Issues

• initiatior filtering

  enhancement
  charles-plessy/CAGEr#137 · Filter by author ferenckata opened on Mar 18, 2026
  1

• alpha value capped at 1.05

  charles-plessy/CAGEr#126 · Filter by author ferenckata opened on Feb 21, 2025
  4

• plotAnnot warnings

  charles-plessy/CAGEr#124 · Filter by author ferenckata opened on Dec 6, 2024

• Brush up function families.

  enhancement
  charles-plessy/CAGEr#118 · Filter by author charles-plessy opened on May 24, 2024

• Remove the redundant tpm column of consensus cluster objects.

  enhancement
  charles-plessy/CAGEr#117 · Filter by author charles-plessy opened on May 17, 2024

• as(tag_cluster, "CTSS") should use the dominant CTSS information.

  enhancement
  charles-plessy/CAGEr#116 · Filter by author charles-plessy opened on May 17, 2024

• no non-missing arguments to max; returning -Inf error when calling tag clusters

  charles-plessy/CAGEr#115 · Filter by author da-bar opened on May 14, 2024
  1

• consensusClustersGR() row.names problem

  charles-plessy/CAGEr#112 · Filter by author MorexV3CAGE opened on Feb 8, 2024
  4

• Can the correctSystematicG = T parameter be used for a BAM file generated from STAR mapping of paired-end reads

  charles-plessy/CAGEr#111 · Filter by author QiliShi opened on Jan 22, 2024
  3

• Parallel load of libraries can be sluggish.

  charles-plessy/CAGEr#107 · Filter by author charles-plessy opened on Oct 10, 2023

• Make the output of summary() of CAGEexp objects more useful.

  enhancement
  charles-plessy/CAGEr#106 · Filter by author charles-plessy opened on Oct 10, 2023

• Sample specific enhancer identificiation

  enhancement
  charles-plessy/CAGEr#105 · Filter by author ferenckata opened on Sep 15, 2023

• getExpressionProfiles gives a warning message about argument length.

  bug
  charles-plessy/CAGEr#100 · Filter by author charles-plessy opened on Jul 27, 2023

• Suggestion: a new, maybe private, acessor CTSScoordinatesGRL

  enhancement
  charles-plessy/CAGEr#99 · Filter by author charles-plessy opened on Jul 27, 2023
  1

• A UCSCData method for TSSlogo

  enhancement
  charles-plessy/CAGEr#95 · Filter by author charles-plessy opened on Jul 19, 2023
  1

• Suggestion: a function to send TSSes to seqArchR

  enhancement
  charles-plessy/CAGEr#92 · Filter by author charles-plessy opened on Jul 6, 2023

• Double-check consistency of consensus clusters.

  charles-plessy/CAGEr#91 · Filter by author charles-plessy opened on Jul 6, 2023

• Sum of the TPM-normalised expression valuse of consensus clusters is higher than one million…

  bug
  charles-plessy/CAGEr#88 · Filter by author charles-plessy opened on Jun 30, 2023

• aggregateTagClusters give a different result on CAGEexp compared with formerly on CAGEset objects.

  charles-plessy/CAGEr#86 · Filter by author charles-plessy opened on Jun 29, 2023
  1

• filteredCTSSidx and .filterCtss are not documented.

  enhancement
  charles-plessy/CAGEr#84 · Filter by author charles-plessy opened on Jun 29, 2023

• exportToTrack crashes when a CTSS object does not not contain filteredCTSSidx information.

  bug
  charles-plessy/CAGEr#83 · Filter by author charles-plessy opened on Jun 29, 2023

• Fix importPublicData to import FANTOM5 data.

  enhancement
  charles-plessy/CAGEr#78 · Filter by author charles-plessy opened on Jun 21, 2023
  1

• Loading FANTOM5 HeliScopeCAGE BAM files does not work

  bug
  charles-plessy/CAGEr#67 · Filter by author charles-plessy opened on Oct 3, 2022
  4

• Add a method to export cluster sequences

  enhancement
  charles-plessy/CAGEr#65 · Filter by author charles-plessy opened on Apr 28, 2022

• Ability to filter/discard CTSSs overlapping some genomic region(s)

  enhancement
  charles-plessy/CAGEr#63 · Filter by author snikumbh opened on Apr 26, 2022