Showing : DEXseq • reset
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43
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 21 hours ago by ★ 1.9k • written 1 day ago by • 0
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1
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69
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Adding columns to DEXSeqResults object
DEXSeq
updated 21 hours ago by ★ 1.9k • written 2 days ago by • 0
0
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1
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45
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 hours ago by 41k • written 1 day ago by • 0
0
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0
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121
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DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
5 weeks ago jean-christophe.helbling • 0
2
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4
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390
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
11 weeks ago • updated 7 weeks ago thomas.heigl.ibk • 0
0
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2
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337
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Swimming downstream: transcript fold changes
DEXSeq stageR
5 months ago jbono ▴ 10
1
vote
1
reply
362
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DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
5 months ago NiKo ▴ 10
0
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2
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534
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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
0
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3
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631
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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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736
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Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 8 months ago by 16k • written 8 months ago by • 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
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5
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815
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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365
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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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373
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Error while performing DEXseq
DEXSeq
10 months ago vipul14 • 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
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0
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410
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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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867
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
14 months ago Ben J • 0
1
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15
replies
3.4k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 16 months ago by • 0 • written 7.0 years ago by • 0
0
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0
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554
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 16 months ago by 41k • written 16 months ago by • 0
0
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1
reply
775
views
plotDEXSeq error?
DEXSeq dex
17 months ago • updated 16 months ago barrypraveen • 0
1
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4
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897
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DEXseq batch removal
DEXSeq
updated 18 months ago by ★ 1.9k • written 18 months ago by ▴ 10
0
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0
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406
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DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
19 months ago Matthias Munz ▴ 10
1
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2
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2.0k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 20 months ago by ▴ 10 • written 4.7 years ago by ▴ 10
0
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0
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484
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
20 months ago osieman52 • 0
1
vote
2
replies
805
views
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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819
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago • updated 22 months ago NIK • 0
0
votes
4
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1.4k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 23 months ago by ▴ 90 • written 23 months ago by • 0
3
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2
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922
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DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.0 years ago • updated 23 months ago Dakarai ▴ 10
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
1
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1
reply
630
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
replies
847
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.4 years ago • updated 2.2 years ago A ▴ 40
1
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1
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1.1k
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DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.2 years ago by ★ 1.9k • written 2.7 years ago by ▴ 10
0
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1
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823
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.2 years ago by ★ 1.9k • written 2.5 years ago by • 0
3
votes
3
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1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 120
3
votes
2
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1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 2.4 years ago by • 0 • written 7.2 years ago by ★ 1.5k
2
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7
replies
1.2k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago • updated 2.6 years ago rbenel ▴ 40
3
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3
replies
1.6k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.6 years ago by ▴ 20 • written 4.0 years ago by ▴ 20
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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797
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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
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0
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620
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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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619
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DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.8 years ago Matthias Munz ▴ 10
1
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6
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1.5k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.8 years ago by ▴ 120 • written 3.0 years ago by ▴ 10
4
votes
5
replies
1.9k
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
3.0 years ago Matthias Munz ▴ 10
0
votes
0
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855
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.0 years ago jbono ▴ 10
0
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2
replies
980
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.1 years ago Gaia • 0
2
votes
2
replies
1.1k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.2 years ago • updated 3.1 years ago n.tear ▴ 20
3
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2
replies
1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.1 years ago Angel ▴ 10
1
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1
reply
965
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
6
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7
replies
1.6k
views
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
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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