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Dexseq
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24
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
1 day ago
Sara
• 0
0
votes
1
reply
86
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Alessia
• 0
0
votes
1
reply
120
views
Adding columns to DEXSeqResults object
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 9 days ago by
Clyde
• 0
0
votes
1
reply
90
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 8 days ago by
09191919
• 0
0
votes
0
replies
128
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
6 weeks ago
jean-christophe.helbling
• 0
2
votes
4
replies
398
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
12 weeks ago • updated 8 weeks ago
thomas.heigl.ibk
• 0
0
votes
2
replies
350
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
5 months ago
jbono
▴ 10
1
vote
1
reply
372
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
5 months ago
NiKo
▴ 10
0
votes
3
replies
641
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 7 months ago by
Alejandro Reyes
★ 1.9k • written 7 months ago by
Alice
• 0
0
votes
3
replies
758
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 8 months ago by
Hervé Pagès
16k • written 9 months ago by
anavmar1
• 0
0
votes
2
replies
544
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
8 months ago • updated 7 months ago
yr542
• 0
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 9 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
1
vote
5
replies
831
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 9 months ago by
Alejandro Reyes
★ 1.9k • written 10 months ago by
zhangpeng1202
• 0
0
votes
0
replies
373
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
10 months ago
nick_brittain55
• 0
0
votes
0
replies
386
views
Error while performing DEXseq
DEXSeq
11 months ago
vipul14
• 0
15 results • Page
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Recent ...
Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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