Showing : DEXseq • reset
15
votes
6
replies
3.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 7.7 years ago by ▴ 90 • written 7.7 years ago by ▴ 170
12
votes
2
replies
4.5k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 9.3 years ago by ★ 3.7k • written 9.3 years ago by ▴ 370
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 9 months ago by ▴ 20 • written 18 months ago by ▴ 20
6
votes
6
replies
2.2k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 5.6 years ago by ★ 1.9k • written 5.6 years ago by • 0
6
votes
3
replies
2.9k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
7.2 years ago fizer ▴ 30
6
votes
11
replies
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
6
votes
4
replies
2.1k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 7.1 years ago by ▴ 30 • written 7.1 years ago by ▴ 20
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.3 years ago by 41k • written 3.5 years ago by ▴ 20
5
votes
18
replies
3.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
8.9 years ago • updated 8.8 years ago elle ▴ 10
5
votes
6
replies
2.3k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by ▴ 110
4
votes
7
replies
1.7k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 7.8 years ago by 65k • written 7.8 years ago by ★ 1.5k
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
4
votes
1
reply
1.4k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 8.9 years ago by ★ 1.9k • written 8.9 years ago by ▴ 10
4
votes
3
replies
1.3k
views
Custom title for DEXseq plot
dexseq
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 10
4
votes
4
replies
2.6k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 8.4 years ago by ★ 13k • written 8.4 years ago by ▴ 20
4
votes
3
replies
1.4k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 5.6 years ago by ▴ 90 • written 5.6 years ago by • 0
3
votes
2
replies
3.1k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 5.8 years ago by 50k • written 5.8 years ago by • 0
3
votes
4
replies
2.2k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by ▴ 10
3
votes
6
replies
3.5k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 8.1 years ago by ★ 1.9k • written 8.1 years ago by • 0
3
votes
2
replies
1.0k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.1 years ago Angel ▴ 10
3
votes
2
replies
1.2k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 9.4 years ago by ★ 1.9k • written 9.4 years ago by ▴ 70
3
votes
2
replies
1.2k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 10
3
votes
3
replies
1.7k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.7 years ago by ▴ 20 • written 4.1 years ago by ▴ 20
3
votes
3
replies
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
replies
934
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
2.1 years ago • updated 24 months ago Dakarai ▴ 10
3
votes
2
replies
1.9k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 2.5 years ago by • 0 • written 7.2 years ago by ★ 1.5k
3
votes
4
replies
1.1k
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
2
votes
1
reply
630
views
"condition" factor name is hardcoded
DEXSeq
7.4 years ago bjoern.gruening • 0
2
votes
4
replies
398
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
12 weeks ago • updated 8 weeks ago thomas.heigl.ibk • 0
2
votes
4
replies
3.1k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 7.3 years ago by 41k • written 7.3 years ago by ▴ 30
2
votes
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.2 years ago • updated 3.1 years ago n.tear ▴ 20
2
votes
1
reply
842
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 4.9 years ago by ★ 1.9k • written 4.9 years ago by • 0
2
votes
3
replies
1.0k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 20
2
votes
6
replies
2.5k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 4.4 years ago by ▴ 380 • written 4.4 years ago by • 0
2
votes
6
replies
1.2k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
5.0 years ago gv ▴ 40
2
votes
3
replies
1.5k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 8.2 years ago by ★ 1.9k • written 8.2 years ago by ▴ 170
2
votes
3
replies
1.1k
views
DEXSeq ignore non-coding regions
dexseq
updated 8.2 years ago by ★ 1.9k • written 8.2 years ago by ▴ 40
2
votes
2
replies
1.1k
views
Subset DEXSeqDataSet In DEXSeq
dexseq
8.1 years ago adelmane ▴ 20
2
votes
3
replies
1.0k
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
5.0 years ago gv ▴ 40
2
votes
3
replies
2.1k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 8.1 years ago by • 0 • written 8.4 years ago by ▴ 30
2
votes
4
replies
1.5k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
8.4 years ago Assa Yeroslaviz ★ 1.5k
2
votes
6
replies
3.4k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
8.8 years ago • updated 8.7 years ago rahel14350 ▴ 10
2
votes
2
replies
874
views
Algorithm behind splice=TRUE in DEXSeq
dexseq
updated 6.6 years ago by ★ 1.9k • written 6.6 years ago by • 0
2
votes
3
replies
1.4k
views
DEXSeqHTML and biomart object
DEXSeq
updated 6.4 years ago by ★ 1.9k • written 6.4 years ago by ▴ 50
2
votes
3
replies
2.0k
views
Issues with DEXSeq: rows did not converge in beta
rnaseq dexseq
7.2 years ago Konstantin Okonechnikov ▴ 40
2
votes
10
replies
2.6k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
9.2 years ago n.kreim ▴ 20
2
votes
5
replies
1.5k
views
proper way to subset columns of a DEXSeqDataset object
DEXSeq
8.5 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
2
votes
2
replies
2.7k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
6.9 years ago craigmonger ▴ 10
2
votes
3
replies
2.0k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
9.6 years ago guffanti.alessandro • 0
2
votes
5
replies
1.6k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.7 years ago António Miguel de Jesus Domingues ▴ 490
50 results • Page 1 of 1
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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