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fgsea
•
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0
votes
0
replies
465
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
8 months ago
GT
• 0
2
votes
2
replies
1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
15 months ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.7k
views
NAs in fgseaMultilevel
fgsea
updated 16 months ago by
alserg
▴ 280 • written 16 months ago by
Danté
• 0
1
vote
13
replies
2.4k
views
Ranking the GSEA Results
fgsea
log2FC
17 months ago • updated 16 months ago
V_Vibes
• 0
0
votes
0
replies
560
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
17 months ago
Tanvi
• 0
4
votes
5
replies
2.0k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
19 months ago
Chris
▴ 20
2
votes
2
replies
1.6k
views
fgsea significant result
fgsea
19 months ago
Chris
▴ 20
4
votes
2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
19 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
540
views
Empty table plot using plotGseaTable()
fgsea
19 months ago
Chris
▴ 20
2
votes
4
replies
2.1k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 19 months ago by
Chris
▴ 20
0
votes
8
replies
2.7k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 18 months ago by
alserg
▴ 280 • written 19 months ago by
sropri
• 0
1
vote
5
replies
1.2k
views
fgsea fork
fgsea
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
yimjohns
• 0
0
votes
2
replies
1.9k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
20 months ago
Gordon
• 0
0
votes
5
replies
1.8k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Gordon
• 0
3
votes
2
replies
856
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
2.3 years ago
luca.s
▴ 50
0
votes
0
replies
1.2k
views
using fgsea to compare two datasets
GSEA
fgsea
2.4 years ago
Cen
• 0
0
votes
0
replies
2.1k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
2.5 years ago
pg45863
▴ 10
7
votes
6
replies
4.7k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.9 years ago by
Gordon Smyth
53k • written 3.0 years ago by
nhaus
▴ 70
0
votes
0
replies
730
views
is it possible to limit fgsea to particular tissue type?
fgsea
3.1 years ago
kavator
▴ 30
0
votes
4
replies
1.8k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
3.2 years ago
dario.beraldi
• 0
0
votes
8
replies
3.8k
views
Problem with fgsea
fgsea
updated 17 months ago by
James W. MacDonald
68k • written 3.7 years ago by
Barista
• 0
2
votes
3
replies
5.9k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
3.9 years ago
amir.khan
• 0
0
votes
1
reply
3.7k
views
Tied Ranks in fgsea
fgsea
updated 4.6 years ago by
Guido Hooiveld
★ 4.1k • written 4.6 years ago by
zli1
• 0
2
votes
3
replies
2.7k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 4.6 years ago by
alserg
▴ 280 • written 4.6 years ago by
julie.hardy
• 0
3
votes
3
replies
6.5k
views
Warning with the example of GSEA
fgsea
fgse
4.6 years ago
julie.hardy
• 0
2
votes
2
replies
3.9k
views
fgsea usage question - what gene set to use?
fgsea
4.8 years ago
alexandr.gopanenko
▴ 50
0
votes
2
replies
2.2k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
yueli7
▴ 20
0
votes
3
replies
3.7k
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 4.8 years ago by
ATpoint
★ 5.0k • written 4.8 years ago by
kavator
▴ 30
0
votes
1
reply
1.7k
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 5.4 years ago by
alserg
▴ 280 • written 5.4 years ago by
kavator
▴ 30
1
vote
2
replies
2.3k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 5.5 years ago by
alserg
▴ 280 • written 5.5 years ago by
kavator
▴ 30
3
votes
2
replies
2.2k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
coulsonr
▴ 20
8
votes
5
replies
5.1k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 6.6 years ago by
Gordon Smyth
53k • written 6.6 years ago by
Biologist
▴ 120
0
votes
3
replies
4.5k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
7.4 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.4k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
7.5 years ago
martin.busch
• 0
1
vote
5
replies
2.9k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 8.4 years ago by
alserg
▴ 280 • written 8.4 years ago by
shawn.w.foley
• 0
0
votes
8
replies
3.8k
views
Does fgsea order the stats argument?
fgsea
8.5 years ago
rubi
▴ 110
6
votes
15
replies
4.3k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 8.6 years ago by
willem.ligtenberg
▴ 150 • written 8.6 years ago by
alserg
▴ 280
2
votes
1
reply
2.2k
views
Direction aware fgsea test
fgsea
gsea
updated 8.9 years ago by
alserg
▴ 280 • written 8.9 years ago by
rubi
▴ 110
38 results • Page
1 of 1
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Hervé Pagès
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▴ 30
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James W. MacDonald
68k
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4.2k
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