Showing : DEXSEq • reset
0
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3
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124
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DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
16 days ago • updated 15 days ago phoebe1354 • 0
0
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5
replies
963
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 3.1 years ago by • 0
3
votes
9
replies
288
views
DEXSeq errors "Error in scan( line ... did not have 3 elements" and "Error in FUN(X[[i]], ...) : subscript out of bounds" (DEXSeqDataSetFromHTSeq)
DEXSeq
4 weeks ago • updated 28 days ago Matthew Thornton ▴ 350
3
votes
2
replies
126
views
DEX-Seq returns Error in FUN(X[[i]], ...) : subscript out of bounds when I use DEXSeqDatasetFromHTseq()
R DEXSeq SequenceAnnotation RNASeqData
6 weeks ago • updated 16 days ago Dakarai ▴ 10
0
votes
1
reply
112
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 8 weeks ago by ★ 1.8k • written 8 weeks ago by • 0
1
vote
2
replies
245
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
5 months ago • updated 3 months ago A ▴ 40
3
votes
3
replies
253
views
Joint disperstion estimation for DEXSeq and DESeq2
DESeq2 DEXseq
updated 4 months ago by 36k • written 4 months ago by ▴ 100
0
votes
1
reply
222
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 3 months ago by ★ 1.8k • written 7 months ago by • 0
0
votes
1
reply
220
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 3 months ago by ★ 1.8k • written 8 months ago by • 0
2
votes
7
replies
377
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
9 months ago • updated 8 months ago rbenel ▴ 20
0
votes
5
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278
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
9 months ago bioinformatic_trainee • 0
0
votes
0
replies
198
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
9 months ago Matthias Munz ▴ 10
0
votes
0
replies
188
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
10 months ago n.tear ▴ 20
0
votes
0
replies
165
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
10 months ago Matthias Munz ▴ 10
1
vote
6
replies
608
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 11 months ago by ▴ 100 • written 13 months ago by ▴ 10
4
votes
5
replies
591
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
12 months ago Matthias Munz ▴ 10
0
votes
0
replies
256
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
13 months ago jbono ▴ 10
0
votes
2
replies
330
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
14 months ago Gaia • 0
3
votes
2
replies
413
views
How to better run DEXSeq with a very large number of samples?
DEXSeq
14 months ago Angel ▴ 10
2
votes
2
replies
448
views
Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
15 months ago • updated 14 months ago n.tear ▴ 20
1
vote
1
reply
379
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 16 months ago by ★ 1.8k • written 16 months ago by • 0
0
votes
2
replies
455
views
DEXSeq - what is the best way to filter out low expressed exons / genes?
dexseq
23 months ago • updated 18 months ago aleksandar.baburski.g • 0
1
vote
6
replies
2.8k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 18 months ago by ▴ 20 • written 7.2 years ago by • 0
0
votes
2
replies
765
views
Interpreting the EstimateDispersion plot from the DEXSeq package
dexseq estimatedispersions
updated 18 months ago by ▴ 20 • written 4.4 years ago by • 0
6
votes
7
replies
748
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 17 months ago by 36k • written 18 months ago by ▴ 20
0
votes
2
replies
303
views
DEXSeq : can we plot from the table of results or/and run DEXSeq from a matrix of counts like in DESeq2?
DEXseq
updated 22 months ago by ★ 3.7k • written 22 months ago by • 0
0
votes
4
replies
522
views
Calculating per-exon PSI from DEXSeq
DEXSeq
22 months ago Angel Liang • 0
1
vote
2
replies
372
views
Detailed explanations for DEXSeq output columns
DEXSeq
updated 22 months ago by ★ 1.8k • written 22 months ago by • 0
0
votes
1
reply
259
views
How to obtain the specific genelists mentioned in the RNASeq DTU workflow?
