Showing : dexseq • reset
0
votes
2
replies
153
views
Swimming downstream: transcript fold changes
DEXSeq stageR
24 days ago jbono ▴ 10
0
votes
1
reply
153
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
4 weeks ago NiKo • 0
0
votes
3
replies
402
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 3 months ago by ★ 1.9k • written 3 months ago by • 0
0
votes
3
replies
487
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 3 months ago by 16k • written 4 months ago by • 0
0
votes
2
replies
320
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
3 months ago • updated 12 weeks ago yr542 • 0
8
votes
7
replies
1.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 5 months ago by ▴ 20 • written 13 months ago by ▴ 20
1
vote
5
replies
578
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 5 months ago by ★ 1.9k • written 5 months ago by • 0
0
votes
0
replies
236
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
5 months ago nick_brittain55 • 0
0
votes
0
replies
247
views
Error while performing DEXseq
DEXSeq
6 months ago vipul14 • 0
0
votes
0
replies
281
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
8 months ago Ben J • 0
0
votes
2
replies
587
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
10 months ago • updated 9 months ago Ben J • 0
0
votes
0
replies
400
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 12 months ago by 41k • written 12 months ago by • 0
0
votes
1
reply
603
views
plotDEXSeq error?
DEXSeq dex
12 months ago barrypraveen • 0
1
vote
4
replies
741
views
DEXseq batch removal
DEXSeq
updated 13 months ago by ★ 1.9k • written 13 months ago by ▴ 10
0
votes
0
replies
315
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
15 months ago Matthias Munz ▴ 10
0
votes
0
replies
371
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
15 months ago osieman52 • 0
1
vote
2
replies
635
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
15 months ago Delta._.43 ▴ 20
0
votes
1
reply
649
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
18 months ago NIK • 0
0
votes
4
replies
1.1k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 18 months ago by ▴ 90 • written 19 months ago by • 0
0
votes
5
replies
1.7k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 4.6 years ago by • 0
6
votes
11
replies
2.4k
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 8 months ago by • 0 • written 19 months ago by ▴ 350
3
votes
2
replies
743
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
20 months ago • updated 19 months ago Dakarai ▴ 10
1
vote
1
reply
523
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
1
vote
2
replies
718
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.0 years ago • updated 22 months ago A ▴ 40
3
votes
3
replies
879
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 22 months ago by 41k • written 23 months ago by ▴ 120
0
votes
1
reply
707
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 22 months ago by ★ 1.9k • written 2.1 years ago by • 0
1
vote
1
reply
907
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 22 months ago by ★ 1.9k • written 2.3 years ago by ▴ 10
2
votes
7
replies
1.1k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.3 years ago • updated 2.2 years ago rbenel ▴ 30
0
votes
5
replies
1.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.3 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
665
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.4 years ago Matthias Munz ▴ 10
0
votes
0
replies
516
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.4 years ago n.tear ▴ 20
0
votes
0
replies
526
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.4 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.3k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.5 years ago by ▴ 120 • written 2.6 years ago by ▴ 10
4
votes
5
replies
1.6k
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
2.6 years ago Matthias Munz ▴ 10
0
votes
0
replies
708
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
2.7 years ago jbono ▴ 10
0
votes
2
replies
838
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
2.7 years ago Gaia • 0
3
votes
2
replies
858
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.7 years ago Angel ▴ 10
2
votes
2
replies
1.0k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
2.8 years ago • updated 2.7 years ago n.tear ▴ 20
1
vote
1
reply
819
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 2.9 years ago by ★ 1.9k • written 2.9 years ago by • 0
0
votes
2
replies
1.0k
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
3.4 years ago • updated 3.0 years ago aleksandar.baburski.g • 0
1
vote
6
replies
3.6k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.1 years ago by ▴ 20 • written 8.7 years ago by • 0
0
votes
2
replies
1.3k
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 3.1 years ago by ▴ 20 • written 5.9 years ago by • 0
6
votes
7
replies
1.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 2.9 years ago by 41k • written 3.1 years ago by ▴ 20
0
votes
2
replies
716
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 3.4 years ago by ★ 3.7k • written 3.4 years ago by • 0
0
votes
4
replies
1.3k
views
Calculating per-exon PSI from DEXSeq
DEXSeq
3.4 years ago Angel Liang • 0
1
vote
2
replies
981
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by • 0
0
votes
1
reply
604
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 10
1
vote
2
replies
968
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
3.5 years ago aleksandar.baburski.g • 0
0
votes
2
replies
748
views
DEXSeq HTML report Error
DEXSeq
updated 3.5 years ago by 3.9k • written 3.5 years ago by • 0
0
votes
0
replies
558
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
3.6 years ago alexis.weinreb • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: NCBI protein conversion to CDNA and NCBI gene (in R) by Gordon Smyth 48k
Continuation of https://support.bioconductor.org/p/9155428/
Comment: Why is DMRcate not available for Bioconductor version 3.18? by Tim Peters ▴ 150
Thanks Daniel, Gordon and Lori for flagging this. DSS is only needed for the vignette so I'll remove that section, plus the dependency, som…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by R_Page • 0
Thank you, this works well. As for CDNA, I figured out what I need to find, and have made a new post regarding it.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hello Michael, I am continuing here and need your expert answer on this again I have performed small rna loci and DNA methylation mappin…
Comment: GOslim missing GO term by amanda • 0
Thank you for the advice and many thanks! It is WGCNA analysis. I will try your method today and see if there are some consistencies.
Votes
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Why is DMRcate not available for Bioconductor version 3.18?
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