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glmGamPoi
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4
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1.5k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2
independentfiltering
glmGamPoi
15 months ago • updated 14 months ago
Bob
▴ 30
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 16 months ago by
Gordon Smyth
53k • written 16 months ago by
Alec
• 0
1
vote
3
replies
1.0k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
20 months ago
I-Hsuan Lin
▴ 10
8
votes
7
replies
3.1k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2
glmGamPoi
DEXSeq
updated 2.4 years ago by
alexandresegers
▴ 20 • written 3.0 years ago by
jeremymsimon
▴ 20
1
vote
1
reply
2.6k
views
Instaling glmGamPoi
glmGamPoi
updated 3.0 years ago by
ATpoint
★ 5.0k • written 3.0 years ago by
sina.tadayon
• 0
0
votes
3
replies
1.9k
views
Can't install packages due to '503 Service Unavailable'
glmGamPoi
BiocManager
updated 3.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 3.0 years ago by
i.am.filippov
• 0
5
votes
4
replies
3.3k
views
Using DESeq2 with GlmGamPoi
DESeq2
glmGamPoi
scRNAseq
4.7 years ago • updated 4.6 years ago
tatyana.perlova
• 0
7 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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