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fgsea
•
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0
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0
replies
60
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
5 days ago
GT
• 0
2
votes
2
replies
867
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
6 months ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.2k
views
NAs in fgseaMultilevel
fgsea
updated 7 months ago by
alserg
▴ 280 • written 7 months ago by
Danté
• 0
1
vote
13
replies
1.6k
views
Ranking the GSEA Results
fgsea
log2FC
8 months ago
V_Vibes
• 0
0
votes
0
replies
402
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
9 months ago
Tanvi
• 0
4
votes
5
replies
1.4k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
10 months ago
Chris
▴ 20
2
votes
2
replies
1.2k
views
fgsea significant result
fgsea
10 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
10 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
370
views
Empty table plot using plotGseaTable()
fgsea
10 months ago
Chris
▴ 20
2
votes
4
replies
1.5k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 10 months ago by
Chris
▴ 20
0
votes
8
replies
1.8k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 9 months ago by
alserg
▴ 280 • written 11 months ago by
sropri
• 0
1
vote
5
replies
933
views
fgsea fork
fgsea
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
yimjohns
• 0
0
votes
2
replies
1.4k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
12 months ago • updated 11 months ago
Gordon
• 0
0
votes
5
replies
1.3k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Gordon
• 0
3
votes
2
replies
675
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
19 months ago
luca.s
▴ 50
0
votes
0
replies
1.0k
views
using fgsea to compare two datasets
GSEA
fgsea
20 months ago
Cen
• 0
0
votes
0
replies
1.7k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
22 months ago
pg45863
▴ 10
7
votes
6
replies
3.9k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.2 years ago by
Gordon Smyth
52k • written 2.3 years ago by
nhaus
▴ 70
0
votes
0
replies
599
views
is it possible to limit fgsea to particular tissue type?
fgsea
2.3 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
2.5 years ago
dario.beraldi
• 0
0
votes
8
replies
3.1k
views
Problem with fgsea
fgsea
updated 9 months ago by
James W. MacDonald
68k • written 3.0 years ago by
Barista
• 0
2
votes
3
replies
4.9k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
3.1 years ago
amir.khan
• 0
0
votes
1
reply
3.3k
views
Tied Ranks in fgsea
fgsea
updated 3.9 years ago by
Guido Hooiveld
★ 4.1k • written 3.9 years ago by
zli1
• 0
2
votes
3
replies
2.4k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 3.9 years ago by
alserg
▴ 280 • written 3.9 years ago by
julie.hardy
• 0
3
votes
3
replies
5.7k
views
Warning with the example of GSEA
fgsea
fgse
3.9 years ago
julie.hardy
• 0
2
votes
2
replies
3.3k
views
fgsea usage question - what gene set to use?
fgsea
4.0 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
2.0k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
yueli7
▴ 20
0
votes
3
replies
2.8k
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 4.1 years ago by
ATpoint
★ 4.7k • written 4.1 years ago by
kavator
▴ 30
0
votes
1
reply
1.4k
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 4.7 years ago by
alserg
▴ 280 • written 4.7 years ago by
kavator
▴ 30
1
vote
2
replies
2.0k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 4.8 years ago by
alserg
▴ 280 • written 4.8 years ago by
kavator
▴ 30
3
votes
2
replies
1.9k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
coulsonr
▴ 20
8
votes
5
replies
4.5k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
Biologist
▴ 120
0
votes
3
replies
3.8k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
6.7 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.8 years ago
martin.busch
• 0
1
vote
5
replies
2.6k
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
3.4k
views
Does fgsea order the stats argument?
fgsea
7.8 years ago
rubi
▴ 110
6
votes
15
replies
3.7k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 7.9 years ago by
willem.ligtenberg
▴ 150 • written 7.9 years ago by
alserg
▴ 280
2
votes
1
reply
1.9k
views
Direction aware fgsea test
fgsea
gsea
updated 8.2 years ago by
alserg
▴ 280 • written 8.2 years ago by
rubi
▴ 110
38 results • Page
1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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