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charles-plessy
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CAGEr
Mirror of Bioconductor's CAGEr package repository
https://bioconductor.org/packages/CAGEr
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genomeName error in getCTSS
#121
ckuanglim85
opened
3 weeks ago
1
distclu/paraclu crashes if I don't set rowRanges(CTSStagCountSE(ce))$filteredCTSSidx <- Rle(TRUE)
#120
a-klarkowska
closed
1 month ago
3
annotateCTSS method for TxDB objects
#119
charles-plessy
closed
3 months ago
0
Brush up function families.
#118
charles-plessy
opened
3 months ago
0
Remove the redundant tpm column of consensus cluster objects.
#117
charles-plessy
opened
3 months ago
0
as(tag_cluster, "CTSS") should use the dominant CTSS information.
#116
charles-plessy
opened
3 months ago
0
no non-missing arguments to max; returning -Inf error when calling tag clusters
#115
da-bar
opened
3 months ago
1
Remove returnInterquantileWidth option
#114
charles-plessy
closed
3 months ago
1
Remove custom method of clusterCTSS
#113
charles-plessy
closed
4 months ago
0
consensusClustersGR() row.names problem
#112
MorexV3CAGE
opened
7 months ago
4
Can the correctSystematicG = T parameter be used for a BAM file generated from STAR mapping of paired-end reads
#111
QiliShi
opened
7 months ago
3
encountered an error when running plotReverseCumulatives
#110
Always-Stude
closed
4 months ago
2
How to create a CAGEexp?
#109
Always-Stude
closed
9 months ago
8
exportToTrack should return a clear error when quantile information is missing.
#108
charles-plessy
closed
4 months ago
0
Parallel load of libraries can be sluggish.
#107
charles-plessy
opened
11 months ago
0
Make the output of summary() of CAGEexp objects more useful.
#106
charles-plessy
opened
11 months ago
0
Sample specific enhancer identificiation
#105
ferenckata
opened
11 months ago
0
Docker container for Bioconductor 3.17 version
#104
ferenckata
closed
4 months ago
1
Annotating clustered CTSS
#103
martino-ugolini
closed
4 months ago
1
getCTSS gives no error but returns 1
#102
martino-ugolini
closed
1 year ago
4
issue with estimation of TC quantile positions
#101
radinagg
closed
1 year ago
2
getExpressionProfiles gives a warning message about argument length.
#100
charles-plessy
opened
1 year ago
0
Suggestion: a new, maybe private, acessor CTSScoordinatesGRL
#99
charles-plessy
opened
1 year ago
1
Allow varying promoter region width in annotation functions.
#98
charles-plessy
closed
1 year ago
0
resetCAGEexp needs to remove non-expressed CTSSes.
#97
charles-plessy
closed
1 year ago
0
CTSSclusteringMethod(exampleCAGEexp) returns NULL in CAGEr 2.6.1 and 2.7.1
#96
charles-plessy
closed
1 year ago
0
A UCSCData method for TSSlogo
#95
charles-plessy
opened
1 year ago
1
Port plotReverseCumulatives to ggplot2
#94
charles-plessy
closed
4 months ago
0
aggregateTagClusters function error in CAGEr
#93
trangng03
closed
1 year ago
10
Suggestion: a function to send TSSes to seqArchR
#92
charles-plessy
opened
1 year ago
0
Double-check consistency of consensus clusters.
#91
charles-plessy
opened
1 year ago
0
Suggestion: a function to plot nice PyPu logos with ggplot2
#90
charles-plessy
closed
4 months ago
3
New flagByUpstreamSequences function.
#89
charles-plessy
closed
1 year ago
0
Sum of the TPM-normalised expression valuse of consensus clusters is higher than one million…
#88
charles-plessy
opened
1 year ago
0
Efficient row sum computation on DataFrames of Rle numericals.
#87
charles-plessy
closed
1 year ago
0
aggregateTagClusters give a different result on CAGEexp compared with formerly on CAGEset objects.
#86
charles-plessy
opened
1 year ago
1
refactor the distclu functions
#85
charles-plessy
closed
3 months ago
2
filteredCTSSidx and .filterCtss are not documented.
#84
charles-plessy
opened
1 year ago
0
exportToTrack crashes when a CTSS object does not not contain filteredCTSSidx information.
#83
charles-plessy
opened
1 year ago
0
Restore import public data function.
#82
charles-plessy
closed
4 months ago
0
Backport bug fixes in 2.6.1
#81
charles-plessy
closed
1 year ago
5
Bug fixes related to cluster aggregation and quantile computation
#80
charles-plessy
closed
1 year ago
0
Broken quantile ranges caused by unsorted cluster objects.
#79
charles-plessy
closed
1 year ago
1
Fix importPublicData to import FANTOM5 data.
#78
charles-plessy
opened
1 year ago
1
aggregateTagClusters looses/misses some TCs...
#77
snikumbh
closed
1 year ago
1
fixes #71 : handles length of groups > 1
#76
snikumbh
closed
1 year ago
0
aggregateTagClusters "address 0x4c13f1c8, cause 'memory not mapped'"
#75
ferenckata
closed
1 year ago
6
exportToTrack (to bed) produces lines invalid for UCSC browser
#74
ferenckata
closed
1 year ago
1
paraclu clusterCTSS method does not return score column
#73
ferenckata
closed
3 months ago
2
Wrap `CAGEfightR::quickEnhancers`
#72
charles-plessy
closed
1 year ago
3
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