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DEXseq
•
reset
5
votes
18
replies
2.2k
views
Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq
bitseq
cuffdiff
Differential exon usage
isoforms
7.8 years ago • updated 7.7 years ago
elle
▴ 10
0
votes
5
replies
1.3k
views
DEXSeq - counts from paired reads and unpaired singletons
dexseq
written 4.0 years ago by
maslane
• 0
2
votes
10
replies
2.0k
views
Undefined log2Foldchanges within DEXSeq for significantly regulated exons
DEXSeq
8.1 years ago
n.kreim
▴ 20
1
vote
15
replies
2.4k
views
DEXSeq: Error in FUN(X[[i]], ...) : subscript out of bounds
dexseq
updated 3 months ago by
Zhuqiang
• 0 • written 5.9 years ago by
cpsosa0006
• 0
0
votes
5
replies
1.7k
views
DEXSeq - Error in estimateSizeFactorsForMatrix(featureCounts(object)
DEXSeq
DESeq2
dexseq
deseq2
alternative splicing
7.5 years ago
Fahmi Nazarie
• 0
0
votes
5
replies
1.5k
views
DEXSeq output "Gene Model"
dexseq
7.9 years ago
atisou
• 0
1
vote
4
replies
1.3k
views
DEXSeqDataSet example code
DEXSeq
updated 7.3 years ago by
zb.picb
• 0 • written 7.3 years ago by
pensona
▴ 10
0
votes
6
replies
1.0k
views
Where is DEXSeq bioconductor package?
DEXSeq
DEXSeq
updated 11.7 years ago by
Simon Anders
★ 3.7k • written 11.7 years ago by
Fabrice Tourre
▴ 970
1
vote
6
replies
3.1k
views
DEXSeq: question about usage coefficient and splicing plot
dexseq
updated 2.4 years ago by
rohitsatyam102
▴ 20 • written 8.0 years ago by
ywu
• 0
0
votes
5
replies
2.1k
views
NA in padj in the DEXSeq package
dexseq
padj
7.2 years ago
gil.hornung
• 0
2
votes
4
replies
1.2k
views
DEXSeqHTML doesn't creates plots
dexseq
DEXSeqHTML
data representation in graphical forms
warning message
7.3 years ago
Assa Yeroslaviz
★ 1.5k
0
votes
13
replies
2.5k
views
Efficiently running DEXSeq for Large Cohorts
DEXSeq
DEXSeq
updated 7.7 years ago by
rahel14350
▴ 10 • written 10.2 years ago by
Fong Chun Chan
▴ 320
1
vote
4
replies
1.1k
views
problems running DEXseq
DEXSeq
DEXSeq
updated 9.7 years ago by
Steve Lianoglou
13k • written 9.7 years ago by
Diya
▴ 10
2
votes
6
replies
2.8k
views
DEXSeq Error in lf[[1]] : subscript out of bounds
DEXSeq
7.7 years ago
rahel14350
▴ 10
1
vote
4
replies
1.7k
views
DEXSeq continous variable in model
RNASeq
TimeCourse
timecourse
DEXSeq
DESeq2
RNASeq
TimeCourse
timecourse
DEXSeq
DESeq2
updated 8.6 years ago by
Alejandro Reyes
★ 1.8k • written 8.6 years ago by
Alex Gutteridge
▴ 650
1
vote
6
replies
901
views
Differential Transcript Usage: complex factorial design
edgeR
DEXSeq
IsoformSwitchAnalyzeR
DTU
updated 21 months ago by
k.vitting.seerup
▴ 120 • written 23 months ago by
jbono
▴ 10
1
vote
23
replies
1.6k
views
Sample label swap in HTML results
dexseq
dexseqhtml
updated 5.7 years ago by
Alejandro Reyes
★ 1.8k • written 5.7 years ago by
maximinio
• 0
15
votes
6
replies
2.5k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 6.6 years ago by
Charity Law
▴ 90 • written 6.6 years ago by
maltethodberg
▴ 160
1
vote
14
replies
2.1k
views
DEXSeq - dexseq_count.py issue
dexseq
dexseq_count
genomicfeatures
updated 4.9 years ago by
hazards
• 0 • written 5.0 years ago by
marija.durdevic
• 0
1
vote
2
replies
957
views
DEXSeq. Error: could not find function "DEXSeqDataSetFromHTSeq"
dexseq
6.9 years ago
peter.thorpe
• 0
0
votes
9
replies
1.4k
views
Where is DEXSeq bioconductor package?
