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47 Open 58 Closed
47 Open 58 Closed
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Issues list

genomeName error in getCTSS
#121 opened Aug 13, 2024 by ckuanglim85
1
Brush up function families. enhancement
#118 opened May 24, 2024 by charles-plessy
Remove the redundant tpm column of consensus cluster objects. enhancement
#117 opened May 17, 2024 by charles-plessy
as(tag_cluster, "CTSS") should use the dominant CTSS information. enhancement
#116 opened May 17, 2024 by charles-plessy
no non-missing arguments to max; returning -Inf error when calling tag clusters
#115 opened May 14, 2024 by da-bar
1
consensusClustersGR() row.names problem
#112 opened Feb 8, 2024 by MorexV3CAGE
4
Can the correctSystematicG = T parameter be used for a BAM file generated from STAR mapping of paired-end reads
#111 opened Jan 22, 2024 by QiliShi
3
Parallel load of libraries can be sluggish.
#107 opened Oct 10, 2023 by charles-plessy
Make the output of summary() of CAGEexp objects more useful. enhancement
#106 opened Oct 10, 2023 by charles-plessy
Sample specific enhancer identificiation enhancement
#105 opened Sep 15, 2023 by ferenckata
getExpressionProfiles gives a warning message about argument length. bug
#100 opened Jul 27, 2023 by charles-plessy
Suggestion: a new, maybe private, acessor CTSScoordinatesGRL enhancement
#99 opened Jul 27, 2023 by charles-plessy
1
A UCSCData method for TSSlogo enhancement
#95 opened Jul 19, 2023 by charles-plessy
1
Suggestion: a function to send TSSes to seqArchR enhancement
#92 opened Jul 6, 2023 by charles-plessy
Double-check consistency of consensus clusters.
#91 opened Jul 6, 2023 by charles-plessy
Sum of the TPM-normalised expression valuse of consensus clusters is higher than one million… bug
#88 opened Jun 30, 2023 by charles-plessy
aggregateTagClusters give a different result on CAGEexp compared with formerly on CAGEset objects.
#86 opened Jun 29, 2023 by charles-plessy
1
filteredCTSSidx and .filterCtss are not documented. enhancement
#84 opened Jun 29, 2023 by charles-plessy
exportToTrack crashes when a CTSS object does not not contain filteredCTSSidx information. bug
#83 opened Jun 29, 2023 by charles-plessy
Fix importPublicData to import FANTOM5 data. enhancement
#78 opened Jun 21, 2023 by charles-plessy
1
Loading FANTOM5 HeliScopeCAGE BAM files does not work bug
#67 opened Oct 3, 2022 by charles-plessy
Add a method to export cluster sequences enhancement
#65 opened Apr 28, 2022 by charles-plessy
Ability to filter/discard CTSSs overlapping some genomic region(s) enhancement
#63 opened Apr 26, 2022 by snikumbh
Remove consensusClustersQuantileLow() and consensusClustersQuantileUp() enhancement
#59 opened Feb 21, 2022 by charles-plessy
Give different names to plus and minus strand when exporting to BedGraph bug regression This worked in a previous release.
#56 opened Jan 16, 2022 by Hami7407
6
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