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DEXSeq
•
reset
0
votes
31
replies
4.3k
views
Error in find DEXSeq package
deseq
dexseq
9.0 years ago
engr.yahya602
• 0
1
vote
23
replies
2.4k
views
Sample label swap in HTML results
dexseq
dexseqhtml
updated 6.8 years ago by
Alejandro Reyes
★ 1.9k • written 6.8 years ago by
maximinio
• 0
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
1
vote
15
replies
3.5k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 16 months ago by
Zhuqiang
• 0 • written 7.0 years ago by
cpsosa0006
• 0
1
vote
15
replies
3.5k
views
junction.bed to GTF to use in DEXSeq
junction.bed
DEXSeq
updated 8.8 years ago by
andrew.j.skelton73
▴ 370 • written 8.8 years ago by
rahel14350
▴ 10
1
vote
14
replies
3.2k
views
DEXSeq - dexseq_count.py issue
dexseq
dexseq_count
genomicfeatures
updated 6.0 years ago by
hazards
• 0 • written 6.2 years ago by
marija.durdevic
• 0
0
votes
13
replies
3.2k
views
Efficiently running DEXSeq for Large Cohorts
DEXSeq
DEXSeq
updated 8.8 years ago by
rahel14350
▴ 10 • written 11.3 years ago by
Fong Chun Chan
▴ 320
0
votes
12
replies
2.4k
views
problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI
DESeq
DEXSeq
GUI
DESeq
DEXSeq
updated 12.0 years ago by
Yue Li
▴ 60 • written 12.0 years ago by
Yue Li
▴ 370
0
votes
12
replies
3.0k
views
Error in strsplit() : non-character argument - using DEXSeq
dexseq_count
DEXSeqDataSetFromHTSeq
DEXSeq
strsplit
updated 8.0 years ago by
aditi
▴ 20 • written 8.0 years ago by
sakura.nussbaum
▴ 10
6
votes
11
replies
3.0k
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 13 months ago by
EChambers
• 0 • written 2.0 years ago by
Matthew Thornton
▴ 350
0
votes
11
replies
1.6k
views
Issue during transcript variant analysis using rnaseqDTU-DRIMseq-DEXseq.
rnaseqDTU
DRIMseq
DEXseq
rna-seq
5.1 years ago
saddamhusain77
• 0
0
votes
11
replies
1.9k
views
DEXSeq- ExonCountSet
DEXSeq
DEXSeq
10.1 years ago
Anitha Sundararajan
▴ 140
2
votes
10
replies
2.6k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
9.2 years ago
n.kreim
▴ 20
0
votes
9
replies
1.6k
views
DEXSeq: Error running dexseq_prepare_annotation.py
dexseq
updated 5.8 years ago by
Alejandro Reyes
★ 1.9k • written 5.8 years ago by
suzanne11
• 0
0
votes
9
replies
1.4k
views
DEXSeq - identical p-values for all exons in a gene
DEXSeq
DEXSeq
updated 10.3 years ago by
Steve Lianoglou
★ 13k • written 10.3 years ago by
Guest User
★ 13k
0
votes
9
replies
1.7k
views
Where is DEXSeq bioconductor package?
DEXSeq
DEXSeq
updated 12.8 years ago by
Sean Davis
21k • written 12.8 years ago by
Jinyan Huang
▴ 190
0
votes
9
replies
1.9k
views
DEXSeq many exons marked as not testable
DEXSeq
DEXSeq
updated 11.6 years ago by
Stefan Dentro
▴ 10 • written 11.6 years ago by
Stefan Dentro
▴ 70
0
votes
8
replies
2.4k
views
DEXSeq - too many exons in gene
Sequencing
Annotation
DEXSeq
Sequencing
Annotation
DEXSeq
updated 10.2 years ago by
Steve Lianoglou
★ 13k • written 10.2 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
8
replies
2.1k
views
DEXSeqHTML Output Trouble
dexseq
dexseqhtml
8.1 years ago
skasowitz
• 0
0
votes
8
replies
1.4k
views
No significant hits!
dexseq
updated 7.8 years ago by
Alejandro Reyes
★ 1.9k • written 7.8 years ago by
saudpabita
• 0
1
vote
7
replies
3.1k
views
DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
dexseq
gtf
gff
reference genome
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
greg.mulhearn
• 0
2
votes
7
replies
1.8k
views
Is possible to apply 'svaseq' with 'DEXSeq' design in order to remove unknown batch effects ?
svaseq
dexseq
updated 7.2 years ago by
Alejandro Reyes
★ 1.9k • written 7.2 years ago by
tofukaj
• 0
6
votes
7
replies
1.7k
views
Strategy to perform DESeq, DEXSeq workflow
DEXSeq
DESeq2
updated 3.4 years ago by
Michael Love
41k • written 3.5 years ago by
rohitsatyam102
▴ 20
0
votes
7
replies
2.1k
views
htseq and dexseq
DEXSeq
DEXSeq
updated 10.9 years ago by
Steve Lianoglou
★ 13k • written 10.9 years ago by
Andreia Fonseca
▴ 810
2
votes
7
replies
1.3k
views
Fold Change for rnaseq DTU
DEXSeq
rnaseqDTU
2.7 years ago
rbenel
▴ 40
0
votes
7
replies
2.9k
views
How to retrieve exon ID and gene ID from exon coordinates?
