Showing : DEXSeq • reset
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11
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Differential splicing from SGSeq analysis
DEXSeq SGSeq
2 hours ago • updated 1 hour ago Sara • 0
0
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1
reply
78
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 6 days ago by ★ 1.9k • written 6 days ago by • 0
0
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1
reply
114
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Adding columns to DEXSeqResults object
DEXSeq
updated 6 days ago by ★ 1.9k • written 7 days ago by • 0
0
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1
reply
84
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 6 days ago by 41k • written 6 days ago by • 0
0
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0
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125
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
6 weeks ago jean-christophe.helbling • 0
2
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4
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394
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 weeks ago • updated 8 weeks ago thomas.heigl.ibk • 0
0
votes
2
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344
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Swimming downstream: transcript fold changes
DEXSeq stageR
5 months ago jbono ▴ 10
1
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1
reply
368
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
5 months ago NiKo ▴ 10
0
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3
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639
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
0
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3
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751
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Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 8 months ago by 16k • written 9 months ago by • 0
0
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2
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541
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DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
8 months ago • updated 7 months ago yr542 • 0
8
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7
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1.7k
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Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
1
vote
5
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826
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 9 months ago by ★ 1.9k • written 9 months ago by • 0
0
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0
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370
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Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
10 months ago nick_brittain55 • 0
0
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0
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382
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Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
0
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0
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413
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DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
13 months ago Ben J • 0
0
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2
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878
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
14 months ago Ben J • 0
0
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0
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563
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 41k • written 17 months ago by • 0
0
votes
1
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784
views
plotDEXSeq error?
DEXSeq dex
17 months ago barrypraveen • 0
1
vote
4
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904
views
DEXseq batch removal
DEXSeq
updated 18 months ago by ★ 1.9k • written 18 months ago by ▴ 10
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0
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408
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
19 months ago Matthias Munz ▴ 10
0
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0
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488
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
20 months ago osieman52 • 0
1
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2
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810
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DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
20 months ago Delta._.43 ▴ 20
0
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1
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823
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DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago NIK • 0
0
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4
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1.4k
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 23 months ago by ▴ 90 • written 24 months ago by • 0
0
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5
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1.9k
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DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.0 years ago by • 0
6
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11
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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 • 0 • written 2.0 years ago by ▴ 350
3
votes
2
replies
929
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
635
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by • 0
1
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2
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851
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Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.2 years ago A ▴ 40
3
votes
3
replies
1.1k
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Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 120
0
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1
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831
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.5 years ago by • 0
1
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1
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1.1k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.3 years ago by ★ 1.9k • written 2.7 years ago by ▴ 10
2
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7
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1.2k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago • updated 2.6 years ago rbenel ▴ 40
0
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5
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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
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0
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811
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.7 years ago Matthias Munz ▴ 10
0
votes
0
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625
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Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago n.tear ▴ 20
0
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0
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625
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 2.9 years ago by ▴ 120 • written 3.0 years ago by ▴ 10
4
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5
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1.9k
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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
0
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0
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860
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
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2
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985
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.1 years ago Gaia • 0
3
votes
2
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1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
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
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1
reply
973
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by • 0
0
votes
2
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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
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DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.4 years ago by ▴ 20 • written 9.1 years ago by • 0
0
votes
2
replies
1.5k
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Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.4 years ago by ▴ 20 • written 6.3 years ago by • 0
6
votes
7
replies
1.7k
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Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.3 years ago by 41k • written 3.5 years ago by ▴ 20
0
votes
2
replies
868
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 ★ 3.7k • written 3.8 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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