Showing : DEXseq • reset
4
votes
4
replies
703
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
5 days ago • updated 3 days ago Elijah • 0
0
votes
0
replies
94
views
My DEXSeqDataSetFromSE is returning an Error, but all of my checks to seem to indicate that this error is not present
DifferentialSplicing RNASeqData DEXSeq
5 weeks ago cftattersfield • 0
0
votes
1
reply
389
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 7 months ago by ★ 4.7k • written 7 months ago by • 0
2
votes
1
reply
536
views
How to design DEXSeq formula for multiple variables
DEXSeq
10 months ago • updated 9 months ago Sara • 0
3
votes
1
reply
627
views
How to save the DEXSeq results
DEXSeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
336
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
10 months ago Sara • 0
0
votes
3
replies
591
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
1
reply
453
views
Adding columns to DEXSeqResults object
DEXSeq
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
1
reply
833
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
379
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
12 months ago jean-christophe.helbling • 0
2
votes
4
replies
851
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
13 months ago • updated 12 months ago thomas.heigl.ibk • 0
0
votes
2
replies
673
views
Swimming downstream: transcript fold changes
DEXSeq stageR
16 months ago jbono ▴ 10
1
vote
1
reply
720
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
16 months ago NiKo ▴ 10
0
votes
3
replies
1.1k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 18 months ago by ★ 1.9k • written 18 months ago by • 0
0
votes
3
replies
1.4k
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 19 months ago by 16k • written 19 months ago by • 0
0
votes
2
replies
976
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
19 months ago • updated 18 months ago yr542 • 0
8
votes
7
replies
2.5k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 20 months ago by ▴ 20 • written 2.4 years ago by ▴ 20
1
vote
5
replies
1.3k
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
0
votes
0
replies
668
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
21 months ago nick_brittain55 • 0
0
votes
0
replies
597
views
Error while performing DEXseq
DEXSeq
21 months ago vipul14 • 0
0
votes
0
replies
605
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
24 months ago Ben J ▴ 20
2
votes
2
replies
1.5k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.1 years ago Ben J ▴ 20
0
votes
0
replies
835
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
1.0k
views
plotDEXSeq error?
DEXSeq dex
2.3 years ago barrypraveen • 0
1
vote
4
replies
1.3k
views
DEXseq batch removal
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 10
0
votes
0
replies
582
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
695
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
2.6 years ago osieman52 • 0
1
vote
2
replies
1.2k
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
2.6 years ago Delta._.43 ▴ 20
0
votes
1
reply
1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.8 years ago NIK • 0
0
votes
4
replies
2.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 2.8 years ago by ▴ 90 • written 2.9 years ago by • 0
0
votes
5
replies
2.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.9 years ago by • 0
8
votes
12
replies
4.2k
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 9 months ago by ▴ 30 • written 2.9 years ago by ▴ 380
3
votes
2
replies
1.4k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.9 years ago Dakarai ▴ 10
1
vote
1
reply
905
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by • 0
1
vote
2
replies
1.2k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.3 years ago • updated 3.1 years ago A ▴ 40
3
votes
3
replies
1.4k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 120
0
votes
1
reply
1.1k
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3.1 years ago by ★ 1.9k • written 3.4 years ago by • 0
1
vote
1
reply
1.5k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3.1 years ago by ★ 1.9k • written 3.5 years ago by ▴ 10
2
votes
7
replies
1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.6 years ago • updated 3.5 years ago rbenel ▴ 40
0
votes
5
replies
1.6k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.6 years ago bioinformatic_trainee ▴ 10
1
vote
0
replies
1.4k
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
3.6 years ago Matthias Munz ▴ 20
0
votes
0
replies
858
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
3.7 years ago n.tear ▴ 20
0
votes
0
replies
838
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
3.7 years ago Matthias Munz ▴ 20
1
vote
6
replies
2.0k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 3.7 years ago by ▴ 120 • written 3.9 years ago by ▴ 10
4
votes
5
replies
2.5k
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
3.9 years ago Matthias Munz ▴ 20
0
votes
0
replies
1.1k
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.9 years ago jbono ▴ 10
0
votes
2
replies
1.3k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
4.0 years ago Gaia • 0
3
votes
2
replies
1.4k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.0 years ago Angel ▴ 10
2
votes
2
replies
1.5k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.1 years ago • updated 4.0 years ago n.tear ▴ 20
1
vote
1
reply
1.3k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 4.2 years ago by ★ 1.9k • written 4.2 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: error in ChAMP loading file by shocked.tick.zyet • 0
Great troubleshooting steps for ChAMP import issues! "ChAMP methylation data import errors" on [Google Search][1] for similar cases. Header…
Comment: orgDB by jenniferping36 • 0
Thanks for the suggestion! I'll check out the resources.
Comment: sesameDataCache is not work properly on my system by Samreen • 0
Any luck with this? I have tried all of the above and it still doesn't work. This is my session info and I'm on a cluster computing environ…
Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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