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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Wrap `CAGEfightR::quickEnhancers`

#72 charles-plessy closed 1 year ago
3
scoreShift does not work with length 1 groupX or groupY.

#71 charles-plessy closed 1 year ago
4
Exporting consensusClusters to BED12 with IQW information is broken

#70 charles-plessy closed 5 months ago
0
Promoter shifting for CAGEexp

#69 snikumbh closed 2 years ago
0
IQW for consensus clusters

#68 snikumbh closed 2 years ago
2
Loading FANTOM5 HeliScopeCAGE BAM files does not work

#67 charles-plessy opened 2 years ago
0
The result is 1

#66 houruiyan closed 2 years ago
4
Add a method to export cluster sequences

#65 charles-plessy opened 2 years ago
0
Create a reset() function that removes everything but the CTSS raw expression value

#64 charles-plessy closed 5 months ago
1
Ability to filter/discard CTSSs overlapping some genomic region(s)

#63 snikumbh opened 2 years ago
0
Loss of genome/seqinfo with tagClustersGR

#62 snikumbh closed 2 years ago
5
getCTSS - correctSystematicG

#61 PavlSi closed 2 years ago
10
Consensus clusters: compute quantile boundaries on the sum of the expression scores of all samples.

#60 charles-plessy closed 1 year ago
1
Remove `consensusClustersQuantileLow()` and `consensusClustersQuantileUp()`

#59 charles-plessy opened 2 years ago
0
The dim() method for DataFrameList objects is deprecated. Please use dims() on these objects instead.

#58 charles-plessy closed 2 years ago
1
Dominant TSS displayed in exported tag cluster files span 2 bases

#57 charles-plessy closed 2 years ago
1
Give different names to plus and minus strand when exporting to BedGraph

#56 Hami7407 opened 2 years ago
6
Find head-to-head promoters

#55 charles-plessy opened 2 years ago
0
Replace clumsy `getRefGenome` with `BSgenome::getBSgenome`

#54 charles-plessy opened 2 years ago
0
annotateCTSS issue using gff3

#53 pna059 opened 2 years ago
10
importPublicData not available any more?

#52 snikumbh opened 2 years ago
4
getCTSS: BiocParallel errors element index: 1 first error: too many positions in 'pos'

#51 pna059 closed 2 years ago
8
The CAGEexp constructor does not support URLs as file source.

#50 mea2712 closed 1 year ago
2
getCTSS() failed for inputFilesType = "bamPairedEnd" in CAGEr 2.0.1 (not CAGEr 1.34.0)

#49 Pentayouth closed 2 years ago
17
Export filelist tables for ZENBU

#48 charles-plessy opened 2 years ago
0
`summariseChrExpr` should work when `genomeName` is `NULL`

#47 charles-plessy opened 3 years ago
0
The dim() method for DataFrameList objects is deprecated

#46 charles-plessy opened 3 years ago
1
getCTSS bug specific to version 1.34.0

#45 orionzhou closed 1 year ago
1
Conservative fix to reinstate/repair paraclu support for CAGEexp objects (fixes charles-plessy/CAGEr#8)

#44 snikumbh closed 3 years ago
2
simple fix for #14

#43 snikumbh closed 3 years ago
0
Debug

#42 da-bar closed 3 years ago
0
Simplify vocabulary

#41 charles-plessy opened 3 years ago
0
Having different result between CAGEexp and CAGEset in aggregateTagClusters

#40 Fushun-Chen closed 3 years ago
4
What to do with genes with multiple cons_clus_ids

#39 mirkocelii closed 3 years ago
3
shifting-promoters HELP！！！

#38 gamemake-rookie closed 3 years ago
0
CAGEset vs CAGEexp

#37 ewong159 closed 3 years ago
1
bam2CTSS() attempts to run promoters() on a CTSS() object.

#36 ewong159 closed 3 years ago
4
CAGEexp from imported bam file

#35 ewong159 closed 3 years ago
1
create CAGEexp from imported bam file

#34 ewong159 closed 3 years ago
4
Reform the CTSS class

#33 charles-plessy closed 3 years ago
0
Subsetting the tagCountMatrix experiment through its CAGEexp container does not work.

#32 charles-plessy opened 4 years ago
0
Prevent from loading paired-end data in single-end mode.

#31 charles-plessy opened 4 years ago
0
annotateCTSS should work out of the box with AnnotationHub data

#30 charles-plessy closed 5 months ago
4
Fix error due to `_R_CHECK_LENGTH_1_LOGIC2_`

#29 snikumbh closed 4 years ago
0
Implement G correction for CAGEexp class

#28 da-bar opened 4 years ago
7
Errors while creating consensus clusters

#27 madalenamrp closed 4 years ago
18
Fix wrong call to f for minus CTSS in .remove.added.G

#26 da-bar closed 5 years ago
0
Issues with clusterCTSS function

#25 dalmiaa closed 4 years ago
35
Use more explicit calls to assay()

#24 charles-plessy opened 6 years ago
0
After merging to CAGEexp objects, the genomeName information is lost.

#23 charles-plessy opened 6 years ago
0

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