Showing : DEXseq • reset
0
votes
31
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5.2k
views
Error in find DEXSeq package
deseq dexseq
9.9 years ago engr.yahya602 • 0
1
vote
23
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3.0k
views
Sample label swap in HTML results
dexseq dexseqhtml
updated 7.7 years ago by ★ 1.9k • written 7.7 years ago by • 0
5
votes
18
replies
3.9k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
9.8 years ago • updated 9.7 years ago elle ▴ 10
1
vote
15
replies
4.2k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 2.3 years ago by • 0 • written 7.9 years ago by • 0
1
vote
15
replies
4.1k
views
junction.bed to GTF to use in DEXSeq
junction.bed DEXSeq
updated 9.6 years ago by ▴ 370 • written 9.6 years ago by ▴ 10
1
vote
14
replies
3.8k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 6.9 years ago by • 0 • written 7.0 years ago by • 0
0
votes
13
replies
3.5k
views
Efficiently running DEXSeq for Large Cohorts
DEXSeq DEXSeq
updated 9.7 years ago by ▴ 10 • written 12.2 years ago by ▴ 320
0
votes
12
replies
3.6k
views
Error in strsplit() : non-character argument - using DEXSeq
dexseq_count DEXSeqDataSetFromHTSeq DEXSeq strsplit
updated 8.9 years ago by ▴ 20 • written 8.9 years ago by ▴ 10
0
votes
12
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2.8k
views
problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI DESeq DEXSeq GUI DESeq DEXSeq
updated 12.9 years ago by ▴ 60 • written 12.9 years ago by ▴ 370
8
votes
12
replies
4.3k
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 9 months ago by ▴ 30 • written 2.9 years ago by ▴ 380
0
votes
11
replies
2.0k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU DRIMseq DEXseq rna-seq
6.0 years ago saddamhusain77 • 0
0
votes
11
replies
2.2k
views
DEXSeq- ExonCountSet
DEXSeq DEXSeq
11.0 years ago Anitha Sundararajan ▴ 140
2
votes
10
replies
3.0k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
10.1 years ago n.kreim ▴ 20
0
votes
9
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2.0k
views
DEXSeq: Error running dexseq_prepare_annotation.py
dexseq
updated 6.7 years ago by ★ 1.9k • written 6.7 years ago by • 0
0
votes
9
replies
1.8k
views
DEXSeq - identical p-values for all exons in a gene
DEXSeq DEXSeq
updated 11.2 years ago by ★ 13k • written 11.2 years ago by ★ 13k
0
votes
9
replies
2.0k
views
Where is DEXSeq bioconductor package?
DEXSeq DEXSeq
updated 13.6 years ago by 21k • written 13.6 years ago by ▴ 190
0
votes
9
replies
2.3k
views
DEXSeq many exons marked as not testable
DEXSeq DEXSeq
updated 12.5 years ago by ▴ 10 • written 12.5 years ago by ▴ 70
0
votes
8
replies
2.8k
views
DEXSeq - too many exons in gene
Sequencing Annotation DEXSeq Sequencing Annotation DEXSeq
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 510
0
votes
8
replies
2.5k
views
DEXSeqHTML Output Trouble
dexseq dexseqhtml
9.0 years ago skasowitz • 0
0
votes
8
replies
1.7k
views
No significant hits!
dexseq
updated 8.6 years ago by ★ 1.9k • written 8.7 years ago by • 0
1
vote
7
replies
3.7k
views
DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
dexseq gtf gff reference genome
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
2
votes
7
replies
2.1k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq dexseq
updated 8.1 years ago by ★ 1.9k • written 8.1 years ago by • 0
6
votes
7
replies
2.1k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq DESeq2
updated 4.3 years ago by 43k • written 4.4 years ago by ▴ 20
0
votes
7
replies
2.4k
views
htseq and dexseq
DEXSeq DEXSeq
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ▴ 810
2
votes
7
replies
1.7k
views
Fold Change for rnaseq DTU
DEXSeq rnaseqDTU
3.6 years ago • updated 3.5 years ago rbenel ▴ 40
0
votes
7
replies
3.2k
views
How to retrieve exon ID and gene ID from exon coordinates?
