charles-plessy CAGEr issues

charles-plessy / CAGEr

Mirror of Bioconductor's CAGEr package repository

https://bioconductor.org/packages/CAGEr

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issues

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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