DEXSeq
DEXSeq
updated 11.6 years ago by
Sean Davis
21k • written 11.6 years ago by
Jinyan Huang
▴ 190
1
vote
6
replies
1.5k
views
Error: could not find function "HTSeqCounts"
HTSeq
HTSeqCounts
Could not find function
DEXSeq
updated 6.9 years ago by
Martin Morgan
25k • written 6.9 years ago by
sakura.nussbaum
▴ 10
1
vote
2
replies
840
views
DEXseq for alternate promoter usage
dexseq
promoter
utr
updated 6.8 years ago by
Alejandro Reyes
★ 1.8k • written 6.8 years ago by
joan.hooper
• 0
3
votes
2
replies
2.5k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 4.7 years ago by
Gordon Smyth
47k • written 4.7 years ago by
jennyl.smith12
• 0
0
votes
2
replies
1.2k
views
DEXSeq package
DEXSeq
DEXSeq
updated 11.5 years ago by
Wolfgang Huber
13k • written 11.5 years ago by
Liu,Bin
▴ 50
0
votes
2
replies
1.2k
views
Using Rscript to run DEXSeq on Linux cluster
DEXSeq
DEXSeq
updated 11.3 years ago by
Wolfgang Huber
13k • written 11.3 years ago by
Christopher T Gregg
▴ 210
1
vote
3
replies
998
views
DEXSeqHTML filenames gone wrong
dexseq
updated 7.3 years ago by
Alejandro Reyes
★ 1.8k • written 7.8 years ago by
jannetta.steyn
▴ 10
6
votes
4
replies
1.7k
views
Problem running dexseq in parallel using BiocParallel
dexseq
updated 6.0 years ago by
s.w.vanderlaan
▴ 30 • written 6.0 years ago by
forestylake
▴ 20
0
votes
2
replies
1.2k
views
DEXSeq: How to get expresion value for each exon?
DEXSeq
7.8 years ago
Peter
• 0
0
votes
5
replies
1.3k
views
deqseq_count and BWA-based SAM files
convert
DEXSeq
convert
DEXSeq
updated 11.3 years ago by
Shona Wood
▴ 70 • written 11.3 years ago by
Guest User
★ 12k
1
vote
6
replies
1.1k
views
Eliminating minor exon bins from DEXSeq / associated python scripts
dexseq
deseq2
7.6 years ago
np
▴ 10
2
votes
3
replies
1.3k
views
DEXSeq for DE of antisense transcription
dexseq
antisense
updated 8.4 years ago by
Wolfgang Huber
13k • written 8.4 years ago by
Alex Gutteridge
▴ 650
0
votes
2
replies
9.1k
views
deseq2: convert ensembl ID to gene symbol.
DEXSeq
DESeq2
DEXSeq
DESeq2
updated 4.6 years ago by
hamidreza_moazzeni20
• 0 • written 8.6 years ago by
Fabrice Tourre
▴ 970
0
votes
2
replies
744
views
install previous version of DEXSeq (1.6.0)
DEXSeq
DEXSeq
updated 8.8 years ago by
Mallon, Eamonn B. Dr.
