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DEXseq
•
reset
0
votes
0
replies
95
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
8 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
3
replies
604
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
505
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
687
views
Error with makeTxDbFromBiomart
DEXSeq
biomaRt
updated 7 months ago by
Hervé Pagès
16k • written 8 months ago by
anavmar1
• 0
1
vote
5
replies
774
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
357
views
Error while performing DEXseq
DEXSeq
10 months ago
vipul14
• 0
0
votes
0
replies
391
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
12 months ago
Ben J
• 0
0
votes
2
replies
826
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
14 months ago • updated 13 months ago
Ben J
• 0
0
votes
0
replies
530
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 16 months ago by
Michael Love
41k • written 16 months ago by
barrypraveen
• 0
0
votes
1
reply
746
views
plotDEXSeq error?
DEXSeq
dex
16 months ago
barrypraveen
• 0
8
votes
7
replies
1.7k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 8 months ago by
alexandresegers
▴ 20 • written 17 months ago by
jeremymsimon
▴ 20
1
vote
4
replies
869
views
DEXseq batch removal
DEXSeq
updated 17 months ago by
Alejandro Reyes
★ 1.9k • written 17 months ago by
ta_awwad
▴ 10
0
votes
0
replies
390
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
18 months ago
Matthias Munz
▴ 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
770
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
785
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
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
3
votes
2
replies
892
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
1
vote
1
reply
604
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
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
1
vote
2
replies
825
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.3 years ago • updated 2.2 years ago
A
▴ 40
0
votes
1
reply
798
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
1
vote
1
reply
1.1k
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
2
votes
7
replies
1.2k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.6 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
2.6 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
605
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
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
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
0
votes
0
replies
834
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq
DEXSeq
3.0 years ago
jbono
▴ 10
0
votes
2
replies
948
views
DRIMSeq + dmFilter
DEXSeq
DRIMSeq
3.0 years ago
Gaia
• 0
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
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
1
vote
1
reply
943
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
4
replies
1.5k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.7 years ago
Angel Liang
• 0
1
vote
2
replies
1.1k
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.7 years ago by
Alejandro Reyes
★ 1.9k • written 3.7 years ago by
Angel Liang
• 0
0
votes
2
replies
832
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
0
votes
1
reply
675
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu
RNASeq
DEXSeq
DESeq2
updated 3.7 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
3.8 years ago • updated 3.4 years ago
aleksandar.baburski.g
• 0
1
vote
2
replies
1.1k
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq
estimateDispersions
3.8 years ago
aleksandar.baburski.g
• 0
0
votes
2
replies
834
views
DEXSeq HTML report Error
DEXSeq
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
aleksandar.baburski.g
• 0
0
votes
0
replies
632
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
3.9 years ago
alexis.weinreb
• 0
1
vote
2
replies
1.4k
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq
python
gtf
gff3
annotation
3.9 years ago
Raito92
▴ 60
50 results • Page
1 of 1
Recent ...
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
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This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
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…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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