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fgsea
•
reset
0
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0
replies
168
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
5 weeks ago
GT
• 0
2
votes
2
replies
938
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
7 months ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.4k
views
NAs in fgseaMultilevel
fgsea
updated 8 months ago by
alserg
▴ 280 • written 8 months ago by
Danté
• 0
1
vote
13
replies
1.8k
views
Ranking the GSEA Results
fgsea
log2FC
10 months ago • updated 9 months ago
V_Vibes
• 0
0
votes
0
replies
434
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
10 months ago
Tanvi
• 0
4
votes
5
replies
1.5k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
11 months ago
Chris
▴ 20
2
votes
2
replies
1.3k
views
fgsea significant result
fgsea
11 months ago
Chris
▴ 20
4
votes
2
replies
1.4k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
11 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
395
views
Empty table plot using plotGseaTable()
fgsea
11 months ago
Chris
▴ 20
2
votes
4
replies
1.6k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 11 months ago by
Chris
▴ 20
0
votes
8
replies
2.0k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 10 months ago by
alserg
▴ 280 • written 12 months ago by
sropri
• 0
1
vote
5
replies
1.0k
views
fgsea fork
fgsea
updated 12 months ago by
James W. MacDonald
68k • written 13 months ago by
yimjohns
• 0
0
votes
2
replies
1.5k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
13 months ago • updated 12 months ago
Gordon
• 0
0
votes
5
replies
1.4k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Gordon
• 0
3
votes
2
replies
691
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
20 months ago
luca.s
▴ 50
0
votes
0
replies
1.1k
views
using fgsea to compare two datasets
GSEA
fgsea
21 months ago
Cen
• 0
0
votes
0
replies
1.8k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
23 months ago
pg45863
▴ 10
7
votes
6
replies
4.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.3 years ago by
Gordon Smyth
52k • written 2.4 years ago by
nhaus
▴ 70
0
votes
0
replies
617
views
is it possible to limit fgsea to particular tissue type?
fgsea
2.4 years ago
kavator
▴ 30
0
votes
4
replies
1.5k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
2.6 years ago
dario.beraldi
• 0
0
votes
8
replies
3.2k
views
Problem with fgsea
fgsea
updated 10 months ago by
James W. MacDonald
68k • written 3.1 years ago by
Barista
• 0
2
votes
3
replies
5.2k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
3.2 years ago
amir.khan
• 0
0
votes
1
reply
3.4k
views
Tied Ranks in fgsea
fgsea
updated 4.0 years ago by
Guido Hooiveld
★ 4.1k • written 4.0 years ago by
zli1
• 0
2
votes
3
replies
2.5k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 4.0 years ago by
alserg
▴ 280 • written 4.0 years ago by
julie.hardy
• 0
3
votes
3
replies
5.9k
views
Warning with the example of GSEA
fgsea
fgse
4.0 years ago
julie.hardy
• 0
2
votes
2
replies
3.4k
views
fgsea usage question - what gene set to use?
fgsea
4.1 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
2.1k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 4.2 years ago by
Kevin Blighe
★ 4.0k • written 4.2 years ago by
yueli7
▴ 20
0
votes
3
replies
2.9k
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 4.2 years ago by
ATpoint
★ 4.8k • written 4.2 years ago by
kavator
▴ 30
0
votes
1
reply
1.5k
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 4.8 years ago by
alserg
▴ 280 • written 4.8 years ago by
kavator
▴ 30
1
vote
2
replies
2.1k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 4.9 years ago by
alserg
▴ 280 • written 4.9 years ago by
kavator
▴ 30
3
votes
2
replies
2.0k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 6.0 years ago by
Michael Love
43k • written 6.0 years ago by
coulsonr
▴ 20
8
votes
5
replies
4.6k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
Biologist
▴ 120
0
votes
3
replies
3.9k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
6.8 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.2k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.9 years ago
martin.busch
• 0
1
vote
5
replies
2.7k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 7.7 years ago by
alserg
▴ 280 • written 7.7 years ago by
shawn.w.foley
• 0
0
votes
8
replies
3.5k
views
Does fgsea order the stats argument?
fgsea
7.8 years ago
rubi
▴ 110
6
votes
15
replies
3.8k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 8.0 years ago by
willem.ligtenberg
▴ 150 • written 8.0 years ago by
alserg
▴ 280
2
votes
1
reply
2.0k
views
Direction aware fgsea test
fgsea
gsea
updated 8.3 years ago by
alserg
▴ 280 • written 8.3 years ago by
rubi
▴ 110
38 results • Page
1 of 1
Recent ...
Replies
Comment: How to convert transcript counts to gene counts in R?
by
ben
• 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open!
by
Ali
• 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets
by
Gordon Smyth
52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install
by
Szabolcs
• 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0
by
Kinnary
▴ 20
Thank you very much for the vis suggestion!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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Gordon Smyth
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shepherl
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Szabolcs
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Mengjun
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James W. MacDonald
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