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stringtie
•
reset
2
votes
3
replies
1.5k
views
how to get the lastest version of tximport
tximport
stringtie
6.2 years ago • updated 6.0 years ago
matrs
▴ 10
2
votes
1
reply
1.7k
views
How to change stringtie gene_id names with ref_gene_id when performing featureCount
featureCount
rna-seq
gene_id
re_gene_id
stringtie
updated 5.3 years ago by
Wei Shi
★ 3.6k • written 5.3 years ago by
IRAIA.MAIALEN
• 0
2
votes
8
replies
5.7k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 7.2 years ago by
linda.boshans
• 0 • written 8.2 years ago by
bhawley1991
▴ 10
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
amy16
• 0
1
vote
3
replies
1.4k
views
Interaction term analysis using ballgown
ballgown
stringtie
voom limma
differential gene expression
rnaseq
updated 7.6 years ago by
Alyssa Frazee
▴ 210 • written 7.6 years ago by
jcalis
▴ 10
0
votes
1
reply
4.4k
views
Usage of prepDE.py with stringtie and deseq2
prepDE
STRINGTIE
deseq2
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
Nancy
▴ 10
0
votes
4
replies
1.3k
views
tximport and its version
tximport
stringtie
RNA-seq analysis
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
Mithil Gaikwad
• 0
0
votes
3
replies
3.5k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2
StringTie
RNA-seq
normalisation
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
JindrichK
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
lakshmi9c
• 0
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform
RNA-seq
hisat2
stringtie
ballgown
3.6 years ago
ra711
• 0
0
votes
0
replies
282
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 5 months ago by
James W. MacDonald
65k • written 5 months ago by
sumitra.20
• 0
0
votes
1
reply
726
views
How to make the data compatible for DESeq2?
DESeq2
TPM
rawcounts
StringTie
updated 20 months ago by
Michael Love
41k • written 20 months ago by
snijesh
▴ 20
0
votes
4
replies
1.8k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown
stringtie
updated 7.8 years ago by
Jeff Leek
▴ 650 • written 7.8 years ago by
alva.james
• 0
0
votes
7
replies
2.5k
views
Handling both technical and biological replicates in Ballgown
ballgown
biologicalreplicates
technical replicates
stringtie
updated 6.4 years ago by
Alyssa Frazee
▴ 210 • written 7.2 years ago by
linda.boshans
• 0
0
votes
0
replies
1.8k
views
RNA-seq with hisat2+stringtie+ballgown
hisat2
stringtie
ballgown
RNAseq
6.2 years ago • updated 6.0 years ago
Nancy
▴ 10
0
votes
0
replies
1.4k
views
Ballgown data processing error
Ballgown
Stringtie
DEG
rnaseq
6.0 years ago
vharshavardhanan
• 0
16 results • Page
1 of 1
Recent ...
Replies
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!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
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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