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msigdb
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0
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How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
4 weeks ago • updated 29 days ago
Seongsu
• 0
4
votes
3
replies
222
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 6 weeks ago by
Georg
• 0
1
vote
1
reply
618
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 5 months ago by
Robert Castelo
★ 3.3k • written 5 months ago by
snijesh
▴ 20
1
vote
1
reply
1.2k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
forlani.luca
• 0
1
vote
1
reply
1.9k
views
Tutorial:
Update gene symbols in GeneSetCollection
gseabase
msigdb
genesetcollection
Tutorial
written 5.9 years ago by
t.kuilman
▴ 170
2
votes
2
replies
4.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler
GSEA
MSIGDB
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
thomasjenner333
• 0
1
vote
2
replies
1.4k
views
Update to MSigDB derivates for romer()?
limma
romer
msigdb
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
Jon Manning
▴ 40
0
votes
0
replies
1.3k
views
hyperGTest for MSigDB categories
category
gostats
msigdb
hypergeometric test
8.8 years ago
petyuk
▴ 70
8 results • Page
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Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM()
by
James W. MacDonald
65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient
by
JKim
• 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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