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DEXSeq
•
reset
0
votes
0
replies
93
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
17 days ago
jean-christophe.helbling
• 0
2
votes
4
replies
336
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
7 weeks ago • updated 4 weeks ago
thomas.heigl.ibk
• 0
0
votes
2
replies
305
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
4 months ago
jbono
▴ 10
0
votes
1
reply
319
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
4 months ago
NiKo
• 0
0
votes
2
replies
504
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq
HTSeq
R
7 months ago • updated 6 months ago
yr542
• 0
0
votes
3
replies
604
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 6 months ago by
Alejandro Reyes
★ 1.9k • written 6 months ago by
Alice
• 0
0
votes
3
replies
686
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 7 months ago by
Hervé Pagès
16k • written 8 months ago by
anavmar1
• 0
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 8 months ago by
alexandresegers
▴ 20 • written 17 months ago by
jeremymsimon
▴ 20
1
vote
5
replies
771
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 9 months ago by
zhangpeng1202
• 0
0
votes
0
replies
345
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
9 months ago
nick_brittain55
• 0
0
votes
0
replies
355
views
Error while performing DEXseq
DEXSeq
10 months ago
vipul14
• 0
6
votes
11
replies
2.9k
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
updated 12 months ago by
EChambers
• 0 • written 23 months ago by
Matthew Thornton
▴ 350
0
votes
0
replies
389
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
12 months ago
Ben J
• 0
0
votes
2
replies
824
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
14 months ago • updated 13 months ago
Ben J
• 0
1
vote
15
replies
3.4k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 15 months ago by
Zhuqiang
• 0 • written 6.9 years ago by
cpsosa0006
• 0
0
votes
0
replies
529
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 16 months ago by
Michael Love
41k • written 16 months ago by
barrypraveen
• 0
0
votes
1
reply
743
views
plotDEXSeq error?
DEXSeq
dex
16 months ago
barrypraveen
• 0
1
vote
4
replies
867
views
DEXseq batch removal
DEXSeq
updated 17 months ago by
Alejandro Reyes
★ 1.9k • written 17 months ago by
ta_awwad
▴ 10
0
votes
0
replies
389
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
18 months ago
Matthias Munz
▴ 10
1
vote
2
replies
1.9k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 19 months ago by
ta_awwad
▴ 10 • written 4.7 years ago by
bruce.hayward
▴ 10
0
votes
0
replies
461
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
19 months ago
osieman52
• 0
1
vote
2
replies
769
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
19 months ago
Delta._.43
▴ 20
0
votes
1
reply
784
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
22 months ago
NIK
• 0
0
votes
4
replies
1.3k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 22 months ago by
jeroen.gilis
▴ 90 • written 23 months ago by
phoebe1354
• 0
3
votes
2
replies
891
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
24 months ago • updated 23 months ago
Dakarai
▴ 10
0
votes
5
replies
1.9k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.0 years ago by
maslane
• 0
1
vote
1
reply
601
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 2.0 years ago by
Alejandro Reyes
★ 1.9k • written 2.0 years ago by
jochen
• 0
1
vote
2
replies
824
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.3 years ago • updated 2.2 years ago
A
▴ 40
1
vote
1
reply
1.0k
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 2.2 years ago by
Alejandro Reyes
★ 1.9k • written 2.6 years ago by
Nirad
▴ 10
0
votes
1
reply
797
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.2 years ago by
Alejandro Reyes
★ 1.9k • written 2.5 years ago by
Hahsooni
• 0
3
votes
3
replies
1.0k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
k.vitting.seerup
▴ 120
3
votes
2
replies
1.8k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq
fit
matrix
warning
updated 2.4 years ago by
koushik
• 0 • written 7.1 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
7
replies
1.2k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.6 years ago
rbenel
▴ 40
3
votes
3
replies
1.6k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq
log2foldchange
Tutorial
updated 2.6 years ago by
rohitsatyam102
▴ 20 • written 4.0 years ago by
tmvarsha
▴ 20
0
votes
5
replies
1.1k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.6 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
774
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
2.7 years ago
Matthias Munz
▴ 10
0
votes
0
replies
604
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.7 years ago
n.tear
▴ 20
0
votes
0
replies
596
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.8 years ago
Matthias Munz
▴ 10
1
vote
6
replies
1.5k
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 2.8 years ago by
k.vitting.seerup
▴ 120 • written 3.0 years ago by
jbono
▴ 10
4
votes
5
replies
1.8k
views
DEXSeq: What's the best way to map an exon counting bin, e.g. E002 to exon(s) or position in transcript(s)
DEXSeq
2.9 years ago
Matthias Munz
▴ 10
0
votes
0
replies
833
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.0 years ago
jbono
▴ 10
0
votes
2
replies
943
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.0 years ago
Gaia
• 0
2
votes
2
replies
1.1k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
3.1 years ago • updated 3.0 years ago
n.tear
▴ 20
3
votes
2
replies
990
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.1 years ago • updated 3.0 years ago
Angel
▴ 10
1
vote
1
reply
938
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.2 years ago by
Alejandro Reyes
★ 1.9k • written 3.2 years ago by
Anubhav
• 0
6
votes
7
replies
1.6k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3.3 years ago by
Michael Love
41k • written 3.4 years ago by
rohitsatyam102
▴ 20
0
votes
2
replies
1.2k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.8 years ago • updated 3.4 years ago
aleksandar.baburski.g
• 0
1
vote
6
replies
3.9k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.4 years ago by
rohitsatyam102
▴ 20 • written 9.0 years ago by
ywu
• 0
0
votes
2
replies
1.4k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq
estimatedispersions
updated 3.4 years ago by
rohitsatyam102
▴ 20 • written 6.2 years ago by
brand
• 0
0
votes
2
replies
830
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.7 years ago by
Simon Anders
★ 3.7k • written 3.7 years ago by
lu.la
• 0
50 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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