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DESeq2 multiple groups comparison issues, incorrect log2FC results in a small proportion of genes
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shepherl
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shepherl
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ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
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Johannes Rainer
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4.8 years ago • updated 4.7 years ago
kayla.interdonato
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News:
Final List of Deprecated Packages for Bioc3.11
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updated 4.8 years ago by
kayla.interdonato
▴ 160 • written 4.9 years ago by
shepherl
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4.8 years ago
kayla.interdonato
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Thomas Maurel
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News:
Bioconductor 3.11 is Released!
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4.8 years ago
shepherl
4.1k
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News:
BridgeDb build fails due to website unavailability
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5.2 years ago • updated 4.8 years ago
egon.willighagen
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News:
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4.8 years ago
shepherl
4.1k
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News:
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4.8 years ago
Martin Morgan
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News:
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4.8 years ago
shepherl
4.1k
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News:
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4.8 years ago
Matthew Ritchie
▴ 1000
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News:
New Package and New Docker Image Submission Deadline for Bioc Release 3.11
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4.9 years ago
shepherl
4.1k
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Comment: Is there a way to do DEG analysis across two batches sharing one sample only?
by
kahunroleh
• 0
Yes, you can perform DEG analysis across two batches with one shared sample by using batch correction methods like ComBat or limma. These t…
Comment: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Martijn
• 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
alexis.weinreb
• 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in
by
James W. MacDonald
67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
jodan
• 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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