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JunctionSeq
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2
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451
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Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
15 months ago • updated 14 months ago
n.tear
▴ 20
0
votes
1
reply
337
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
2.5 years ago
stuart
▴ 10
0
votes
1
reply
536
views
JunctionSeq Can't produce Summary Plots
JunctionSeq
5.1 years ago
rachelrodgers12
• 0
0
votes
0
replies
550
views
Setting relevel with the JunctionSeq package
junctionseq
relevel
reference
5.3 years ago
Assa Yeroslaviz
★ 1.5k
1
vote
0
replies
625
views
JunctionSeq on multiple conditions
junctionseq
qorts
multiple factor design
relevel
5.3 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
965
views
JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2
junctionseq
dexseq
estimatedispersions
rnaseq
updated 5.4 years ago by
Steve Lianoglou
13k • written 5.4 years ago by
l.frank
• 0
0
votes
0
replies
570
views
Problems running JunctionSeq
junctionseq
5.5 years ago
jbono
▴ 10
0
votes
0
replies
502
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq
design and contrast matrix
5.6 years ago
stuart
• 0
8 results • Page
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Replies
Comment: error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
by
James W. MacDonald
59k
It's not clear from this what the problem is. Rather than running under `snakemake` you might run the R code directly. I mean it's obvious …
Comment: CPM after RUVseq
by
James W. MacDonald
59k
I am unfamiliar with a `counts` function (your `counts(set)`), so it's not clear what exactly you are putting into that `DGEList`. But if i…
Comment: error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
by
rsnorman
• 0
Thanks for the advice! I need to use this particular bacterial strain, but I did locate a more recent annotation for it and that cleared th…
Comment: Error in h(simpleError(msg, call)) : when calling makeOrgPackagefromNCBI()
by
shepherl
3.1k
I'm not able to reproduce this. Maybe it was a temporary issue with biomaRt? ``` > makeOrgPackageFromNCBI( + version = "0.1", + …
Comment: CPM after RUVseq
by
Jess
• 0
Ah I think I know where the communication breakdown is occurring. When I think of RUVr, I'm including fitting the preliminary model in edge…
Votes
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
Answer: CPM after RUVseq
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
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Guido Hooiveld
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Teacher
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Gordon Smyth
45k
Teacher
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Aaron Lun
★ 27k
Scholar
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James W. MacDonald
59k
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Lluís Revilla Sancho
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Wageningen University, Wageningen, the Netherlands,
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