RNASeq DEXSeq RNASeq DEXSeq
updated 12.5 years ago by 68k • written 12.5 years ago by ▴ 340
0
votes
7
replies
2.5k
views
Detecting differential usage of introns from RNA-seq data.
DEXSeq DEXSeq
updated 12.1 years ago by ★ 1.9k • written 12.1 years ago by ▴ 320
0
votes
7
replies
2.7k
views
DEXSeqHTML getListElement GRanges error
dexseq software error bug
updated 6.3 years ago by ▴ 140 • written 6.4 years ago by • 0
4
votes
7
replies
2.0k
views
assigning differential exons to trascripts
dexseq rsem differential exon usage differential gene expression
updated 8.7 years ago by 68k • written 8.7 years ago by ★ 1.5k
8
votes
7
replies
2.6k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 20 months ago by ▴ 20 • written 2.4 years ago by ▴ 20
0
votes
7
replies
4.3k
views
DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or indefinite
dexseq estimateexonfoldchanges
updated 9.0 years ago by ★ 1.9k • written 9.0 years ago by ▴ 20
0
votes
6
replies
1.6k
views
DEXSeq error with estimateExonFoldChanges
software error dexseq R
7.5 years ago Chen • 0
5
votes
6
replies
2.7k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 9.4 years ago by ★ 1.9k • written 9.4 years ago by ▴ 110
1
vote
6
replies
1.8k
views
Eliminating minor exon bins from DEXSeq / associated python scripts
dexseq deseq2
9.6 years ago np ▴ 10
0
votes
6
replies
2.2k
views
DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
dexseq
8.0 years ago badribio • 0
0
votes
6
replies
1.8k
views
DEXSeq for 1 gene
DEXSeq DEXSeq
updated 11.8 years ago by ★ 1.9k • written 11.8 years ago by ▴ 120
0
votes
6
replies
1.7k
views
Where is DEXSeq bioconductor package?
DEXSeq DEXSeq
updated 13.7 years ago by ★ 3.8k • written 13.7 years ago by ▴ 970
3
votes
6
replies
3.8k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 9.0 years ago by ★ 1.9k • written 9.0 years ago by • 0
0
votes
6
replies
2.0k
views
DEXSeq dispersion outlier
DEXSeq dispersion pvalue
5.9 years ago fiona.dick91 ▴ 60
1
vote
6
replies
2.3k
views
Error: could not find function "HTSeqCounts"
HTSeq HTSeqCounts Could not find function DEXSeq
updated 8.9 years ago by 25k • written 8.9 years ago by ▴ 10
16
votes
6
replies
3.8k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 8.6 years ago by ▴ 90 • written 8.6 years ago by ▴ 180
2
votes
6
replies
1.6k
views
estimateDispersions calculation for > 500,000 exons for 2 conditions taking forever
deseq2 dexseq
5.9 years ago gv ▴ 40
6
votes
6
replies
2.8k
views
Kallisto output with DEXSeq
dexseq kallisto NH_tag
updated 6.5 years ago by ★ 1.9k • written 6.5 years ago by • 0
0
votes
6
replies
1.8k
views
DEXSeq output - count file
Annotation limma DEXSeq Annotation limma DEXSeq
updated 11.0 years ago by ▴ 310 • written 11.0 years ago by ★ 1.9k
0
votes
6
replies
1.8k
views
DEXseq: fitDispersionFunction error
DEXSeq DEXSeq
updated 13.1 years ago by ★ 1.9k • written 13.1 years ago by ▴ 160
2
votes
6
replies
3.7k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
9.7 years ago rahel14350 ▴ 10
0
votes
6
replies
1.6k
views
DEXseq error on estimatelog2FoldChanges
DEXSeq DEXSeq
11.1 years ago Fabrice Tourre ▴ 970
1
vote
6
replies
4.6k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 4.4 years ago by ▴ 20 • written 10.0 years ago by • 0
1
vote
6
replies
1.6k
views
How to install DEXSeq on R 3.4.4
DEXSEq Linux
updated 5.9 years ago by ★ 1.9k • written 5.9 years ago by ▴ 10
2
votes
6
replies
3.4k
views
featureCount error - cannot identify gene_id
dexseq rsubread featureCount software error
updated 5.3 years ago by ▴ 450 • written 5.3 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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