Showing : DEXSeq • reset
4
votes
5
replies
923
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 3 days ago by • 0 • written 17 days ago by • 0
0
votes
0
replies
108
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
7 weeks ago cftattersfield • 0
0
votes
1
reply
396
views
Run DEXSeq successfully but got a result that padj==1 in all genes
DEXSeq
updated 8 months ago by ★ 4.7k • written 8 months ago by • 0
2
votes
1
reply
565
views
How to design DEXSeq formula for multiple variables
DEXSeq
10 months ago • updated 9 months ago Sara • 0
3
votes
1
reply
646
views
How to save the DEXSeq results
DEXSeq
updated 10 months ago by 43k • written 10 months ago by • 0
0
votes
0
replies
345
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
11 months ago • updated 10 months ago Sara • 0
0
votes
3
replies
601
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 10 months ago by ★ 1.9k • written 11 months ago by • 0
0
votes
1
reply
464
views
Adding columns to DEXSeqResults object
DEXSeq
updated 11 months ago by ★ 1.9k • written 11 months ago by • 0
0
votes
1
reply
875
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
0
replies
383
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
12 months ago jean-christophe.helbling • 0
2
votes
4
replies
869
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
13 months ago thomas.heigl.ibk • 0
0
votes
2
replies
686
views
Swimming downstream: transcript fold changes
DEXSeq stageR
16 months ago jbono ▴ 10
1
vote
1
reply
731
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 20 months ago by • 0
0
votes
2
replies
985
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
2.6k
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 21 months ago by • 0
0
votes
0
replies
676
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
21 months ago nick_brittain55 • 0
0
votes
0
replies
609
views
Error while performing DEXseq
DEXSeq
22 months ago vipul14 • 0
0
votes
0
replies
608
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
2.0 years ago Ben J ▴ 20
2
votes
2
replies
1.6k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.1 years ago Ben J ▴ 20
0
votes
0
replies
845
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
1.1k
views
plotDEXSeq error?
DEXSeq dex
2.3 years ago barrypraveen • 0
1
vote
4
replies
1.3k
views
DEXseq batch removal
DEXSeq
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 10
0
votes
0
replies
588
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
2.5 years ago Matthias Munz ▴ 20
0
votes
0
replies
702
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
2.2k
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
2.4k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 6.0 years ago by • 0
8
votes
12
replies
4.3k
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
3.0 years ago • updated 2.9 years ago Dakarai ▴ 10
1
vote
1
reply
919
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
1.3k
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
3.3 years ago • updated 3.1 years ago A ▴ 60
3
votes
3
replies
1.5k
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 3.2 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 3.2 years ago by ★ 1.9k • written 3.6 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
1.7k
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
3.7 years ago Matthias Munz ▴ 20
0
votes
0
replies
865
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
848
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 3.8 years ago by ▴ 120 • written 4.0 years ago by ▴ 10
4
votes
5
replies
2.6k
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
4.0 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
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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