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    27 repositories

    • PRDM16_CtBP_Project

      Public
      Workflows and documentation for Baizabal Group genomics projects on neural stem cells
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•1•Updated Nov 24, 2024Nov 24, 2024

    • CTBPprj

      Public
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jul 9, 2024Jul 9, 2024

    • TSRbuild

      Public
      Scripts and workflows for transcription start region (TSR) exploration
      Shell
      •5•0•0•2•Updated Jun 3, 2024Jun 3, 2024

    • AEGeAn

      Public
      Integrated toolkit for analysis and evaluation of annotated genomes
      C
      •
      ISC License
      •10•24•15•0•Updated Jan 17, 2024Jan 17, 2024

    • iLoci_SLB22NARGB

      Public
      Procedures and data for the iLoci study described in Standage, Lai and Brendel (2022)
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 17, 2024Jan 17, 2024

    • GAinSAW

      Public
      Workflows for genome alignment chain file selection and annotation tasks
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 27, 2023Oct 27, 2023

    • BWASP

      Public
      Bisulfite-seq data Workflow Automation Software and Protocols
      Shell
      •
      GNU General Public License v2.0
      •5•2•0•0•Updated May 23, 2023May 23, 2023

    • TSRchitect

      Public
      Promoter identification from diverse types of large-scale TSS profiling data
      R
      •
      GNU General Public License v3.0
      •4•1•2•1•Updated Jan 3, 2023Jan 3, 2023

    • GoSTRIPES

      Public
      Computational workflows for STRIPE-seq data analyses
      Perl
      •5•4•0•0•Updated Dec 25, 2022Dec 25, 2022

    • bgSingularityHub

      Public
      A portal to our collection of Singularity/Apptainer definition and image files
      2•1•0•0•Updated Apr 4, 2022Apr 4, 2022

    • AllRice

      Public
      Code for rice genome analyses (but not necessarily only rice)
      Shell
      •1•0•0•0•Updated Mar 28, 2022Mar 28, 2022

    • mRNAmarkup

      Public
      Evaluation and annotation of assembled transcripts
      C
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • SRAssembler

      Public
      Selective and Recursive local Assembler
      C++
      •
      GNU General Public License v3.0
      •6•15•4•0•Updated Jan 31, 2022Jan 31, 2022

    • BWASPR

      Public
      R functions and scripts to process output from the BWASP workflow
      R
      •5•1•0•0•Updated Jan 31, 2022Jan 31, 2022

    • brendelgroup.github.io

      Public
      Brendel Group - github.io presence
      SCSS
      •
      Other
      •0•0•0•0•Updated Jan 30, 2022Jan 30, 2022

    • GeneSeqer

      Public
      Sensitive spliced-alignment of cDNAs or proteins
      C
      •
      GNU General Public License v3.0
      •2•1•0•1•Updated Jan 26, 2022Jan 26, 2022

    • IntervalLoci

      Public
      Supplemental documentation for the iLocus paper
      Jupyter Notebook
      •1•0•1•0•Updated Apr 3, 2020Apr 3, 2020

    • MoVRs

      Public
      Motif set Reduction and Validation (MoVRs) - a workflow for the derivation of genome-wide DNA motif detection and vetting
      Perl
      •
      GNU General Public License v2.0
      •5•7•5•0•Updated Sep 25, 2019Sep 25, 2019

    • bghandbook

      Public
      Handbook for Brendel Group students, postdocs, and staff
      Python
      •23•4•0•0•Updated Feb 13, 2019Feb 13, 2019

    • GoRAMPAGE

      Public
      GoRAMPAGE - a workflow for promoter detection by 5'-read mapping
      Shell
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Oct 5, 2018Oct 5, 2018

    • Bismark

      Public
      A tool to map bisulfite converted sequence reads and determine cytosine methylation states
      Smarty
      •
      GNU General Public License v3.0
      •103•0•0•0•Updated May 24, 2018May 24, 2018

    • code4Rice3K

      Public
      code developed for the analysis of the Rice 3000 Genomes project data
      Shell
      •
      GNU General Public License v3.0
      •3•1•0•0•Updated Nov 22, 2017Nov 22, 2017

    • xGDBvm

      Public
      Code for the xGDBvm iPlant Atmosphere enabled genome annotation platform
      PHP
      •
      GNU General Public License v3.0
      •3•0•7•0•Updated May 16, 2017May 16, 2017

    • TRegGA

      Public
      Targeted reference-guided genome assembly for comparative rice genomics
      Shell
      •4•3•2•1•Updated Jan 9, 2017Jan 9, 2017

    • FMAB

      Public
      Fundamental Models and Algorithms in Bioinformatics
      Python
      •8•3•0•0•Updated Oct 25, 2016Oct 25, 2016

    • HymHub

      Public
      HymHub is now GenHub
      2•1•4•0•Updated Feb 26, 2016Feb 26, 2016

    • pdom-genome-project

      Public
      Polistes dominula genome project, a collaboration between the Insect Sociogenomics Lab at Iowa State University and the Computational Genome Science Lab at Indiana University
      Makefile
      •1•7•1•0•Updated Jul 25, 2015Jul 25, 2015