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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
880
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
216
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
818
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
Recent ...
Replies
Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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