Showing : DEXSeq • reset
16
votes
6
replies
3.3k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 7.8 years ago by ▴ 90 • written 7.8 years ago by ▴ 180
12
votes
2
replies
4.6k
views
DEXSeq Usage and Expression Confusion
dexseq
updated 9.4 years ago by ★ 3.7k • written 9.4 years ago by ▴ 370
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 10 months ago by ▴ 20 • written 19 months ago by ▴ 20
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
7.3 years ago fizer ▴ 30
6
votes
6
replies
2.3k
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
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 3.4 years ago by 42k • written 3.5 years ago by ▴ 20
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
11
replies
3.1k
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 14 months ago by • 0 • written 2.1 years ago by ▴ 360
5
votes
18
replies
3.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
9.0 years ago • updated 8.9 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 7.9 years ago by 65k • written 7.9 years ago by ★ 1.5k
4
votes
3
replies
1.4k
views
Custom title for DEXseq plot
dexseq
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 10
4
votes
1
reply
1.4k
views
DEXSeq with mutliple experimental conditions - definig contrasts
DEXSeq
updated 9.0 years ago by ★ 1.9k • written 9.0 years ago by ▴ 10
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
4
votes
4
replies
2.6k
views
DEXSeq and Independent filtering
dexseq deseq2 genefilter
updated 8.5 years ago by ★ 13k • written 8.5 years ago by ▴ 20
4
votes
1
reply
897
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 5.0 years ago by ★ 1.9k • written 5.0 years ago by ▴ 10
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
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
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 ▴ 20
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 42k • written 6.9 years ago by • 0
3
votes
2
replies
1.2k
views
DEXSeq analysis with large number of samples
dexseq estimatedispersions
updated 5.8 years ago by 42k • written 5.8 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 8.2 years ago by ★ 1.9k • written 8.2 years ago by • 0
3
votes
2
replies
1.3k
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 9.5 years ago by ★ 1.9k • written 9.5 years ago by ▴ 70
3
votes
1
reply
143
views
How to save the DEXSeq results
DEXSeq
updated 10 days ago by 42k • written 10 days ago by • 0
3
votes
2
replies
965
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 2.0 years ago Dakarai ▴ 10
3
votes
2
replies
1.1k
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
3.2 years ago Angel ▴ 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 7.3 years ago by ★ 1.5k
3
votes
3
replies
1.1k
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 2.3 years ago by 42k • written 2.3 years ago by ▴ 120
2
votes
5
replies
1.3k
views
DEXSeq time course design
DEXSeq differential exon usage
updated 5.9 years ago by ★ 1.9k • written 5.9 years ago by ▴ 40
2
votes
6
replies
2.6k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 4.5 years ago by ▴ 380 • written 4.5 years ago by • 0
2
votes
4
replies
439
views
DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 11 weeks ago thomas.heigl.ibk • 0
2
votes
2
replies
1.2k
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
1.1k
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 5.0 years ago by 16k • written 5.0 years ago by ▴ 20
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 ▴ 50
2
votes
4
replies
1.5k
views
DEXSeqHTML doesn't creates plots
dexseq DEXSeqHTML data representation in graphical forms warning message
8.5 years ago Assa Yeroslaviz ★ 1.5k
2
votes
1
reply
650
views
"condition" factor name is hardcoded
DEXSeq
7.4 years ago bjoern.gruening • 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
2
replies
1.2k
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
3.2 years ago n.tear ▴ 20
2
votes
6
replies
3.4k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
8.8 years ago rahel14350 ▴ 10
2
votes
2
replies
888
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
2.1k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 8.1 years ago by • 0 • written 8.5 years ago by ▴ 30
2
votes
3
replies
1.4k
views
DEXSeqHTML and biomart object
DEXSeq
updated 6.4 years ago by ★ 1.9k • written 6.5 years ago by ▴ 60
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
3
replies
1.6k
views
DEXSeq for DE of antisense transcription
dexseq antisense
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 650
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
1.6k
views
DEXSeq: DEXSeqHTML, plotDEXSeq and interaction tests
dexseq
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by ▴ 20
2
votes
3
replies
1.5k
views
DEXSeq error upon executing testForDEU()
dexseq
updated 8.3 years ago by ★ 1.9k • written 8.3 years ago by ▴ 170
2
votes
5
replies
1.6k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.8 years ago • updated 9.7 years ago António Miguel de Jesus Domingues ▴ 510
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Michael Love 42k
Popular Question to Vincent J. Carey, Jr. 6.7k
Locations • All
The Netherlands, 6 minutes ago
Poland, 14 minutes ago
United States, 22 minutes ago
Greece, 52 minutes ago
Spain, 57 minutes ago
Traffic: 701 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6