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Showing :
fgsea
•
reset
2
votes
2
replies
622
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
8 weeks ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
739
views
NAs in fgseaMultilevel
fgsea
updated 3 months ago by
alserg
▴ 280 • written 3 months ago by
Danté
• 0
1
vote
13
replies
1.1k
views
Ranking the GSEA Results
fgsea
log2FC
4 months ago • updated 3 months ago
V_Vibes
• 0
0
votes
0
replies
274
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
4 months ago
Tanvi
• 0
4
votes
5
replies
924
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
6 months ago • updated 5 months ago
Chris
▴ 20
2
votes
2
replies
812
views
fgsea significant result
fgsea
6 months ago
Chris
▴ 20
4
votes
2
replies
1.0k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
6 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
281
views
Empty table plot using plotGseaTable()
fgsea
6 months ago
Chris
▴ 20
2
votes
2
replies
654
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
6 months ago
Chris
▴ 20
0
votes
8
replies
1.2k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 4 months ago by
alserg
▴ 280 • written 6 months ago by
sropri
• 0
1
vote
5
replies
697
views
fgsea fork
fgsea
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
yimjohns
• 0
0
votes
2
replies
866
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
7 months ago
Gordon
• 0
0
votes
5
replies
973
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 8 months ago by
James W. MacDonald
67k • written 9 months ago by
Gordon
• 0
3
votes
2
replies
574
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
15 months ago • updated 14 months ago
luca.s
▴ 50
0
votes
0
replies
866
views
using fgsea to compare two datasets
GSEA
fgsea
15 months ago
Cen
• 0
0
votes
0
replies
1.4k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
17 months ago
pg45863
▴ 10
7
votes
6
replies
2.9k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 22 months ago by
Gordon Smyth
51k • written 23 months ago by
nhaus
▴ 70
0
votes
0
replies
524
views
is it possible to limit fgsea to particular tissue type?
fgsea
23 months ago
kavator
▴ 30
0
votes
4
replies
1.3k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
2.1 years ago
dario.beraldi
• 0
0
votes
8
replies
2.4k
views
Problem with fgsea
fgsea
updated 4 months ago by
James W. MacDonald
67k • written 2.6 years ago by
Barista
• 0
2
votes
3
replies
3.7k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
2.8 years ago
amir.khan
• 0
0
votes
1
reply
2.9k
views
Tied Ranks in fgsea
fgsea
updated 3.5 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
zli1
• 0
2
votes
3
replies
2.2k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 3.5 years ago by
alserg
▴ 280 • written 3.5 years ago by
julie.hardy
• 0
3
votes
3
replies
5.1k
views
Warning with the example of GSEA
fgsea
fgse
3.6 years ago • updated 3.5 years ago
julie.hardy
• 0
2
votes
2
replies
2.8k
views
fgsea usage question - what gene set to use?
fgsea
3.7 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
1.9k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
yueli7
▴ 20
0
votes
3
replies
2.5k
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 3.7 years ago by
ATpoint
★ 4.5k • written 3.7 years ago by
kavator
▴ 30
0
votes
1
reply
1.3k
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 4.4 years ago by
alserg
▴ 280 • written 4.4 years ago by
kavator
▴ 30
1
vote
2
replies
1.8k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 4.4 years ago by
alserg
▴ 280 • written 4.4 years ago by
kavator
▴ 30
3
votes
2
replies
1.7k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
coulsonr
▴ 20
8
votes
5
replies
4.1k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.5 years ago by
Gordon Smyth
51k • written 5.5 years ago by
Biologist
▴ 120
0
votes
3
replies
3.4k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
6.3 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.4 years ago
martin.busch
• 0
1
vote
5
replies
2.4k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 7.3 years ago by
alserg
▴ 280 • written 7.3 years ago by
shawn.w.foley
• 0
0
votes
8
replies
3.2k
views
Does fgsea order the stats argument?
fgsea
7.4 years ago
rubi
▴ 110
6
votes
15
replies
3.4k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 7.6 years ago by
willem.ligtenberg
▴ 150 • written 7.6 years ago by
alserg
▴ 280
2
votes
1
reply
1.8k
views
Direction aware fgsea test
fgsea
gsea
updated 7.8 years ago by
alserg
▴ 280 • written 7.8 years ago by
rubi
▴ 110
37 results • Page
1 of 1
Recent ...
Replies
Comment: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
by
Ai
• 0
Hi Gordon, Thank you so much for answering my question and confirming that this is expected! I will go ahead note this down. Sincerely, …
Answer: Annotation for EPICv2
by
icecreamlover
• 0
Hello, I am also working on analyzing my data from EPICv2 using ChAMP. I used this resource as a guide: https://github.com/YuanTian1991/ChA…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
And it doesn't matter if you're doing gene set analyses after, if the statistics are questionable to begin with.
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
James W. MacDonald
67k
If you're saying that (as an example) you have treated and control in both assay types, and you want to combine and make comparisons betwee…
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
I have contacted NCBI, and meanwhile got an an answer. See below. It turns out that the official, HGNC-approved symbols are present in the…
Votes
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Answer: DecideTest vs topTAGs in edgeR
Comment: DESeq Input from Salmon + tximport/tximeta
Comment: DESeq Input from Salmon + tximport/tximeta
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