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seqgsea
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1.2k
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Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
5.6 years ago
kentfung
▴ 20
0
votes
1
reply
1.1k
views
install SeqGSEA problem
seqgsea
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
jial2
• 0
0
votes
1
reply
1.3k
views
accounting for gene length with SeqGSEA
goseq
SeqGSEA
goseq
SeqGSEA
updated 9.2 years ago by
Xi Wang
• 0 • written 11.7 years ago by
Julie Leonard
▴ 110
0
votes
3
replies
2.1k
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Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 10.9 years ago by
Steve Lianoglou
★ 13k • written 10.9 years ago by
Leif Väremo
▴ 70
0
votes
5
replies
3.7k
views
Running the GSEA algorithm
Infrastructure
PGSEA
GSEABase
SeqGSEA
Infrastructure
PGSEA
GSEABase
SeqGSEA
updated 10.9 years ago by
Julian Gehring
★ 1.3k • written 10.9 years ago by
enricoferrero
▴ 680
5 results • Page
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Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `ntd()` or `vst/…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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