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Splicing
•
reset
1
vote
6
replies
2.1k
views
SGSeq error on analyzeFeatures
SGSeq
analyzeFeatures
Splicing
9.4 years ago • updated 9.3 years ago
Paolo Guarnieri
▴ 20
1
vote
3
replies
1.7k
views
Microarray data analysis for detecting alternative splicing
microarray
splicing
updated 8.2 years ago by
Sonika Tyagi
▴ 20 • written 9.5 years ago by
gv
▴ 40
1
vote
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 4.5 years ago by
Michael Lawrence
★ 11k • written 7.1 years ago by
rasi1983
▴ 10
2
votes
2
replies
1.7k
views
Deseq2 alternative splicing in understudied organism
deseq2
splicing
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
yannickwurm
• 0
0
votes
1
reply
1.1k
views
About CIRI's output
ciri
splicing
splicesites
updated 4.2 years ago by
lhddiallo
• 0 • written 5.9 years ago by
csijst
• 0
0
votes
1
reply
879
views
Can DEXseq be used for splicing QTL analysis?
dexseq
splicing
sqtl
qtl
updated 5.2 years ago by
Alejandro Reyes
★ 1.9k • written 5.3 years ago by
rtunney2
• 0
0
votes
1
reply
491
views
Transcriptome assembly: single individual or pooled samples
transcriptome
splicing
assembly
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Marianna
▴ 20
3
votes
16
replies
2.6k
views
Read counts generated by SGSeq are always 0
sgseq
splicing
alternative splicing
updated 8.2 years ago by
Leonard Goldstein
▴ 180 • written 8.2 years ago by
vakul.mohanty
▴ 10
1
vote
2
replies
1.5k
views
Is it possible to get Isoform-level differential isoform usage form DRIMSeq?
DRIMSeq
splicing
differential isoform usage
updated 7.2 years ago by
Gosia Nowicka
▴ 90 • written 7.2 years ago by
kristoffer.vittingseerup
▴ 20
2
votes
7
replies
2.2k
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger
normalization
differential exon usage
splicing
updated 3.5 years ago by
Yunshun Chen
▴ 840 • written 3.5 years ago by
oakhamwolf
• 0
0
votes
1
reply
214
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
scoops_streams_06
• 0
0
votes
0
replies
1.5k
views
DEXSeq analysis of alternative splicing: error 'SAM optional field tag NH not found'
DEXSeq
splicing
python
SAM
8.5 years ago
Fiona
▴ 70
0
votes
0
replies
678
views
Psichomics Suppa Input issue
psichomics
SUPPA
Splicing
Alternative Splicing
Retained Introns
3.5 years ago
noahhelton98
▴ 20
0
votes
1
reply
823
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 0
0
votes
1
reply
817
views
JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq
splicing
RNAseq
DEXSeq
4.4 years ago
stuart
▴ 10
0
votes
3
replies
1.1k
views
DEXSeq Splicing Result with incomplete lines between exons
DEXSeq
Splicing
Exon Usage
4.2 years ago
gunjan.dikshit
• 0
16 results • Page
1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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