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Dexseq
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15
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
20 hours ago • updated 19 hours ago
Sara
• 0
0
votes
1
reply
82
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 6 days ago by
Alessia
• 0
0
votes
1
reply
116
views
Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
0
replies
125
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
6 weeks ago
jean-christophe.helbling
• 0
2
votes
4
replies
394
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 weeks ago • updated 8 weeks ago
thomas.heigl.ibk
• 0
0
votes
2
replies
348
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
5 months ago
jbono
▴ 10
1
vote
1
reply
369
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
5 months ago
NiKo
▴ 10
0
votes
3
replies
639
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
755
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
543
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
828
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 9 months ago by
Alejandro Reyes
★ 1.9k • written 9 months ago by
zhangpeng1202
• 0
0
votes
0
replies
371
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
10 months ago
nick_brittain55
• 0
0
votes
0
replies
384
views
Error while performing DEXseq
DEXSeq
11 months ago
vipul14
• 0
15 results • Page
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Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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