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    47 repositories

    • trinityrnaseq

      Public
      Trinity RNA-Seq de novo transcriptome assembly
      Perl
      •
      BSD 3-Clause "New" or "Revised" License
      •317•897•311•0•Updated Apr 23, 2026Apr 23, 2026

    • bamsifter

      Public
      normalizes coverage depth by position-specific read sampling in a bam file to give a target max depth
      C++
      •6•2•4•0•Updated Mar 16, 2026Mar 16, 2026

    • CSHLProgForBio

      Public
      Python
      •2•2•0•0•Updated Oct 22, 2025Oct 22, 2025

    • minigenome

      Public
      makes a mini-genome, shrinks introns, useful for developing small test sets and small data sets for workshops
      Perl
      •0•3•0•0•Updated Dec 10, 2024Dec 10, 2024

    • TrinityFusion

      Public
      TrinityFusion software
      Perl
      •1•5•3•0•Updated Jun 27, 2024Jun 27, 2024

    • keepsakes

      Public
      milestones and momentos
      0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • trinity_ext_sample_data

      Public
      more extensive sample data for exploring various Trinity supported analysis modules
      Go
      •4•7•0•1•Updated Sep 26, 2023Sep 26, 2023

    • Chrysalis

      Public
      Chrysalis codebase
      C++
      •3•0•0•1•Updated May 30, 2023May 30, 2023

    • KrumlovTrinityWorkshopMay2023

      Public
      The first edition of the abridged version of the workshop
      1•0•0•0•Updated May 23, 2023May 23, 2023

    • KrumlovTrinityWorkshopMay2022

      Public
      Krumlov Trinity Workshop, May 2022
      Perl
      •1•3•0•0•Updated May 30, 2022May 30, 2022

    • Butterfly

      Public
      Butterfly codebase
      Java
      •1•0•0•1•Updated Mar 10, 2022Mar 10, 2022

    • seqtk-trinity

      Public
      Toolkit for processing sequences in FASTA/Q formats
      C
      •
      MIT License
      •325•1•0•1•Updated Nov 8, 2021Nov 8, 2021

    • Inchworm

      Public
      Inchworm codebase
      C++
      •
      Other
      •2•2•1•1•Updated Nov 8, 2021Nov 8, 2021

    • wgsim-trans

      Public
      Reads simulator
      C
      •92•0•0•0•Updated Mar 3, 2021Mar 3, 2021

    • KrumlovTrinityWorkshopJan2020

      Public
      Trinity rnaseq workshop in Cesky Krumlov, Czech Republic, Jan 2020
      2•5•0•0•Updated Jan 15, 2020Jan 15, 2020

    • KrumlovTrinityWorkshopJan2018

      Public
      Trinity RNA-Seq workshop in Krumlov 2018
      Pep8
      •6•3•2•0•Updated Jan 8, 2020Jan 8, 2020

    • KrumlovTrinityWorkshopJan2019

      Public
      Trinity workshop in Krumlov, Jan 2019
      Pep8
      •2•4•0•0•Updated Jan 8, 2020Jan 8, 2020

    • misc_tests

      Public
      Perl
      •1•0•0•0•Updated Nov 3, 2019Nov 3, 2019

    • CSHLProgForBiol2019

      Public
      CSHL Prog for Bio course 2019, rna-seq section
      Python
      •2•1•0•0•Updated Oct 24, 2019Oct 24, 2019

    • RNAseq_2019

      Public
      Content for RNAseq 2019 workshop
      Perl
      •9•0•0•0•Updated Jun 9, 2019Jun 9, 2019

    • BiCG_2019

      Public
      Workshop content for Bioinformatics for Cancer Genomics workshop 2019
      R
      •4•1•0•0•Updated Jun 7, 2019Jun 7, 2019

    • trinity_community_codebase

      Public
      Software contributed by Trinity community users to facilitate studies of Trinity-assembled transcriptomes.
      Perl
      •1•3•0•0•Updated Apr 30, 2019Apr 30, 2019

    • CSHLadvSeqTech

      Public
      basic rna-seq tutorial, leveraging Trinity, StringTie, HISAT2, and IGV
      2•1•0•0•Updated Nov 14, 2018Nov 14, 2018

    • CSHLProgForBiol2018

      Public
      CSHL Prog for Bio 2018, trinity rnaseq section
      2•0•0•0•Updated Oct 24, 2018Oct 24, 2018

    • UsageTracker

      Public
      Tracks software version usage via URL ping
      HTML
      •1•0•0•0•Updated Sep 1, 2018Sep 1, 2018

    • BernWorkshop2018

      Public
      Workshop in Bern, Switzerland in June, 2018
      Python
      •2•0•0•0•Updated Jun 28, 2018Jun 28, 2018

    • BerlinTrinityWorkshop2018

      Public
      week-long Trinity workshop in Berlin, June 2018
      Shell
      •3•0•1•0•Updated Jun 12, 2018Jun 12, 2018

    • RNAseq_2018

      Public
      Perl
      •3•1•0•0•Updated May 30, 2018May 30, 2018

    • BiCG_2018

      Public
      R
      •8•0•0•0•Updated Mar 15, 2018Mar 15, 2018

    • tracer

      Public
      TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
      Python
      •
      Other
      •48•0•0•0•Updated Mar 8, 2018Mar 8, 2018
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