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MSIGDB
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reset
0
votes
2
replies
167
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How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
25 days ago • updated 24 days ago
Seongsu
• 0
4
votes
3
replies
211
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 5 weeks ago by
Georg
• 0
1
vote
1
reply
600
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea
GSVA
biotype
proteincoding
msigdb
updated 4 months ago by
Robert Castelo
★ 3.3k • written 4 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 5.8 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
8.7 years ago
petyuk
▴ 70
8 results • Page
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Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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