hartleys JunctionSeq issues

hartleys / JunctionSeq

The JunctionSeq R package is a powerful tool for testing and visualizing differential usage of exons and splice junctions in next-generation, high-throughput RNA-Seq experiments.

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issues

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Can JunctionSeq be used in long-read RNA-seq ONT data?

#60 kaanokay opened 1 year ago
0
Error : attempt to select less than one element in OneIndex

#59 ChoiJi-Hye closed 2 years ago
0
QoRTs/JunctionSeq with Rsubread alignment

#58 jmbono opened 3 years ago
2
Normalized gene counts of 0?

#57 alanbergland opened 3 years ago
1
Sig gene wtih the P-value as NA

#56 zhouqz opened 3 years ago
2
Junctionseq marked as deprecated in bioconductor.

#55 tbrittoborges opened 3 years ago
0
weird dispersion plot

#54 scseekers opened 3 years ago
1
writeCompleteResults : Error in data.frame(..., check.names = FALSE)

#53 YanliangDou opened 3 years ago
0
Unable to view splice junction tracks on ucsc browser

#52 varsha090597 opened 4 years ago
1
Error: all samples have 0 counts for all genes. check the counting script

#51 HeenaBioinfo opened 4 years ago
0
Error in estimateSizeFactorsForMatrix(counts.byGenes)

#50 HeenaBioinfo opened 4 years ago
2
estimateEffectSizes: Error in if (any(dispersion < 0)) stop("dispersion values must be non-negative")

#49 ashish674675 opened 4 years ago
2
independent filtering on the gene counts

#48 shivarice opened 4 years ago
1
Error: C stack usage 50949656 is too close to the limit"

#47 CS791 closed 4 years ago
5
error in reading decoder file

#46 CS791 opened 4 years ago
1
labels of gene of interest in MA plot

#45 kaanokay closed 4 years ago
0
Error in cf[[pvn]] : subscript out of bounds

#44 nicholas-owen opened 5 years ago
0
plot interpretation

#43 natallah opened 5 years ago
4
can't install the packages 'backports','nlme'

#42 HL2007 opened 5 years ago
1
How can I write all results to JunctionSeq Object (jscs data) in R ?

#41 kaanokay closed 3 years ago
1
Multiple conditions comparsion

#40 LOYON2019 opened 5 years ago
1
parallel run (nCores > 1) always fails

#39 slowsmile opened 5 years ago
1
How To Calculate PSI with JunctionSeq

#38 xysj1989 opened 5 years ago
1
Missing genes in allGenes.results.txt

#37 sagarutturkar opened 5 years ago
4
DESeq2 version collision

#36 gfucile opened 6 years ago
7
Annotation file appears to be missing information! Are you sure you are using the correct flattened annotation file, created by the QoRTs QC command?

#35 kaanokay closed 3 years ago
2
Unable to locate counts file

#34 sanchari24 closed 6 years ago
0
C stack usage is too close to the limit

#33 jxf413 closed 6 years ago
1
Zero counts for whole LY75

#32 cwtkiwi opened 6 years ago
2
Error in names(res) <- nms

#31 mebbert closed 6 years ago
10
Estimated runtime and progress indicator

#30 mebbert closed 6 years ago
3
Dead links on JunctionSeq page

#29 mebbert opened 6 years ago
1
Two-pass alignment?

#28 mebbert opened 6 years ago
0
Alterative junctionseq pipeline inquiry

#27 dejonggr closed 6 years ago
6
splice junction usage between multiple tissues

#26 frankbioinfo opened 6 years ago
3
File interpretation problem

#25 Ambreen06 opened 7 years ago
4
LogFC sign in sigGenes.results.txt

#24 ewilkie opened 7 years ago
4
Two libraries

#23 cwtkiwi closed 7 years ago
2
Fix to readJunctionSeqCounts() countdata handling

#22 ALysaght opened 7 years ago
5
Required features in GTF file.

#21 brgew closed 7 years ago
1
Summary Plots created by JunctionSeq

#20 Tomoya89 closed 7 years ago
2
Comparing JunctionSeq to DEXSeq

#19 brgew closed 7 years ago
1
Annotation file appears to be missing information!

#18 misik opened 7 years ago
24
error about fitDisp

#17 aiminy closed 7 years ago
2
Gene-level expression estimates

#16 hooperj closed 7 years ago
3
Can't successfully use numeric covariate with runJunctionSeqAnalyses()

#15 davemcg closed 7 years ago
2
Differential Usage Numbers only

#14 FallenAzazel closed 7 years ago
6
buildAllPlotsForGene unable to create new directories

#13 hobrien closed 8 years ago
4
dead link in help docs

#12 hobrien closed 8 years ago
2
C stack usage 17723277 is too close to the limit

#11 KateK closed 8 years ago
8