Issues

• get annotation end

  New Tool
  CEGRcode/scriptmanager#190 · Filter by author owlang opened on May 28, 2026

• Calculate scaling factor loads control array for every bam

  enhancement
  CEGRcode/scriptmanager#189 · Filter by author jcha40 opened on Mar 4, 2025

• add generic and track comment support for BED files

  bug
  CEGRcode/scriptmanager#188 · Filter by author owlang opened on Feb 14, 2025
  1

• catch Sort BED case of non-unique BED ids

  bug
  CEGRcode/scriptmanager#186 · Filter by author owlang opened on Nov 26, 2024

• Unexpected file outputs by sort-bed in GUI

  bug
  CEGRcode/scriptmanager#185 · Filter by author jcha40 opened on Nov 20, 2024

• Format code and set-up linter

  streamline
  CEGRcode/scriptmanager#183 · Filter by author owlang opened on Nov 19, 2024

• AWTError when running graphics tools on headless remote server

  bug
  CEGRcode/scriptmanager#182 · Filter by author owlang opened on Nov 19, 2024

• ExpandGFFCLI expands by border when center selected

  bugeasy
  CEGRcode/scriptmanager#180 · Filter by author owlang opened on Nov 13, 2024

• TagPileup low memory mode

  enhancementtagpileup-related
  CEGRcode/scriptmanager#177 · Filter by author owlang opened on Oct 15, 2024

• FRiX score denominator much lower than total read count

  bug
  CEGRcode/scriptmanager#176 · Filter by author jcha40 opened on Oct 9, 2024

• Test ScriptManager using X11 forwarding

  CEGRcode/scriptmanager#175 · Filter by author owlang opened on Sep 26, 2024
  1

• Filter BAM by BED

  New Tool
  CEGRcode/scriptmanager#174 · Filter by author owlang opened on Sep 5, 2024

• Aggregate Data Row/Column index specification

  easy
  CEGRcode/scriptmanager#154 · Filter by author WilliamKMLai opened on Mar 12, 2024
  

• update DNAShape tool with new shapes DB

  CEGRcode/scriptmanager#152 · Filter by author owlang opened on Dec 6, 2023
  

• Add @PG tag to BAM header in Filter PIP-seq tool

  CEGRcode/scriptmanager#144 · Filter by author owlang opened on Sep 4, 2023

• Write an Anaconda recipe for bioconda

  CEGRcode/scriptmanager#141 · Filter by author owlang opened on Aug 24, 2023
  

• Calculate scaling factor by regions (NFR normalization)

  New Tool
  CEGRcode/scriptmanager#139 · Filter by author owlang opened on Aug 9, 2023

• Filter BED/GFF by limits on chrom ends

  New Tool
  CEGRcode/scriptmanager#135 · Filter by author owlang opened on Jul 21, 2023

• Add FASTA Chr Name Converter

  New Tool
  CEGRcode/scriptmanager#131 · Filter by author owlang opened on Jun 21, 2023
  1

  

• Add more picard options to MarkDuplicatesWrapper

  easyfeature-request
  CEGRcode/scriptmanager#128 · Filter by author owlang opened on Jun 9, 2023

• Add support for separate composite output files in TagPileup

  streamlinetagpileup-related
  CEGRcode/scriptmanager#125 · Filter by author owlang opened on Jun 8, 2023

• Write Galaxy wrappers for ChIP-exo Tutorial

  CEGRcode/scriptmanager#124 · Filter by author owlang opened on Jun 7, 2023
  

• Wrap priority Picard tools into GUI

  CEGRcode/scriptmanager#122 · Filter by author owlang opened on Jun 6, 2023
  

• Gradle Shadow minimize()

  bug
  CEGRcode/scriptmanager#116 · Filter by author owlang opened on Apr 7, 2023

• JUnit tests for CI development of all tools

  CEGRcode/scriptmanager#114 · Filter by author owlang opened on Apr 6, 2023