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DEXSeq
•
reset
0
votes
0
replies
64
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
7 days ago • updated 2 days ago
Sara
• 0
0
votes
3
replies
148
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 1 day ago by
Alejandro Reyes
★ 1.9k • written 13 days ago by
Alessia
• 0
0
votes
1
reply
99
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 13 days ago by
Michael Love
41k • written 13 days ago by
09191919
• 0
0
votes
1
reply
144
views
Adding columns to DEXSeqResults object
DEXSeq
updated 13 days ago by
Alejandro Reyes
★ 1.9k • written 15 days ago by
Clyde
• 0
0
votes
0
replies
130
views
DEXSeq plot error
DEXSeq
DEXSeqNAvalues
DEXseq
7 weeks ago
jean-christophe.helbling
• 0
2
votes
4
replies
402
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 9 weeks ago
thomas.heigl.ibk
• 0
0
votes
2
replies
358
views
Swimming downstream: transcript fold changes
DEXSeq
stageR
5 months ago
jbono
▴ 10
1
vote
1
reply
380
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq
DRIMSeq
DEXSeqDataSet
columnduplication
6 months ago
NiKo
▴ 10
0
votes
3
replies
648
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 8 months ago by
Alejandro Reyes
★ 1.9k • written 8 months ago by
Alice
• 0
0
votes
2
replies
553
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
768
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
842
views
DEXSeq output included non-exist exons
DEXSeq
exon_definition
exon
updated 10 months ago by
Alejandro Reyes
★ 1.9k • written 10 months ago by
zhangpeng1202
• 0
0
votes
0
replies
376
views
Recommendation sought for differential exon usage of a single gene
isofor
DEXSeq
DifferentialSplicing
10 months ago
nick_brittain55
• 0
0
votes
0
replies
392
views
Error while performing DEXseq
DEXSeq
11 months ago
vipul14
• 0
0
votes
0
replies
419
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
13 months ago
Ben J
• 0
0
votes
2
replies
893
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago
Ben J
• 0
0
votes
0
replies
571
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by
Michael Love
41k • written 17 months ago by
barrypraveen
• 0
0
votes
1
reply
793
views
plotDEXSeq error?
DEXSeq
dex
17 months ago
barrypraveen
• 0
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
1
vote
4
replies
922
views
DEXseq batch removal
DEXSeq
updated 18 months ago by
Alejandro Reyes
★ 1.9k • written 18 months ago by
ta_awwad
▴ 10
0
votes
0
replies
414
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago
Matthias Munz
▴ 10
0
votes
0
replies
496
views
DEXSeq aggregated genes/exons result in NA values
RNASeq
R
DEXSeq
20 months ago
osieman52
• 0
1
vote
2
replies
820
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
21 months ago
Delta._.43
▴ 20
0
votes
1
reply
832
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
0
votes
4
replies
1.4k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq
DRIMSeq
updated 23 months ago by
jeroen.gilis
▴ 90 • written 2.0 years ago by
phoebe1354
• 0
6
votes
11
replies
3.0k
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 13 months ago by
EChambers
• 0 • written 2.0 years ago by
Matthew Thornton
▴ 350
3
votes
2
replies
941
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R
DEXSeq
SequenceAnnotation
RNASeqData
2.1 years ago • updated 24 months ago
Dakarai
▴ 10
1
vote
1
reply
646
views
Increased number of exons in DEXSeq
DEXSeq
exon
updated 2.1 years ago by
Alejandro Reyes
★ 1.9k • written 2.1 years ago by
jochen
• 0
3
votes
3
replies
1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2
DEXseq
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
k.vitting.seerup
▴ 120
1
vote
2
replies
861
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.2 years ago
A
▴ 40
0
votes
1
reply
839
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by
Alejandro Reyes
★ 1.9k • written 2.5 years ago by
Hahsooni
• 0
1
vote
1
reply
1.1k
views
DTU using DEXSeq (time series data with condition factor)
DTU
DEXSeq
RNADTU
updated 2.3 years ago by
Alejandro Reyes
★ 1.9k • written 2.7 years ago by
Nirad
▴ 10
2
votes
7
replies
1.2k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.7 years ago
rbenel
▴ 40
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
2.7 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
819
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures
DEXSeq
2.8 years ago
Matthias Munz
▴ 10
0
votes
0
replies
630
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago
n.tear
▴ 20
0
votes
0
replies
630
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 years ago
Matthias Munz
▴ 10
4
votes
5
replies
1.9k
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
3.0 years ago
Matthias Munz
▴ 10
1
vote
6
replies
1.5k
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 2.9 years ago by
k.vitting.seerup
▴ 120 • written 3.1 years ago by
jbono
▴ 10
0
votes
0
replies
869
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.1 years ago
jbono
▴ 10
0
votes
2
replies
994
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.1 years ago
Gaia
• 0
3
votes
2
replies
1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.2 years ago • updated 3.1 years ago
Angel
▴ 10
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq
JunctionSeq
RNAseq
QoRTs
3.2 years ago • updated 3.1 years ago
n.tear
▴ 20
1
vote
1
reply
982
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.3 years ago by
Alejandro Reyes
★ 1.9k • written 3.3 years ago by
Anubhav
• 0
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3.4 years ago by
Michael Love
41k • written 3.5 years ago by
rohitsatyam102
▴ 20
0
votes
4
replies
1.6k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.8 years ago
Angel Liang
• 0
1
vote
2
replies
1.2k
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.8 years ago by
Alejandro Reyes
★ 1.9k • written 3.8 years ago by
Angel Liang
• 0
0
votes
2
replies
880
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.8 years ago by
Simon Anders
★ 3.7k • written 3.8 years ago by
lu.la
• 0
0
votes
1
reply
705
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
debatosh das
▴ 10
0
votes
2
replies
1.2k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.9 years ago • updated 3.4 years ago
aleksandar.baburski.g
• 0
50 results • Page
1 of 1
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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