Showing : DEXseq • reset
16
votes
6
replies
3.6k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 8.3 years ago by ▴ 90 • written 8.3 years ago by ▴ 180
13
votes
2
replies
4.9k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 9.9 years ago by ★ 3.8k • written 9.9 years ago by ▴ 370
8
votes
12
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3.9k
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 6 months ago by ▴ 30 • written 2.6 years ago by ▴ 380
8
votes
7
replies
2.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 17 months ago by ▴ 20 • written 2.1 years ago by ▴ 20
6
votes
3
replies
3.3k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
7.8 years ago fizer ▴ 40
6
votes
4
replies
2.3k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 7.7 years ago by ▴ 30 • written 7.7 years ago by ▴ 30
6
votes
6
replies
2.6k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 6.2 years ago by ★ 1.9k • written 6.2 years ago by • 0
6
votes
7
replies
1.9k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 4.0 years ago by 43k • written 4.1 years ago by ▴ 20
5
votes
18
replies
3.7k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
9.5 years ago • updated 9.4 years ago elle ▴ 10
5
votes
6
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2.6k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 9.1 years ago by ★ 1.9k • written 9.1 years ago by ▴ 110
4
votes
1
reply
1.1k
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 5.5 years ago by ★ 1.9k • written 5.5 years ago by ▴ 10
4
votes
5
replies
2.3k
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
3.6 years ago Matthias Munz ▴ 20
4
votes
3
replies
1.5k
views
Custom title for DEXseq plot
dexseq
updated 10.1 years ago by 67k • written 10.1 years ago by ▴ 10
4
votes
7
replies
1.9k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 8.4 years ago by 67k • written 8.4 years ago by ★ 1.5k
4
votes
3
replies
1.7k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 6.2 years ago by ▴ 90 • written 6.2 years ago by • 0
4
votes
1
reply
1.5k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 9.6 years ago by ★ 1.9k • written 9.6 years ago by ▴ 10
4
votes
4
replies
2.9k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 9.0 years ago by ★ 13k • written 9.0 years ago by ▴ 20
3
votes
3
replies
2.0k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 3.3 years ago by ▴ 20 • written 4.7 years ago by ▴ 20
3
votes
4
replies
3.6k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 40
3
votes
2
replies
1.4k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
3
votes
4
replies
1.2k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
3
votes
2
replies
3.4k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 6.4 years ago by 52k • written 6.4 years ago by • 0
3
votes
4
replies
2.5k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 9.1 years ago by ★ 1.9k • written 9.1 years ago by ▴ 20
3
votes
2
replies
1.4k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 10.0 years ago by ★ 1.9k • written 10.0 years ago by ▴ 70
3
votes
2
replies
1.2k
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.7 years ago • updated 2.6 years ago Dakarai ▴ 10
3
votes
1
reply
465
views
How to save the DEXSeq results
DEXSeq
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
2
replies
1.3k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.7 years ago Angel ▴ 10
3
votes
2
replies
2.2k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 3.1 years ago by • 0 • written 7.8 years ago by ★ 1.5k
3
votes
3
replies
1.3k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.9 years ago by 43k • written 2.9 years ago by ▴ 120
3
votes
6
replies
3.7k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 8.7 years ago by ★ 1.9k • written 8.7 years ago by • 0
2
votes
5
replies
1.6k
views
DEXSeq time course design
DEXSeq differential exon usage
updated 6.5 years ago by ★ 1.9k • written 6.5 years ago by ▴ 40
2
votes
6
replies
3.1k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.0 years ago by ▴ 450 • written 5.0 years ago by • 0
2
votes
6
replies
1.5k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
5.6 years ago gv ▴ 40
2
votes
3
replies
1.2k
views
DEXSeq ignore non-coding regions
dexseq
updated 8.8 years ago by ★ 1.9k • written 8.8 years ago by ▴ 50
2
votes
3
replies
1.2k
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
5.6 years ago gv ▴ 40
2
votes
4
replies
2.0k
views
DEXSeqDataSet example code
DEXSeq
updated 9.0 years ago by • 0 • written 9.0 years ago by ▴ 20
2
votes
3
replies
1.7k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 8.8 years ago by ★ 1.9k • written 8.9 years ago by ▴ 170
2
votes
2
replies
1.3k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
8.7 years ago adelmane ▴ 20
2
votes
3
replies
1.3k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 20
2
votes
4
replies
730
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
10 months ago • updated 9 months ago thomas.heigl.ibk • 0
2
votes
6
replies
3.6k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
9.4 years ago rahel14350 ▴ 10
2
votes
3
replies
1.5k
views
DEXSeqHTML and biomart object
DEXSeq
updated 7.0 years ago by ★ 1.9k • written 7.0 years ago by ▴ 60
2
votes
10
replies
2.9k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
9.8 years ago n.kreim ▴ 20
2
votes
2
replies
2.9k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
7.5 years ago craigmonger ▴ 10
2
votes
2
replies
1.1k
views
Algorithm behind splice=TRUE in DEXSeq
dexseq
updated 7.2 years ago by ★ 1.9k • written 7.2 years ago by • 0
2
votes
3
replies
2.2k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
10.2 years ago guffanti.alessandro • 0
2
votes
3
replies
2.3k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 8.7 years ago by • 0 • written 9.0 years ago by ▴ 30
2
votes
4
replies
1.7k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
9.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.7k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 9.0 years ago by ★ 1.9k • written 9.0 years ago by ▴ 20
2
votes
5
replies
1.6k
views
proper way to subset columns of a DEXSeqDataset object
DEXSeq
9.1 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k
You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…
Comment: contrast matrix design for a continuous variable by dtzhu337 • 0
Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…
Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k
Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …
Comment: fail to use addPerROIQC in Rmd by liu.n • 0
That's odd. So it can run successfully within markdown but would be failed when knitting?
Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0
> dim(spe) [1] 19962 425
Votes
Answer: contrast matrix design for a continuous variable
A: What's the difference between p.adjust and qvalue?
Answer: DESeq2- merging technical vs biological replicates
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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