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roast
•
reset
1
vote
3
replies
340
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 9 weeks ago by
Jiahao Tian
• 0
3
votes
2
replies
2.0k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 4.9 years ago by
Gordon Smyth
53k • written 4.9 years ago by
prabin.dm
• 0
2
votes
2
replies
2.5k
views
Finding genes in a gene set detected by ROAST (or FRY) in limma
roast
fry
limma
updated 6.3 years ago by
Gordon Smyth
53k • written 6.3 years ago by
kentfung
▴ 20
4
votes
4
replies
2.0k
views
Interpreting mroast results
mroast
limma
roast
6.9 years ago
SB
• 0
1
vote
4
replies
1.7k
views
Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma
roast
statistics
source code
gene set testing
7.2 years ago
Andrea Carenzo
• 0
2
votes
2
replies
2.1k
views
limma roast results not in accordance with barcodeplot
roast
limma
7.5 years ago
b.nota
▴ 370
3
votes
2
replies
1.6k
views
ROAST after edgeR glmTreat and average RPKM filter
roast
edgeR
glmtreat
updated 9.2 years ago by
Aaron Lun
★ 29k • written 9.2 years ago by
b.nota
▴ 370
2
votes
2
replies
1.8k
views
limma roast/mroast with patient-matched pre-/post- treatment
limma
roast
mroast
block
updated 9.3 years ago by
Ryan C. Thompson
★ 7.9k • written 9.3 years ago by
barbara.shih
• 0
2
votes
2
replies
1.6k
views
Running Roast with Gene Symbols of Curated Genes
mroast
roast
gene set
gene set analysis
edgeR
updated 9.4 years ago by
James W. MacDonald
68k • written 9.4 years ago by
lattalic
• 0
0
votes
3
replies
1.9k
views
ROAST using curated gene sets
edgeR
mroast
roast
9.4 years ago
lattalic
• 0
2
votes
1
reply
1.7k
views
limma symbols2indices from gmt files versus rdata files
limma
romer
roast
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
biominer
▴ 10
6
votes
10
replies
2.5k
views
Possible implementation of roast/mroast for testing common DE patterns across two different experiments
gene set testing
roast
mroast
differential gene expression
bioconductor
10.5 years ago
svlachavas
▴ 840
3
votes
4
replies
3.0k
views
edgeR: no replicates & mroast
edger
roast
updated 11.0 years ago by
Gordon Smyth
53k • written 11.0 years ago by
Daniel
▴ 10
4
votes
6
replies
4.6k
views
limma roast syntax and interpretation
limma
roast
updated 11.0 years ago by
Gordon Smyth
53k • written 11.0 years ago by
Juliet Hannah
▴ 360
14 results • Page
1 of 1
Recent ...
Replies
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type
by
Kevin Blighe
★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction
by
Kevin Blighe
★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
Kevin Blighe
★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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