Repositories list

• 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

• CSHLProgForBio

  Public
  Python

  •2•2•0•0•Updated Oct 22, 2024Oct 22, 2024

• trinityrnaseq

  Public
  Trinity RNA-Seq de novo transcriptome assembly

  Perl

  •

  BSD 3-Clause "New" or "Revised" License

  •320•840•297•0•Updated Aug 1, 2024Aug 1, 2024

• bamsifter

  Public
  normalizes coverage depth by position-specific read sampling in a bam file to give a target max depth

  C++

  •6•2•3•0•Updated Jul 30, 2024Jul 30, 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

  •307•1•0•1•Updated Nov 8, 2021Nov 8, 2021

• Inchworm

  Public
  Inchworm codebase

  C++

  •

  Other

  •2•1•1•1•Updated Nov 8, 2021Nov 8, 2021

• wgsim-trans

  Public
  Reads simulator

  C

  •90•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