CEGRcode/scriptmanager

Issues

• fix edge case on peak-align

  #169 opened 13 days ago
  0

• Add strand-matching for peak-align-ref

  #168 opened 18 days ago
  0

• Aggregate Data Row/Column index specification

  #154 opened 4 months ago
  0

• Incorrect 3 prime R1 encoding for SE data

  #153 opened 5 months ago
  0

• update DNAShape tool with new shapes DB

  #152 opened 7 months ago
  0

• fix "seperate" typo in TagPileup

  #150 opened 7 months ago
  1

• bugfix 4-color plot - add support for multi-line FASTA input

  #149 opened 7 months ago
  0

• Modify se-stats GUI output format

  #148 opened 7 months ago
  0

• Upgrade PE Statistics with new features

  #146 opened 7 months ago
  2

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

  #144 opened 10 months ago
  0

• Write an Anaconda recipe for bioconda

  #141 opened 10 months ago
  0

• Calculate scaling factor by regions (NFR normalization)

  #139 opened a year ago
  0

• Reduce repetitive code in ScriptManagerGUI

  #138 opened a year ago
  0

• Filter BED/GFF by limits on chrom ends

  #135 opened a year ago
  0

• TagPileup GUI tag extend - 2bp by default - should be 1bp

  #133 opened 7 months ago
  0

• Add Logging support for core tools

  #132 opened 7 months ago
  0

• Add FASTA Chr Name Converter

  #131 opened a year ago
  1

• Write FRiX tool to calculate fraction of reads in reference

  #130 opened a year ago
  1

• Aggregate data tool includes NAME column of CDT file if it is numeric

  #129 opened a year ago
  1

• Add more picard options to MarkDuplicatesWrapper

  #128 opened a year ago
  0

• Add support for CDT/TAB matrix output in DNAShape tools

  #126 opened 7 months ago
  0

• Add support for separate composite output files in TagPileup

  #125 opened a year ago
  0

• Write Galaxy wrappers for ChIP-exo Tutorial

  #124 opened a year ago
  0

• Wrap priority Picard tools into GUI

  #122 opened a year ago
  0

• Add Logging Framework

  #121 opened a year ago
  0

• BAM Genome Correlation Progress Bar not updating

  #118 opened a year ago
  1

• Add ArchTEx Cross-Correlation analysis

  #117 opened a year ago
  0

• Gradle Shadow minimize()

  #116 opened a year ago
  0

• TagPileup Facelift

  #115 opened a year ago
  0

• JUnit tests for CI development of all tools

  #114 opened a year ago
  0

• Upgrade Gradle to support java 17 build

  #112 opened a year ago
  0

• Redo file structure to standard Java project format

  #110 opened a year ago
  0

• ChIP-seq TagPileup Data Cutoff and Full Fragment issue

  #109 opened a year ago
  2

• Refactor existing tools to natively call Picard commands

  #108 opened a year ago
  1

• TagPileup Blacklist function not working

  #106 opened 2 years ago
  1

• Normalize cdt (per row) by histone occupancy

  #105 opened 2 years ago
  1

• BAM Correlation ColorMap Options

  #102 opened a year ago
  0

• BAM Genome Correlation Read selection

  #101 opened 2 years ago
  0

• Composite CLI parameters reversed

  #97 opened 2 years ago
  0

• Composite Plot image making tool

  #96 opened 2 years ago
  0

• Add new tools based on Perl script collection

  #92 opened 2 years ago
  0

• add support for gzipped BED/text files across all tools

  #91 opened 7 months ago
  1

• Switch gzip file type check from extension to "magic" bytes

  #88 opened 2 years ago
  1

• TwoColorHeatMapCLI GZip Incompatibility

  #85 opened 2 years ago
  0

• Parameter tool-tips on TagPileup

  #84 opened 2 years ago
  0

• PE-stats only processing single file at a time

  #83 opened 2 years ago
  1

• Update charting dependencies

  #82 opened 2 years ago
  1

• Scale Matrix GUI results in zero matrices

  #81 opened 2 years ago
  1

• GrCh38 TileGenome and RandCoord

  #80 opened 2 years ago
  0

• Alert user to odd-sized sliding window requirement in TP

  #79 opened 2 years ago
  0