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fgsea
•
reset
0
votes
4
replies
66
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
15 hours ago • updated 13 hours ago
sropri
• 0
1
vote
5
replies
285
views
fgsea fork
fgsea
updated 20 days ago by
James W. MacDonald
65k • written 21 days ago by
yimjohns
• 0
0
votes
2
replies
304
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
27 days ago • updated 16 days ago
Gordon
• 0
0
votes
5
replies
430
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 9 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Gordon
• 0
3
votes
2
replies
371
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
8 months ago
luca.s
▴ 50
0
votes
0
replies
590
views
using fgsea to compare two datasets
GSEA
fgsea
9 months ago
Cen
• 0
0
votes
0
replies
803
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
10 months ago
pg45863
▴ 10
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 15 months ago by
Gordon Smyth
50k • written 16 months ago by
nhaus
▴ 30
0
votes
0
replies
358
views
is it possible to limit fgsea to particular tissue type?
fgsea
17 months ago
kavator
▴ 30
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
18 months ago
dario.beraldi
• 0
0
votes
7
replies
1.8k
views
Problem with fgsea
fgsea
updated 2.1 years ago by
alserg
▴ 240 • written 2.1 years ago by
Barista
• 0
2
votes
3
replies
2.9k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
2.2 years ago
amir.khan
• 0
0
votes
1
reply
2.3k
views
Tied Ranks in fgsea
fgsea
updated 2.9 years ago by
Guido Hooiveld
★ 3.9k • written 2.9 years ago by
zli1
• 0
2
votes
3
replies
1.7k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 3.0 years ago by
alserg
▴ 240 • written 3.0 years ago by
julie.hardy
• 0
3
votes
3
replies
4.0k
views
Warning with the example of GSEA
fgsea
fgse
3.0 years ago
julie.hardy
• 0
2
votes
2
replies
2.2k
views
fgsea usage question - what gene set to use?
fgsea
3.1 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
1.6k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 3.1 years ago by
Kevin Blighe
★ 3.9k • written 3.1 years ago by
yueli7
▴ 20
0
votes
3
replies
2.1k
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 3.2 years ago by
ATpoint
★ 4.0k • written 3.2 years ago by
kavator
▴ 30
0
votes
1
reply
1.0k
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 3.8 years ago by
alserg
▴ 240 • written 3.8 years ago by
kavator
▴ 30
1
vote
2
replies
1.5k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 3.8 years ago by
alserg
▴ 240 • written 3.8 years ago by
kavator
▴ 30
3
votes
2
replies
1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
coulsonr
▴ 20
8
votes
5
replies
3.4k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Biologist
▴ 110
0
votes
3
replies
2.8k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
5.8 years ago
atakanekiz
▴ 30
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.8 years ago
martin.busch
• 0
1
vote
5
replies
2.0k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 6.7 years ago by
alserg
▴ 240 • written 6.7 years ago by
shawn.w.foley
• 0
0
votes
8
replies
2.7k
views
Does fgsea order the stats argument?
fgsea
6.8 years ago
rubi
▴ 110
6
votes
15
replies
2.9k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 7.0 years ago by
willem.ligtenberg
▴ 150 • written 7.0 years ago by
alserg
▴ 240
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea
gsea
updated 7.3 years ago by
alserg
▴ 240 • written 7.3 years ago by
rubi
▴ 110
28 results • Page
1 of 1
Recent ...
Replies
Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
• 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR
by
prity6459
• 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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