
      Python
      •
      MIT License
      •0•0•2•0•Updated Apr 4, 2024Apr 4, 2024

    • minos

      Public
      The labyrinth king judges your gene models.
      Python
      •
      GNU Lesser General Public License v3.0
      •0•8•13•0•Updated Feb 14, 2024Feb 14, 2024

    • go-patterns

      Public
      Curated list of Go design patterns, recipes and idioms
      Go
      •
      Apache License 2.0
      •2.3k•0•0•0•Updated Aug 7, 2022Aug 7, 2022

    • portcullis

      Public
      Splice junction analysis and filtering from BAM files
      bam-filesfilterportcullis
      bam-filesfilterportcullisjunctionsplice-junctions
      C++
      •
      GNU General Public License v3.0
      •9•42•26•0•Updated Mar 31, 2022Mar 31, 2022

    • annotation-workshop-2022

      Public
      MIT License
      •5•1•0•0•Updated Sep 16, 2021Sep 16, 2021

    • DToL_asm_hifi

      Public
      Assembly (Hifi), Breaking (10X), Scaffolding (10X) and Polishing (10X) pipeline
      Python
      •0•0•9•0•Updated Jul 23, 2021Jul 23, 2021

    • annotation-workshop-2021

      Public
      Repository for preparing the workshop of April 2021
      MIT License
      •0•3•2•0•Updated Apr 9, 2021Apr 9, 2021

    • CPC2

      Public
      Verbatim Copy of CPC 2.0
      Java
      •3•0•0•0•Updated Jan 29, 2021Jan 29, 2021

    • barcode_retrieval

      Public
      Primer-based barcode retrieval and counting from barcoded samples
      R
      •0•1•0•0•Updated Jul 15, 2020Jul 15, 2020

    • bgrrl

      Public
      Python
      •0•0•11•0•Updated Mar 19, 2020Mar 19, 2020

    • MultiQC

      Public
      Aggregate results from bioinformatics analyses across many samples into a single report.
      Python
      •
      GNU General Public License v3.0
      •658•0•0•0•Updated Mar 13, 2020Mar 13, 2020

    • qaa

      Public
      Quality Assurance for Assemblies
      Python
      •
      MIT License
      •0•1•1•0•Updated Sep 11, 2019Sep 11, 2019

    • AnnotF

      Public
      AnnotF - A functional Annotation pipeline
      Perl
      •
      MIT License
      •2•0•0•0•Updated Apr 17, 2019Apr 17, 2019

    • CRISPRanto

      Public
      CRISPR off-target analysis (i.e. CRISPRs second language)
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 19, 2018Sep 19, 2018
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