Showing : DEXseq • reset
15
votes
6
replies
3.0k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 7.3 years ago by ▴ 90 • written 7.3 years ago by ▴ 170
12
votes
2
replies
4.3k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 8.9 years ago by ★ 3.7k • written 8.9 years ago by ▴ 370
8
votes
7
replies
1.3k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 5 months ago by ▴ 20 • written 13 months ago by ▴ 20
6
votes
4
replies
2.0k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 6.7 years ago by ▴ 30 • written 6.7 years ago by ▴ 20
6
votes
11
replies
2.4k
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 8 months ago by • 0 • written 19 months ago by ▴ 350
6
votes
7
replies
1.4k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.0 years ago by 41k • written 3.1 years ago by ▴ 20
6
votes
6
replies
2.0k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 5.2 years ago by ★ 1.9k • written 5.2 years ago by • 0
6
votes
3
replies
2.7k
views
plotDEXSeq error in plot.window(xlim = c(0, 1), ylim = c(0, max(matr))) : need finite 'ylim' values
dexseq differential exon usage
6.8 years ago fizer ▴ 30
5
votes
18
replies
2.8k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
8.5 years ago • updated 8.4 years ago elle ▴ 10
5
votes
6
replies
2.1k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 8.1 years ago by ★ 1.9k • written 8.1 years ago by ▴ 110
4
votes
7
replies
1.5k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 7.4 years ago by 64k • written 7.4 years ago by ★ 1.5k
4
votes
4
replies
2.4k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 8.0 years ago by 13k • written 8.0 years ago by ▴ 20
4
votes
5
replies
1.6k
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
2.6 years ago Matthias Munz ▴ 10
4
votes
1
reply
1.3k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 8.6 years ago by ★ 1.9k • written 8.6 years ago by ▴ 10
4
votes
3
replies
1.2k
views
Custom title for DEXseq plot
dexseq
updated 9.1 years ago by 64k • written 9.1 years ago by ▴ 10
4
votes
3
replies
1.3k
views
DEXSeq and DRIMSeq on paired samples?
DRIMSeq DEXSeq
updated 5.2 years ago by ▴ 90 • written 5.2 years ago by • 0
3
votes
3
replies
880
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 23 months ago by 41k • written 23 months ago by ▴ 120
3
votes
3
replies
1.5k
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 2.3 years ago by ▴ 20 • written 3.7 years ago by ▴ 20
3
votes
2
replies
1.1k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
3
votes
6
replies
3.3k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 7.7 years ago by ★ 1.9k • written 7.7 years ago by • 0
3
votes
4
replies
2.0k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 8.1 years ago by ★ 1.9k • written 8.1 years ago by ▴ 10
3
votes
2
replies
1.1k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 9.0 years ago by ★ 1.9k • written 9.0 years ago by ▴ 70
3
votes
4
replies
985
views
deseq2 and dexseq for multiple tissue from wildtype only
deseq2 dexseq rnaseq
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
3
votes
2
replies
859
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
2.7 years ago Angel ▴ 10
3
votes
2
replies
1.7k
views
DEXSeq throws a warning - rank-deficient matrix
dexseq fit matrix warning
updated 2.1 years ago by • 0 • written 6.8 years ago by ★ 1.5k
3
votes
2
replies
743
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
20 months ago • updated 19 months ago Dakarai ▴ 10
3
votes
2
replies
2.9k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread featurecounts dexseq rnaseq
updated 5.4 years ago by 48k • written 5.4 years ago by • 0
2
votes
1
reply
547
views
"condition" factor name is hardcoded
DEXSeq
7.0 years ago bjoern.gruening • 0
2
votes
4
replies
2.8k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 30
2
votes
2
replies
1.0k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
2.8 years ago • updated 2.7 years ago n.tear ▴ 20
2
votes
1
reply
732
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 4.5 years ago by ★ 1.9k • written 4.5 years ago by • 0
2
votes
3
replies
984
views
DEXSeq ignore non-coding regions
dexseq
updated 7.8 years ago by ★ 1.9k • written 7.8 years ago by ▴ 40
2
votes
7
replies
1.6k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 6.8 years ago by ★ 1.9k • written 6.8 years ago by • 0
2
votes
6
replies
2.2k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 4.0 years ago by ▴ 380 • written 4.0 years ago by • 0
2
votes
7
replies
1.1k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.3 years ago • updated 2.2 years ago rbenel ▴ 30
2
votes
3
replies
1.9k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 7.7 years ago by • 0 • written 8.0 years ago by ▴ 30
2
votes
6
replies
3.2k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
8.4 years ago rahel14350 ▴ 10
2
votes
3
replies
1.3k
views
DEXSeqHTML and biomart object
DEXSeq
updated 6.0 years ago by ★ 1.9k • written 6.0 years ago by ▴ 40
2
votes
4
replies
1.4k
views
stageR: Error in stageWiseAdjustment
stageR rnaseqDTU DRIMSeq DEXSeq
4.8 years ago d-joester ▴ 20
2
votes
10
replies
2.4k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
8.8 years ago n.kreim ▴ 20
2
votes
2
replies
2.5k
views
DEXSeq prepare annotation on Stringtie outputGTF - KeyError: 'gene_id'
dexseq
6.5 years ago craigmonger ▴ 10
2
votes
4
replies
1.4k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
8.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
5
replies
1.4k
views
proper way to subset columns of a DEXSeqDataset object
DEXSeq
8.1 years ago Narayanan, Manikandan NIH/NIAID [E] ▴ 60
2
votes
3
replies
1.9k
views
DEXSeqDataSetFromHTSeq object creation error
dexseq
9.2 years ago guffanti.alessandro • 0
2
votes
5
replies
1.4k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.3 years ago António Miguel de Jesus Domingues ▴ 490
2
votes
3
replies
1.5k
views
DEXSeq for DE of antisense transcription
dexseq antisense
updated 9.1 years ago by 13k • written 9.1 years ago by ▴ 650
2
votes
2
replies
1.5k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 8.0 years ago by ★ 1.9k • written 8.0 years ago by ▴ 20
2
votes
3
replies
1.4k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 7.9 years ago by ★ 1.9k • written 7.9 years ago by 170
2
votes
3
replies
917
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 20
2
votes
3
replies
1.9k
views
Issues with DEXSeq: rows did not converge in beta
rnaseq dexseq
6.8 years ago Konstantin Okonechnikov ▴ 40
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl down??? by James W. MacDonald 64k
I normally caution against mapping between annotation sources (NCBI and Ensembl), as it usually doesn't work well. However, it is possible.…
Answer: NCBI protein conversion to CDNA and NCBI gene (in R) by James W. MacDonald 64k
I already showed you how to do this for gene symbols, and it's analogous for any other annotation ID. Please see the `AnnotationDbi` [vigne…
Comment: Obtaining rsIDs with ENSG and variant ID information by Robert Castelo ★ 3.0k
This is a large package, and when downloading and installing large packages it's often the case to get timeouts. Try setting a longer time …
Comment: How does Deseq2 deal with the row with zero when calculating size factors by ATpoint ★ 3.6k
> Because I found that if there is at least one gene without zero among all of the samples, the deseq2 runs smoothly. No, it doesn't. ``…
Comment: Obtaining rsIDs with ENSG and variant ID information by bd2000 • 0
Thank you for your answer. I've tried to download the package but it didn't work: Error in download.file(url, destfile, method, mode =…
Votes
Answer: biomaRt not working - lazy table error
Answer: Confused about the CPM and TMM normalization in edgeR
Answer: Differential gene expression analysis
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Comment: Why is DMRcate not available for Bioconductor version 3.18?
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