rnaseqdtu RNASeq DEXSeq DESeq2
updated 22 months ago by 36k • written 22 months ago by ▴ 10
1
vote
2
replies
443
views
DEXSeq dispersion estimation optimisation for large number of samples
DEXSeq estimateDispersions
23 months ago aleksandar.baburski.g • 0
0
votes
2
replies
350
views
DEXSeq HTML report Error
DEXSeq
updated 23 months ago by 3.5k • written 23 months ago by • 0
0
votes
0
replies
207
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq DRIMSeq
2.0 years ago alexis.weinreb • 0
1
vote
2
replies
481
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
2.0 years ago Raito92 ▴ 60
0
votes
1
reply
339
views
DEXseq conversion of GTF to GFF creating incorrect exon coordinates
software error DEXSeq
2.1 years ago knuppdav • 0
1
vote
3
replies
469
views
DEXSeq with large(ish) number of samples
DEXSeq exon memory dispersions estimateDispersions
2.1 years ago andreismolnikov00 • 0
0
votes
0
replies
569
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 2.1 years ago by 25k • written 2.1 years ago by ▴ 10
3
votes
3
replies
545
views
Calculation of Log2 fold change in DEXSeq
DEXSeq log2foldchange Tutorial
updated 8 months ago by ▴ 20 • written 2.1 years ago by ▴ 20
1
vote
2
replies
272
views
How to set model formulae in DEXSeq when 2 shRNAs were used to target a same gene
DEXSeq
updated 2.1 years ago by ★ 1.8k • written 2.1 years ago by • 0
0
votes
3
replies
499
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq Splicing Exon Usage
2.3 years ago gunjan.dikshit • 0
2
votes
6
replies
963
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 2.5 years ago by ▴ 340 • written 2.5 years ago by • 0
0
votes
1
reply
330
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
2.5 years ago stuart ▴ 10
0
votes
1
reply
282
views
error in DEXSeq estimateExonFoldChanges
dexseq
2.5 years ago brown.annaleigh • 0
0
votes
2
replies
385
views
A question about DEXSeq of estimateDispersions
dexseq
updated 2.6 years ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
466
views
Issue/Error with DEXSeq design formulae in testForDEU function
deseq2 DEXSeq BioCParallel
updated 2.7 years ago by ★ 1.8k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 2.8 years ago by 59k • written 2.8 years ago by • 0
0
votes
2
replies
535
views
DEXSeq error in dexseq_count.py. ValueError: need more than 4 values to unpack
DEXSeq
updated 2.9 years ago by ★ 3.7k • written 2.9 years ago by • 0
2
votes
1
reply
404
views
Print Differentially Expressed Exons From Dexseq Results
DEXSeq RNA-Seq
updated 3.0 years ago by ★ 1.8k • written 3.0 years ago by • 0
2
votes
3
replies
468
views
exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
DEXSeq
updated 3.0 years ago by 15k • written 3.0 years ago by ▴ 10
0
votes
6
replies
720
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
3.0 years ago fiona.dick91 ▴ 10
1
vote
3
replies
583
views
null model and DEXSeqDataSet object in DEXSEQ
deseq2 dexseq
3.0 years ago gv ▴ 40
50 results • Page 1 of 1
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Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by James W. MacDonald 59k
We have progressed past the point where I show you how to do things using Bioconductor packages, and into the realm where I start telling y…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Yang Shi • 0
Thanks sir! As your mentioned here, 12-15 means cutoff value about 4? Could I select the reflection point as the "point" that starts to ha…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by James W. MacDonald 59k
It's a non-scientific selection. The Nonspecific probes are meant to be sequences that are not found in nature, so any binding is due to cr…
Comment: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array by Yang Shi • 0
Thanks for your excellent reply sir! But there are still some points confused me. (1).dbGetQuery get 93 kinds of probes. Would be okay for …
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook by Kevin Blighe 3.5k
Great! problem solved, then?
Votes
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Answer: Methods for removing unexpressed probes of Affymetrix Human Genome U219 Array
Comment: Quantile Normalization after rma or not?
Comment: Print EnhancedVolcano Plot as jpeg or similar in R Notebook
Comment: How to best visualize multi-level transcriptomics experiment data?
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