Showing : DEXseq • reset
16
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6
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3.9k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 8.7 years ago by ▴ 90 • written 8.7 years ago by ▴ 180
13
votes
2
replies
5.2k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 10.3 years ago by ★ 3.8k • written 10.3 years ago by ▴ 370
8
votes
7
replies
2.6k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 22 months ago by ▴ 20 • written 2.5 years ago by ▴ 20
8
votes
12
replies
4.4k
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 11 months ago by ▴ 30 • written 3.0 years ago by ▴ 380
6
votes
7
replies
2.1k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 4.3 years ago by 43k • written 4.5 years ago by ▴ 20
6
votes
6
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2.9k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 6.6 years ago by ★ 1.9k • written 6.6 years ago by • 0
6
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3
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3.5k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
8.2 years ago fizer ▴ 40
6
votes
4
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2.5k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 8.1 years ago by ▴ 30 • written 8.1 years ago by ▴ 30
5
votes
6
replies
2.8k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 9.5 years ago by ★ 1.9k • written 9.5 years ago by ▴ 110
5
votes
18
replies
4.0k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
9.9 years ago • updated 9.8 years ago elle ▴ 10
4
votes
1
reply
1.2k
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 5.9 years ago by ★ 1.9k • written 5.9 years ago by ▴ 10
4
votes
3
replies
1.6k
views
Custom title for DEXseq plot
dexseq
updated 10.5 years ago by 68k • written 10.5 years ago by ▴ 10
4
votes
5
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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
4.0 years ago Matthias Munz ▴ 20
4
votes
1
reply
1.6k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 9.9 years ago by ★ 1.9k • written 9.9 years ago by ▴ 10
4
votes
3
replies
1.8k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by • 0
4
votes
6
replies
1.2k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
4
votes
4
replies
3.1k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 9.4 years ago by ★ 13k • written 9.4 years ago by ▴ 20
4
votes
7
replies
2.1k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 8.8 years ago by 68k • written 8.8 years ago by ★ 1.5k
3
votes
3
replies
2.4k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 3.7 years ago by ▴ 20 • written 5.1 years ago by ▴ 20
3
votes
2
replies
1.4k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
3
votes
4
replies
2.6k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 9.5 years ago by ★ 1.9k • written 9.5 years ago by ▴ 20
3
votes
6
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3.9k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 9.1 years ago by ★ 1.9k • written 9.1 years ago by • 0
3
votes
4
replies
1.3k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
3
votes
2
replies
3.5k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
3
votes
2
replies
1.5k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 10.4 years ago by ★ 1.9k • written 10.4 years ago by ▴ 70
3
votes
2
replies
1.5k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.1 years ago • updated 3.0 years ago Dakarai ▴ 10
3
votes
1
reply
711
views
How to save the DEXSeq results
DEXSeq
updated 11 months ago by 43k • written 11 months ago by • 0
3
votes
4
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3.9k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 40
3
votes
2
replies
1.4k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
4.1 years ago Angel ▴ 10
3
votes
2
replies
2.3k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 3.5 years ago by • 0 • written 8.2 years ago by ★ 1.5k
3
votes
3
replies
1.5k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 120
2
votes
5
replies
1.7k
views
DEXSeq time course design
DEXSeq differential exon usage
updated 6.9 years ago by ★ 1.9k • written 6.9 years ago by ▴ 60
2
votes
6
replies
3.4k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.4 years ago by ▴ 450 • written 5.4 years ago by • 0
2
votes
6
replies
1.6k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
6.0 years ago gv ▴ 40
2
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3
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1.3k
views
DEXSeq ignore non-coding regions
dexseq
updated 9.2 years ago by ★ 1.9k • written 9.2 years ago by ▴ 50
2
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3
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1.4k
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
6.0 years ago gv ▴ 40
2
votes
4
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2.1k
views
DEXSeqDataSet example code
DEXSeq
updated 9.4 years ago by • 0 • written 9.4 years ago by ▴ 20
2
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3
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1.8k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 9.2 years ago by ★ 1.9k • written 9.2 years ago by ▴ 170
2
votes
2
replies
1.4k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
9.1 years ago adelmane ▴ 20
2
votes
3
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1.4k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 5.9 years ago by 16k • written 5.9 years ago by ▴ 20
2
votes
4
replies
900
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
14 months ago thomas.heigl.ibk • 0
2
votes
6
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3.8k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
9.8 years ago • updated 9.7 years ago rahel14350 ▴ 10
2
votes
3
replies
1.6k
views
DEXSeqHTML and biomart object
DEXSeq
updated 7.4 years ago by ★ 1.9k • written 7.4 years ago by ▴ 60
2
votes
10
replies
3.1k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
10.2 years ago n.kreim ▴ 20
2
votes
2
replies
3.2k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
7.9 years ago craigmonger ▴ 10
2
votes
2
replies
1.2k
views
Algorithm behind splice=TRUE in DEXSeq
dexseq
updated 7.6 years ago by ★ 1.9k • written 7.6 years ago by • 0
2
votes
3
replies
2.4k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 9.1 years ago by • 0 • written 9.4 years ago by ▴ 30
2
votes
4
replies
1.8k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
9.4 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.8k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 9.4 years ago by ★ 1.9k • written 9.4 years ago by ▴ 20
2
votes
3
replies
2.3k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
10.6 years ago guffanti.alessandro • 0
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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