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fgsea
•
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0
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0
replies
590
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
10 months ago
GT
• 0
2
votes
2
replies
1.3k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
16 months ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.9k
views
NAs in fgseaMultilevel
fgsea
updated 17 months ago by
alserg
▴ 280 • written 18 months ago by
Danté
• 0
1
vote
13
replies
2.7k
views
Ranking the GSEA Results
fgsea
log2FC
19 months ago • updated 18 months ago
V_Vibes
• 0
0
votes
0
replies
618
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
19 months ago
Tanvi
• 0
4
votes
5
replies
2.1k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
20 months ago
Chris
▴ 20
2
votes
2
replies
1.9k
views
fgsea significant result
fgsea
21 months ago • updated 20 months ago
Chris
▴ 20
4
votes
2
replies
1.9k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
21 months ago • updated 20 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
570
views
Empty table plot using plotGseaTable()
fgsea
21 months ago
Chris
▴ 20
2
votes
4
replies
2.3k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 21 months ago by
Chris
▴ 20
0
votes
8
replies
3.3k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 19 months ago by
alserg
▴ 280 • written 21 months ago by
sropri
• 0
1
vote
5
replies
1.3k
views
fgsea fork
fgsea
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
yimjohns
• 0
0
votes
2
replies
2.1k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
22 months ago
Gordon
• 0
0
votes
5
replies
2.0k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Gordon
• 0
3
votes
2
replies
924
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
2.5 years ago • updated 2.4 years ago
luca.s
▴ 50
0
votes
0
replies
1.3k
views
using fgsea to compare two datasets
GSEA
fgsea
2.5 years ago
Cen
• 0
0
votes
0
replies
2.3k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
2.7 years ago
pg45863
▴ 10
7
votes
6
replies
5.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
nhaus
▴ 70
0
votes
0
replies
771
views
is it possible to limit fgsea to particular tissue type?
fgsea
3.2 years ago
kavator
▴ 30
0
votes
4
replies
1.9k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
3.3 years ago
dario.beraldi
• 0
0
votes
8
replies
3.9k
views
Problem with fgsea
fgsea
updated 19 months ago by
James W. MacDonald
68k • written 3.8 years ago by
Barista
• 0
2
votes
3
replies
6.1k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
4.0 years ago
amir.khan
• 0
0
votes
1
reply
3.8k
views
Tied Ranks in fgsea
fgsea
updated 4.7 years ago by
Guido Hooiveld
★ 4.1k • written 4.7 years ago by
zli1
• 0
2
votes
3
replies
2.8k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 4.7 years ago by
alserg
▴ 280 • written 4.7 years ago by
julie.hardy
• 0
3
votes
3
replies
6.7k
views
Warning with the example of GSEA
fgsea
fgse
4.8 years ago • updated 4.7 years ago
julie.hardy
• 0
2
votes
2
replies
4.1k
views
fgsea usage question - what gene set to use?
fgsea
4.9 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
2.3k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 4.9 years ago by
Kevin Blighe
★ 4.0k • written 4.9 years ago by
yueli7
▴ 20
0
votes
3
replies
3.9k
views
why does stat column disappears after lfcshrink on deseq 2 and why does fgsea uses stat column (not affected by shrinking) for fgsea?
fgsea
DESeq2
updated 4.9 years ago by
ATpoint
★ 5.0k • written 4.9 years ago by
kavator
▴ 30
0
votes
1
reply
1.8k
views
do expression of leading edges within a negative NES term reflect the same direction as it's enrichment score? aka downregulation of leading edges
fgsea
updated 5.6 years ago by
alserg
▴ 280 • written 5.6 years ago by
kavator
▴ 30
1
vote
2
replies
2.4k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 5.6 years ago by
alserg
▴ 280 • written 5.6 years ago by
kavator
▴ 30
3
votes
2
replies
2.3k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 6.7 years ago by
Michael Love
43k • written 6.7 years ago by
coulsonr
▴ 20
8
votes
5
replies
5.3k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
Biologist
▴ 120
0
votes
3
replies
4.6k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
7.5 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.5k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
7.6 years ago
martin.busch
• 0
1
vote
5
replies
3.0k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 8.5 years ago by
alserg
▴ 280 • written 8.5 years ago by
shawn.w.foley
• 0
0
votes
8
replies
3.9k
views
Does fgsea order the stats argument?
fgsea
8.6 years ago
rubi
▴ 110
6
votes
15
replies
4.5k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 8.8 years ago by
willem.ligtenberg
▴ 150 • written 8.8 years ago by
alserg
▴ 280
2
votes
1
reply
2.3k
views
Direction aware fgsea test
fgsea
gsea
updated 9.0 years ago by
alserg
▴ 280 • written 9.0 years ago by
rubi
▴ 110
38 results • Page
1 of 1
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Replies
Comment: Bile acid analysis with limpa
by
ATpoint
★ 5.0k
Wilcox/Mann-Whitney-U cannot work because it is bound to sample size even when all of group X are lower than all of group Y. At 4 vs 3 the …
Comment: chemmineOB install help
by
Jeremy
• 0
I could install ChemmineOB on my MacBook Pro M1 Max using this procedure **1. Install open-babel and eigen using homebrew and create a cus…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Gordon Smyth
53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
• 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
Michael Love
43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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