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initiatior filtering

enhancement

Status: Open.

#137 In charles-plessy/CAGEr;

· ferenckata opened on Mar 18, 2026

alpha value capped at 1.05

Status: Open.

#126 In charles-plessy/CAGEr;

· ferenckata opened on Feb 21, 2025

plotAnnot warnings

Status: Open.

#124 In charles-plessy/CAGEr;

· ferenckata opened on Dec 6, 2024

Brush up function families.

enhancement

Status: Open.

#118 In charles-plessy/CAGEr;

· charles-plessy opened on May 24, 2024

Remove the redundant tpm column of consensus cluster objects.

enhancement

Status: Open.

#117 In charles-plessy/CAGEr;

· charles-plessy opened on May 17, 2024

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

enhancement

Status: Open.

#116 In charles-plessy/CAGEr;

· charles-plessy opened on May 17, 2024

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

Status: Open.

#115 In charles-plessy/CAGEr;

· da-bar opened on May 14, 2024

consensusClustersGR() row.names problem

Status: Open.

#112 In charles-plessy/CAGEr;

· MorexV3CAGE opened on Feb 8, 2024

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

Status: Open.

#111 In charles-plessy/CAGEr;

· QiliShi opened on Jan 22, 2024

Parallel load of libraries can be sluggish.

Status: Open.

#107 In charles-plessy/CAGEr;

· charles-plessy opened on Oct 10, 2023

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

enhancement

Status: Open.

#106 In charles-plessy/CAGEr;

· charles-plessy opened on Oct 10, 2023

Sample specific enhancer identificiation

enhancement

Status: Open.

#105 In charles-plessy/CAGEr;

· ferenckata opened on Sep 15, 2023