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junctionseq
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2
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1.2k
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Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
3.2 years ago
n.tear
▴ 20
1
vote
0
replies
943
views
JunctionSeq on multiple conditions
junctionseq
qorts
multiple factor design
relevel
7.2 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.4k
views
JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2
junctionseq
dexseq
estimatedispersions
rnaseq
updated 7.4 years ago by
Steve Lianoglou
★ 13k • written 7.4 years ago by
l.frank
• 0
0
votes
0
replies
831
views
Problems running JunctionSeq
junctionseq
7.5 years ago
jbono
▴ 10
0
votes
1
reply
833
views
JunctionSeq Can't produce Summary Plots
JunctionSeq
7.0 years ago
rachelrodgers12
• 0
0
votes
1
reply
825
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
4.4 years ago
stuart
▴ 10
0
votes
0
replies
826
views
Setting relevel with the JunctionSeq package
junctionseq
relevel
reference
7.2 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
0
replies
845
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq
design and contrast matrix
7.6 years ago
stuart
• 0
8 results • Page
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Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Comment: Help with running egsea()
by
James W. MacDonald
65k
I don't understand the last question, but do look at the msigdb.gsets argument to `buildIdx` in the help page for that function.
Answer: Help with running egsea()
by
James W. MacDonald
65k
There are no arguments to `egsea.base`, as it is meant only as a helper function to return the different methods. In addition, if you are u…
Votes
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Answer: How to save the DEXSeq results
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