RNASeq
DEXSeq
RNASeq
DEXSeq
updated 11.7 years ago by
James W. MacDonald
65k • written 11.7 years ago by
ying chen
▴ 340
0
votes
7
replies
2.1k
views
Detecting differential usage of introns from RNA-seq data.
DEXSeq
DEXSeq
updated 11.2 years ago by
Alejandro Reyes
★ 1.9k • written 11.2 years ago by
Fong Chun Chan
▴ 320
0
votes
7
replies
2.2k
views
DEXSeqHTML getListElement GRanges error
dexseq
software error
bug
updated 5.5 years ago by
nitesh.turaga
▴ 140 • written 5.5 years ago by
Lance Parsons
• 0
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
James W. MacDonald
65k • written 7.9 years ago by
Assa Yeroslaviz
★ 1.5k
8
votes
7
replies
1.8k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 10 months ago by
alexandresegers
▴ 20 • written 18 months ago by
jeremymsimon
▴ 20
0
votes
7
replies
3.7k
views
DEXSeq Error in estimateExonFoldChanges: the matrix is either rank-deficient or indefinite
dexseq
estimateexonfoldchanges
updated 8.1 years ago by
Alejandro Reyes
★ 1.9k • written 8.1 years ago by
aditi
▴ 20
0
votes
6
replies
1.4k
views
DEXSeq error with estimateExonFoldChanges
software error
dexseq
R
6.6 years ago
Chen
• 0
5
votes
6
replies
2.3k
views
Translating model formula from DESeq to DEXSeq
dexseq
linear model
formula
updated 8.5 years ago by
Alejandro Reyes
★ 1.9k • written 8.5 years ago by
Cornwell, Adam
▴ 110
1
vote
6
replies
1.5k
views
Eliminating minor exon bins from DEXSeq / associated python scripts
dexseq
deseq2
8.7 years ago
np
▴ 10
0
votes
6
replies
1.9k
views
DEXSeq Error in FUN(X[[i]], ...) : subscript out of bounds not sure why
dexseq
7.1 years ago
badribio
• 0
0
votes
6
replies
1.5k
views
DEXSeq for 1 gene
DEXSeq
DEXSeq
updated 10.9 years ago by
Alejandro Reyes
★ 1.9k • written 11.0 years ago by
Mallon, Eamonn B. Dr.
▴ 120
0
votes
6
replies
1.4k
views
Where is DEXSeq bioconductor package?
DEXSeq
DEXSeq
updated 12.8 years ago by
Simon Anders
★ 3.7k • written 12.8 years ago by
Fabrice Tourre
▴ 970
3
votes
6
replies
3.5k
views
DEXSeq Error: unable to find an inherited method for function ‘mcols’ for signature ‘"matrix"’
DEXSeq
updated 8.1 years ago by
Alejandro Reyes
★ 1.9k • written 8.1 years ago by
MedwayC
• 0
0
votes
6
replies
1.6k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
5.0 years ago
fiona.dick91
▴ 60
1
vote
6
replies
1.9k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 8.0 years ago by
Martin Morgan
25k • written 8.0 years ago by
sakura.nussbaum
▴ 10
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
Charity Law
▴ 90 • written 7.8 years ago by
maltethodberg
▴ 180
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
6
votes
6
replies
2.2k
views
Kallisto output with DEXSeq
dexseq
kallisto
NH_tag
updated 5.6 years ago by
Alejandro Reyes
★ 1.9k • written 5.6 years ago by
j2h2k2
• 0
0
votes
6
replies
1.6k
views
DEXSeq output - count file
Annotation
limma
DEXSeq
Annotation
limma
DEXSeq
updated 10.1 years ago by
Jose M Garcia Manteiga
▴ 310 • written 10.1 years ago by
Alejandro Reyes
★ 1.9k
0
votes
6
replies
1.5k
views
DEXseq: fitDispersionFunction error
DEXSeq
DEXSeq
updated 12.2 years ago by
Alejandro Reyes
★ 1.9k • written 12.2 years ago by
Elena Sorokin
▴ 150
2
votes
6
replies
3.4k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
8.8 years ago
rahel14350
▴ 10
0
votes
6
replies
1.4k
views
DEXseq error on estimatelog2FoldChanges
DEXSeq
DEXSeq
10.3 years ago
Fabrice Tourre
▴ 970
1
vote
6
replies
4.0k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 3.5 years ago by
rohitsatyam102
▴ 20 • written 9.1 years ago by
ywu
• 0
1
vote
6
replies
1.3k
views
How to install DEXSeq on R 3.4.4
DEXSEq
Linux
updated 5.0 years ago by
Alejandro Reyes
★ 1.9k • written 5.0 years ago by
justinkablan225
• 0
2
votes
6
replies
2.5k
views
featureCount error - cannot identify gene_id
dexseq
rsubread
featureCount
software error
updated 4.4 years ago by
Yang Liao
▴ 380 • written 4.4 years ago by
seung.ho.steven.choi
• 0
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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