Showing : DEXseq • reset
17
votes
6
replies
4.4k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 9.6 years ago by ▴ 100 • written 9.6 years ago by ▴ 180
13
votes
2
replies
5.6k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 11.2 years ago by ★ 3.8k • written 11.2 years ago by ▴ 370
8
votes
7
replies
3.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.7 years ago by ▴ 20 • written 3.4 years ago by ▴ 20
8
votes
12
replies
5.2k
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 21 months ago by ▴ 30 • written 3.9 years ago by ▴ 390
6
votes
7
replies
2.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 5.2 years ago by 43k • written 5.4 years ago by ▴ 20
6
votes
6
replies
3.3k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 7.4 years ago by ★ 1.9k • written 7.4 years ago by • 0
6
votes
3
replies
3.9k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
9.1 years ago fizer ▴ 40
6
votes
4
replies
2.8k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 8.9 years ago by ▴ 30 • written 9.0 years ago by ▴ 30
5
votes
6
replies
3.1k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 10.3 years ago by ★ 1.9k • written 10.3 years ago by ▴ 110
5
votes
18
replies
4.8k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
10.8 years ago • updated 10.7 years ago elle ▴ 10
4
votes
1
reply
1.4k
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 6.8 years ago by ★ 1.9k • written 6.8 years ago by ▴ 10
4
votes
3
replies
1.8k
views
Custom title for DEXseq plot
dexseq
updated 11.3 years ago by 68k • written 11.3 years ago by ▴ 10
4
votes
5
replies
3.1k
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
4.9 years ago Matthias Munz ▴ 20
4
votes
1
reply
1.8k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 10.8 years ago by ★ 1.9k • written 10.8 years ago by ▴ 10
4
votes
3
replies
2.1k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 7.5 years ago by ▴ 90 • written 7.5 years ago by • 0
4
votes
6
replies
1.8k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 11 months ago by ★ 5.0k • written 12 months ago by • 0
4
votes
4
replies
3.5k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 10.3 years ago by ★ 13k • written 10.3 years ago by ▴ 20
4
votes
7
replies
2.5k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 9.7 years ago by 68k • written 9.7 years ago by ★ 1.5k
3
votes
3
replies
2.8k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 4.5 years ago by ▴ 20 • written 5.9 years ago by ▴ 20
3
votes
2
replies
1.7k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
3
votes
4
replies
2.8k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 10.3 years ago by ★ 1.9k • written 10.3 years ago by ▴ 20
3
votes
6
replies
4.2k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 10.0 years ago by ★ 1.9k • written 10.0 years ago by • 0
3
votes
4
replies
1.5k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 8.8 years ago by 43k • written 8.8 years ago by • 0
3
votes
2
replies
4.0k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
3
votes
2
replies
1.7k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 11.3 years ago by ★ 1.9k • written 11.3 years ago by ▴ 70
3
votes
2
replies
2.0k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
3.9 years ago Dakarai ▴ 10
3
votes
1
reply
1.0k
views
How to save the DEXSeq results
DEXSeq
updated 22 months ago by 43k • written 22 months ago by • 0
3
votes
4
replies
4.4k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 40
3
votes
2
replies
1.7k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
5.0 years ago Angel ▴ 10
3
votes
2
replies
2.6k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 4.3 years ago by • 0 • written 9.1 years ago by ★ 1.5k
3
votes
3
replies
1.8k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 120
2
votes
5
replies
2.0k
views
DEXSeq time course design
DEXSeq differential exon usage
updated 7.8 years ago by ★ 1.9k • written 7.8 years ago by ▴ 60
2
votes
6
replies
4.0k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 6.3 years ago by ▴ 450 • written 6.3 years ago by • 0
2
votes
6
replies
1.9k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
6.9 years ago gv ▴ 30
2
votes
3
replies
1.5k
views
DEXSeq ignore non-coding regions
dexseq
updated 10.1 years ago by ★ 1.9k • written 10.1 years ago by ▴ 50
2
votes
3
replies
1.6k
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
6.9 years ago gv ▴ 30
2
votes
4
replies
2.3k
views
DEXSeqDataSet example code
DEXSeq
updated 10.3 years ago by • 0 • written 10.3 years ago by ▴ 20
2
votes
3
replies
2.0k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 10.1 years ago by ★ 1.9k • written 10.1 years ago by ▴ 170
2
votes
2
replies
1.6k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
10.0 years ago adelmane ▴ 20
2
votes
3
replies
1.7k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 6.8 years ago by 16k • written 6.8 years ago by ▴ 20
2
votes
4
replies
1.3k
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
2.1 years ago • updated 2.0 years ago thomas.heigl.ibk • 0
2
votes
6
replies
4.1k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
10.6 years ago rahel14350 ▴ 10
2
votes
3
replies
1.8k
views
DEXSeqHTML and biomart object
DEXSeq
updated 8.3 years ago by ★ 1.9k • written 8.3 years ago by ▴ 60
2
votes
10
replies
3.5k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
11.1 years ago n.kreim ▴ 20
2
votes
2
replies
3.6k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
8.8 years ago craigmonger ▴ 10
2
votes
2
replies
1.3k
views
Algorithm behind splice=TRUE in DEXSeq
dexseq
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by • 0
2
votes
3
replies
2.7k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 9.9 years ago by • 0 • written 10.3 years ago by ▴ 30
2
votes
4
replies
2.1k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
10.3 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
2.0k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 10.3 years ago by ★ 1.9k • written 10.3 years ago by ▴ 20
2
votes
3
replies
2.4k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
11.5 years ago guffanti.alessandro • 0
364 results • Page 1 of 8
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Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
Votes
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
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