Issues

• Inquiry Regarding Incorrect Assignment of Root Cells to Termini During URD Trajectory Tree Construction (Despite Normal Pseudotime Results)

  farrellja/URD#91 · Filter by author Yukaixu666 opened on Sep 16, 2025

• How to fast the calculation of CalcDM

  farrellja/URD#90 · Filter by author Yukaixu666 opened on Sep 13, 2025

• limit.single.sigmoid.slopes

  farrellja/URD#89 · Filter by author Ruismart opened on Apr 14, 2024
  1

• what is tip.walk.files?

  farrellja/URD#87 · Filter by author wangzitiner opened on May 22, 2023

• SupplementaryAnalysis.pdf --- Page 19 --- Batch correct data --- mnnCorrect

  farrellja/URD#86 · Filter by author zzy0630 opened on May 3, 2023

• Installation: big trouble in many packages

  farrellja/URD#85 · Filter by author wangzitiner opened on Apr 14, 2023

• Error in floodPseudotimeProcess

  farrellja/URD#84 · Filter by author mary77 opened on Jan 31, 2023
  2

• Error in visit.data[cells.in.tip, ] : incorrect number of dimensions

  farrellja/URD#83 · Filter by author zhang929821416 opened on Sep 18, 2022
  2

• where is walks.to.do object

  farrellja/URD#82 · Filter by author xujiahao778899 opened on Aug 21, 2022

• determine.timing: Error in peak.rle[peak, "start"]:peak.rle[peak, "end"] : NA/NaN argument

  farrellja/URD#81 · Filter by author grimwoo opened on Jun 16, 2022

• aucprTestByFactor

  farrellja/URD#80 · Filter by author MedCYLIU opened on Mar 21, 2022

• Error in calcTsne and calcDM: length of 'dimnames' [1] not equal to array extent

  farrellja/URD#79 · Filter by author Sophia409 opened on Dec 6, 2021
  2

• Markers for Trajectory Branches.

  farrellja/URD#78 · Filter by author hzuzu opened on Nov 15, 2021

• floodPseudotime

  farrellja/URD#77 · Filter by author allisoncheney opened on Oct 28, 2021
  1

• n_pcs is needed to be specified in calcDM

  farrellja/URD#76 · Filter by author mimi3421 opened on Aug 25, 2021
  1

• Supplementary Analysis Count and Meta data files out of date on Broad SC Portal

  farrellja/URD#75 · Filter by author gonzalezdavidmatthew opened on Jul 9, 2021

• Cholmod error

  farrellja/URD#73 · Filter by author rojinsafavi opened on Jun 1, 2021
  1

• error when installing destiny

  farrellja/URD#72 · Filter by author liuweihanty opened on May 17, 2021
  1

• macOS: Can't install because of package 'destiny'

  farrellja/URD#71 · Filter by author francoiskroll opened on Apr 1, 2021
  1

• gene cascade heatmap

  farrellja/URD#70 · Filter by author tracytktran opened on Jan 21, 2021

• Link to processed URD object is out of date

  farrellja/URD#68 · Filter by author jlchang opened on Jan 7, 2021

• seuratToURD2 (previous issue #29)

  farrellja/URD#67 · Filter by author Sa753 opened on Dec 30, 2020
  3

• Force directed layout fails to show even though it is loaded and calculated

  farrellja/URD#66 · Filter by author shiromchabra opened on Nov 19, 2020
  1

• Parallelization and scalibility

  farrellja/URD#65 · Filter by author macros29 opened on Oct 17, 2020

• Pseudotime discontinuous at zero

  farrellja/URD#64 · Filter by author corwms opened on Aug 28, 2020
  1