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Dexseq
•
reset
0
votes
0
replies
16
views
Differential splicing from SGSeq analysis
DEXSeq
SGSeq
1 day ago
Sara
• 0
0
votes
1
reply
83
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 7 days ago by
Alessia
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 7 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
118
views
Adding columns to DEXSeqResults object
DEXSeq
updated 7 days ago by
Alejandro Reyes
★ 1.9k • written 8 days ago by
Clyde
• 0
0
votes
0
replies
127
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
12 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
370
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
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
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
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 10 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
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
15 results • Page
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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