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Ballgown
•
reset
1
vote
1
reply
1.9k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 8.0 years ago by
k.vitting.seerup
▴ 120 • written 8.1 years ago by
amy16
• 0
0
votes
1
reply
2.2k
views
Ballgown with replicates and the adjustvars option
ballgown
rnaseq
differential gene expression
updated 8.1 years ago by
Alyssa Frazee
▴ 210 • written 8.3 years ago by
o.diogosilva
• 0
2
votes
0
replies
1.3k
views
p-values, q-values, duplicated entries in output - ballgown
ballgown
rna-seq
q value
r
8.2 years ago
mkhasin
▴ 20
0
votes
1
reply
3.4k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq
ballgown
updated 8.3 years ago by
Alyssa Frazee
▴ 210 • written 8.3 years ago by
vinayjrao
• 0
1
vote
7
replies
2.5k
views
Ballgown object construction error
ballgown
scan
error
package
8.5 years ago
spaque57
• 0
0
votes
0
replies
1.1k
views
Discordant Differential Expression
ballgown
8.5 years ago
lindsaynhayes
• 0
1
vote
3
replies
2.3k
views
limma regularization on Ballgown
ballgown
limma
updated 8.5 years ago by
Alyssa Frazee
▴ 210 • written 8.5 years ago by
rodri2006
▴ 10
0
votes
1
reply
2.2k
views
P value <0.05 and Q values~ 1
ballgown
updated 8.5 years ago by
Jeff Leek
▴ 650 • written 8.5 years ago by
akilabioinfo
• 0
3
votes
5
replies
8.0k
views
Ballgown up and down regulated genes
ballgown
differential expression
updated 8.6 years ago by
kapeelc
• 0 • written 9.9 years ago by
psbpedrobarbosa
▴ 10
0
votes
4
replies
2.3k
views
Results with very few genes with qval <0.05
ballgown
updated 8.7 years ago by
aiwa
• 0 • written 8.8 years ago by
jdchc
• 0
2
votes
8
replies
6.7k
views
StringTie + Ballgown: handling biological replicates
ballgown
stringtie
updated 8.8 years ago by
linda.boshans
• 0 • written 9.8 years ago by
bhawley1991
▴ 10
0
votes
0
replies
1.5k
views
Please help with ballgown problem
ballgown
differential expression
8.8 years ago
Sara
▴ 20
0
votes
2
replies
1.7k
views
IRanges error loading rsem data into ballgown
ballgown
updated 8.8 years ago by
Jeff Leek
▴ 650 • written 8.8 years ago by
jchenpku
• 0
0
votes
8
replies
4.6k
views
The common error with ballgown has not been solved!
ballgown
software error
updated 8.8 years ago by
Jeff Leek
▴ 650 • written 8.8 years ago by
Sara
▴ 20
1
vote
7
replies
4.2k
views
How fold change is calculated in Ballgown?
ballgown
8.9 years ago
Ir
• 0
0
votes
2
replies
2.8k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown
rna-seq
updated 8.9 years ago by
Alyssa Frazee
▴ 210 • written 8.9 years ago by
Ir
• 0
0
votes
3
replies
2.5k
views
Error in ball gown command
rnaseq
ballgown
differential gene expression
updated 9.0 years ago by
Jeff Leek
▴ 650 • written 9.0 years ago by
kritikamish99
▴ 10
2
votes
5
replies
4.6k
views
processing data with 2 rep or one replicate by ballgown
ballgown
differential gene expression
updated 9.1 years ago by
Alyssa Frazee
▴ 210 • written 9.2 years ago by
boyashuang
• 0
0
votes
2
replies
2.2k
views
I'm worried that I can't use "ballgown" well
ballgown
rnaseq
updated 9.1 years ago by
James W. MacDonald
68k • written 9.1 years ago by
noset2769
• 0
1
vote
3
replies
1.8k
views
Interaction term analysis using ballgown
ballgown
stringtie
voom limma
differential gene expression
rnaseq
updated 9.2 years ago by
Alyssa Frazee
▴ 210 • written 9.2 years ago by
jcalis
▴ 10
2
votes
2
replies
1.4k
views
Ballgown Custom Model Question
ballgown
rnaseq
updated 9.3 years ago by
Jeff Leek
▴ 650 • written 9.3 years ago by
daniel.gaston
• 0
0
votes
4
replies
2.4k
views
Ballgown from StringTie results transcripts which are not expressed in both conditions as Differentially expressed ones
ballgown
stringtie
updated 9.4 years ago by
Jeff Leek
▴ 650 • written 9.4 years ago by
alva.james
• 0
2
votes
7
replies
3.8k
views
ballgown custom models
ballgown
linear model
model matrix
custom model
9.7 years ago • updated 9.6 years ago
sbcn
▴ 80
0
votes
1
reply
2.5k
views
trying to use ballgown with Sailfish/Salmon pipeline
rnaseq
multi-mapped reads
ballgown
salmon
timecourse
10.4 years ago
friederike.mgh
• 0
3
votes
3
replies
2.2k
views
Specifying a Default Model in Ballgown
ballgown
updated 10.5 years ago by
Alyssa Frazee
▴ 210 • written 10.5 years ago by
andrea.hodgins.davis
• 0
75 results • Page
2 of 2
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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