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geneset
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How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
10 weeks ago
Seongsu
• 0
0
votes
1
reply
962
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 11 months ago by
James W. MacDonald
66k • written 11 months ago by
manuelsokolov
• 0
2
votes
4
replies
2.5k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 3.4 years ago by
Dharmesh D Bhuva
• 0 • written 5.3 years ago by
Pietro
▴ 40
0
votes
0
replies
1.1k
views
Tumor subtype classification when genes of gene set are missing from samples - GSVA approach
GSVA
geneset
RNASeq
TCGA
subtypes
5.4 years ago
Pietro
▴ 40
2
votes
4
replies
1.8k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 6.8 years ago by
Gordon Smyth
51k • written 6.8 years ago by
sup230
▴ 30
1
vote
2
replies
1.5k
views
Question on GeneSetCollection in GSEABase
gseabase
geneset
updated 7.4 years ago by
Martin Morgan
25k • written 7.4 years ago by
siajunren
• 0
0
votes
0
replies
1.4k
views
Problems in building Cummerbundcuff Database
cummerbund
readcufflinks
geneset
8.5 years ago
alessio.stevano
• 0
7 results • Page
1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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