Showing : dexseq • reset
2
votes
1
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67
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 2 days ago by ★ 1.9k • written 4 days ago by • 0
3
votes
1
reply
147
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How to save the DEXSeq results
DEXSeq
updated 11 days ago by 42k • written 11 days ago by • 0
0
votes
3
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187
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Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 17 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
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0
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99
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how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
23 days ago • updated 19 days ago Sara • 0
0
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1
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166
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Adding columns to DEXSeqResults object
DEXSeq
updated 29 days ago by ★ 1.9k • written 4 weeks ago by • 0
0
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1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 29 days ago by 42k • written 4 weeks ago by • 0
0
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0
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143
views
DEXSeq plot error
DEXSeq DEXSeqNAvalues DEXseq
9 weeks ago jean-christophe.helbling • 0
2
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4
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444
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DEXSeq: summarizeOverlaps() crashes Rstudio with too many samples
DEXSeq
3 months ago • updated 11 weeks ago thomas.heigl.ibk • 0
0
votes
2
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394
views
Swimming downstream: transcript fold changes
DEXSeq stageR
6 months ago jbono ▴ 10
1
vote
1
reply
414
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
6 months ago NiKo ▴ 10
0
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2
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582
views
DEXSeqDataSet object DEXSeqDataSetFromHTSeq Error: line number did not have 3 elements
DEXSeq HTSeq R
9 months ago • updated 8 months ago yr542 • 0
0
votes
3
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689
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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3
replies
807
views
Error with makeTxDbFromBiomart
DEXSeq biomaRt
updated 9 months ago by 16k • written 9 months ago by • 0
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
1
vote
5
replies
883
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
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0
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399
views
Recommendation sought for differential exon usage of a single gene
isofor DEXSeq DifferentialSplicing
11 months ago nick_brittain55 • 0
0
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0
replies
409
views
Error while performing DEXseq
DEXSeq
11 months ago vipul14 • 0
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
0
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0
replies
433
views
DEXSeq Subsetting pre or post dispersion calculation?
DEXSeq
14 months ago Ben J • 0
0
votes
2
replies
922
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
15 months ago Ben J • 0
1
vote
15
replies
3.5k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 17 months ago by • 0 • written 7.1 years ago by • 0
0
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0
replies
589
views
DESXSEQ warning (Fit for gene/exon ENSG0000002121 threw the next warning(s): the matrix is either rank-deficient or indefinite)?
DEXSeq
updated 17 months ago by 42k • written 17 months ago by • 0
0
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1
reply
815
views
plotDEXSeq error?
DEXSeq dex
18 months ago • updated 17 months ago barrypraveen • 0
1
vote
4
replies
957
views
DEXseq batch removal
DEXSeq
updated 19 months ago by ★ 1.9k • written 19 months ago by ▴ 10
0
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0
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431
views
DEXSeq: mcols(dxd)$fullBetaConv either contains TRUE or NA
DEXSeq
20 months ago Matthias Munz ▴ 10
1
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2
replies
2.0k
views
DEXseq error unable to find an inherited method for function NSBS for signature CompressedIntegerList
Dexseq
updated 21 months ago by ▴ 10 • written 4.8 years ago by ▴ 10
0
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0
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515
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
21 months ago osieman52 • 0
1
vote
2
replies
842
views
DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscript out of bounds"
DEXSeq
21 months ago Delta._.43 ▴ 20
0
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1
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865
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
24 months ago • updated 23 months ago NIK • 0
0
votes
4
replies
1.5k
views
DEXSeq: samples$sample_id %in% colnames(counts) is not TRUE
DEXSeq DRIMSeq
updated 24 months ago by ▴ 90 • written 2.0 years ago by • 0
3
votes
2
replies
966
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
0
votes
5
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2.0k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 5.1 years ago by • 0
1
vote
1
reply
664
views
Increased number of exons in DEXSeq
DEXSeq exon
updated 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
1
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2
replies
884
views
Normalizing exonic reads and then log transforming or variance stabilising
DEXSeq
2.5 years ago • updated 2.3 years ago A ▴ 40
1
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1
reply
1.1k
views
DTU using DEXSeq (time series data with condition factor)
DTU DEXSeq RNADTU
updated 2.3 years ago by ★ 1.9k • written 2.7 years ago by ▴ 10
0
votes
1
reply
859
views
DEXSeq prepare annotation script throws "object has no attribute 'next'" for Ensemble GTFs
DEXSeq
updated 2.3 years ago by ★ 1.9k • written 2.6 years ago by • 0
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
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
2
votes
7
replies
1.3k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
2.7 years ago rbenel ▴ 40
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
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
votes
0
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844
views
DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
2.8 years ago Matthias Munz ▴ 10
0
votes
0
replies
646
views
Disabling aggregation with the option -r no, still combines genes into single “aggregate genes"
DEXSeq
2.8 years ago n.tear ▴ 20
0
votes
0
replies
649
views
DEXSeq: Error in perGeneQValue with a single gene
DEXSeq
2.9 years ago Matthias Munz ▴ 10
1
vote
6
replies
1.6k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 2.9 years ago by ▴ 120 • written 3.1 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
0
votes
0
replies
885
views
Error generating counts df for use with DRIMSeq/DEXseq
DRIMSeq DEXSeq
3.1 years ago jbono ▴ 10
0
votes
2
replies
1.0k
views
DRIMSeq + dmFilter
DEXSeq DRIMSeq
3.2 years ago Gaia • 0
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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
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