▴ 120 • written 8.8 years ago by
Guest User
★ 12k
2
votes
5
replies
1.2k
views
DEXSeq update results change
Sequencing
DESeq
DEXSeq
Sequencing
DESeq
DEXSeq
8.6 years ago
António Miguel de Jesus Domingues
▴ 490
1
vote
4
replies
824
views
DEXSeq count differential exons
dexseq
7.2 years ago
jarod_v6@libero.it
▴ 40
0
votes
2
replies
1.0k
views
DEXSeq error during fold change calculation
Alignment
DEXSeq
Alignment
DEXSeq
updated 11.0 years ago by
Wolfgang Huber
13k • written 11.0 years ago by
Guest User
★ 12k
0
votes
8
replies
1.9k
views
DEXSeq - too many exons in gene
Sequencing
Annotation
DEXSeq
Sequencing
Annotation
DEXSeq
updated 9.1 years ago by
Steve Lianoglou
13k • written 9.1 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
3
replies
950
views
multifactorial analysis
DEXSeq
DEXSeq
updated 11.0 years ago by
Gordon Smyth
47k • written 11.0 years ago by
Andreia Fonseca
▴ 810
0
votes
3
replies
3.9k
views
p-value vs adjusted p-value in DEXSeq
DEXSeq
DEXSeq
updated 9.8 years ago by
Simon Anders
★ 3.7k • written 9.8 years ago by
Delasa Aghamirzaie
▴ 70
0
votes
3
replies
1.5k
views
dexseq_count.py SAM "NH" taq
DEXSeq
DEXSeq
9.1 years ago
Jose M Garcia Manteiga
▴ 310
3
votes
2
replies
947
views
How to calculate "This" and "Others" exons in DEXseq
dexseq
updated 8.3 years ago by
Alejandro Reyes
★ 1.8k • written 8.3 years ago by
Sindre
▴ 70
0
votes
5
replies
867
views
A few Q's on using DEXSeq with mucho data
Cancer
DEXSeq
Cancer
DEXSeq
updated 11.0 years ago by
Simon Anders
★ 3.7k • written 11.0 years ago by
Steve Lianoglou
13k
0
votes
6
replies
1.2k
views
DEXseq: fitDispersionFunction error
DEXSeq
DEXSeq
updated 11.1 years ago by
Alejandro Reyes
★ 1.8k • written 11.1 years ago by
Elena Sorokin
▴ 150
0
votes
3
replies
1.6k
views
Query about DEXSeq
dexseq
batch effect
PCA
7.5 years ago
n.deshpande
• 0
0
votes
9
replies
1.4k
views
DEXSeq many exons marked as not testable
DEXSeq
DEXSeq
updated 10.5 years ago by
Stefan Dentro
▴ 10 • written 10.5 years ago by
Stefan Dentro
▴ 70
0
votes
6
replies
1.1k
views
DEXSeq for 1 gene
DEXSeq
DEXSeq
updated 9.8 years ago by
Alejandro Reyes
★ 1.8k • written 9.8 years ago by
Mallon, Eamonn B. Dr.
▴ 120
2
votes
3
replies
1.8k
views
dexseq_count.py 'SAM optional field tag NH not found'
dexseq
updated 7.0 years ago by
juls.jaeger
• 0 • written 7.3 years ago by
Dimitra Alexopoulou
▴ 30
0
votes
2
replies
807
views
a question in merging sam files for DEXSeq
DEXSeq
DEXSeq
updated 9.8 years ago by
Simon Anders
★ 3.7k • written 9.8 years ago by
chunjiang he
▴ 80
0
votes
3
replies
1.7k
views
dexseq read.HTSeqCounts error
DEXSeq
DEXSeq
updated 8.9 years ago by
Alejandro Reyes
★ 1.8k • written 8.9 years ago by
Rao,Xiayu
▴ 550
50 results • Page
1 of 1
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Replies
Comment: KEGG enrichment in R and gene IDs
by
Laia
▴ 10
I could finally solve this and I could get KEGG results :) Thank you so much for your help and quick replies. Best, Laia
Comment: KEGG enrichment in R and gene IDs
by
James W. MacDonald
62k
This part is the main issue. ``` ‘GOSemSim’ 2.22.0 is already loaded, but >= 2.23.1 is required ``` You should restart R and then re-insta…
Comment: Correct script for featurecounts in Rsubread
by
rmoorehe
• 0
Thanks for the help. I was able to work through it using the bioconductor link. For some reason, I thought I had to create a new tab delimi…
Comment: DispEsts plot
by
Michael Love
39k
Are the pairs nested within batch or across?
Comment: KEGG enrichment in R and gene IDs
by
Laia
▴ 10
I managed installing the 3.16 version of BiocManager. R said there were 91 packages to be updated, so I did. However, some warning messages…
Votes
Comment: RUVr batch correction doubling number of DEGs
Comment: RUVr batch correction doubling number of DEGs
Answer: RUVr batch correction doubling number of DEGs
A: LogFC: how do you determine the cutoff for differentially expressed genes?
Confused about design for RNA seq experiment
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