1. 11 Nov, 2019 1 commit
  2. 31 Oct, 2019 4 commits
  3. 13 Mar, 2019 1 commit
  4. 20 Sep, 2018 1 commit
  5. 11 Sep, 2018 1 commit
    • Jamie Gearing's avatar
      No longer rounding matrix similarity score. · 2abdea52
      Jamie Gearing authored
      Correct import of input CSL file.
      Some BED file outputs.
      Cluster can now get sum of deficit squared compared to any transcription factor.
      Changed default CHAMP seed similarity to 0.85 because default scan deficit is 0.15.
      2abdea52
  6. 27 Apr, 2017 1 commit
  7. 07 Apr, 2017 1 commit
    • Jamie Gearing's avatar
      Improvements to CHAMP clustering options in Iterative Clustering and... · 45bc0ac4
      Jamie Gearing authored
      Improvements to CHAMP clustering options in Iterative Clustering and KClusters. Clustering can now be repeated for the same number of clusters, but using different start sites. Start sites can be chosen based on similarity to the original TranscriptionFactor or at random. TFSites with identical sequences are grouped in a LinkedHashMap. Clustering is performed using unique sites; once assigned to a cluster, all other sites with the same sequence are added to the same cluster. This seems to give a marginal performance gain.
      45bc0ac4
  8. 06 Apr, 2017 1 commit
  9. 05 Apr, 2017 2 commits
  10. 04 Apr, 2017 1 commit
    • Jamie Gearing's avatar
      Site toString() includes getSequence(); when writing sites to file in CSV... · 694f0b71
      Jamie Gearing authored
      Site toString() includes getSequence(); when writing sites to file in CSV format, sequence is now also given. Added CHAMPUSEENRICHMENT parameter. If "true", CHAMP uses sites at the most signfificant deficit; if "false" CHAMP uses sites at the scan deficit (e.g. 0.15) for all transcription factors. Re-ordered author list.
      694f0b71
  11. 13 Feb, 2017 2 commits
  12. 01 Feb, 2017 3 commits
  13. 13 Jan, 2017 1 commit