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fgsea
•
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0
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0
replies
418
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
6 months ago
GT
• 0
2
votes
2
replies
1.1k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
13 months ago
Assa Yeroslaviz
★ 1.5k
4
votes
4
replies
1.7k
views
NAs in fgseaMultilevel
fgsea
updated 14 months ago by
alserg
▴ 280 • written 14 months ago by
Danté
• 0
1
vote
13
replies
2.2k
views
Ranking the GSEA Results
fgsea
log2FC
15 months ago • updated 14 months ago
V_Vibes
• 0
0
votes
0
replies
513
views
Filtering the genesets for fgseaMultiLevel
msigdb
fgsea
msig
15 months ago
Tanvi
• 0
4
votes
5
replies
1.9k
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
17 months ago • updated 16 months ago
Chris
▴ 20
2
votes
2
replies
1.6k
views
fgsea significant result
fgsea
17 months ago
Chris
▴ 20
4
votes
2
replies
1.7k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
17 months ago
gene_bioconductor
▴ 10
0
votes
0
replies
493
views
Empty table plot using plotGseaTable()
fgsea
17 months ago
Chris
▴ 20
2
votes
4
replies
2.0k
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 17 months ago by
Chris
▴ 20
0
votes
8
replies
2.5k
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 16 months ago by
alserg
▴ 280 • written 17 months ago by
sropri
• 0
1
vote
5
replies
1.2k
views
fgsea fork
fgsea
updated 18 months ago by
James W. MacDonald
68k • written 18 months ago by
yimjohns
• 0
0
votes
2
replies
1.8k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
18 months ago
Gordon
• 0
0
votes
5
replies
1.7k
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 19 months ago by
James W. MacDonald
68k • written 20 months ago by
Gordon
• 0
3
votes
2
replies
806
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
2.1 years ago
luca.s
▴ 50
0
votes
0
replies
1.2k
views
using fgsea to compare two datasets
GSEA
fgsea
2.2 years ago
Cen
• 0
0
votes
0
replies
2.0k
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
2.4 years ago
pg45863
▴ 10
7
votes
6
replies
4.6k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
nhaus
▴ 70
0
votes
0
replies
688
views
is it possible to limit fgsea to particular tissue type?
fgsea
2.9 years ago
kavator
▴ 30
0
votes
4
replies
1.7k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
3.0 years ago
dario.beraldi
• 0
0
votes
8
replies
3.6k
views
Problem with fgsea
fgsea
updated 15 months ago by
James W. MacDonald
68k • written 3.5 years ago by
Barista
• 0
2
votes
3
replies
5.8k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
3.7 years ago
amir.khan
• 0
0
votes
1
reply
3.6k
views
Tied Ranks in fgsea
fgsea
updated 4.4 years ago by
Guido Hooiveld
★ 4.1k • written 4.4 years ago by
zli1
• 0
2
votes
3
replies
2.6k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 4.4 years ago by
alserg
▴ 280 • written 4.4 years ago by
julie.hardy
• 0
3
votes
3
replies
6.4k
views
Warning with the example of GSEA
fgsea
fgse
4.5 years ago • updated 4.4 years ago
julie.hardy
• 0
2
votes
2
replies
3.8k
views
fgsea usage question - what gene set to use?
fgsea
4.6 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 4.6 years ago by
Kevin Blighe
★ 4.0k • written 4.6 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 4.6 years ago by
ATpoint
★ 4.9k • written 4.6 years ago by
kavator
▴ 30
0
votes
1
reply
1.6k
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 5.3 years ago by
alserg
▴ 280 • written 5.3 years ago by
kavator
▴ 30
1
vote
2
replies
2.3k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 5.3 years ago by
alserg
▴ 280 • written 5.3 years ago by
kavator
▴ 30
3
votes
2
replies
2.1k
views
Calculate S/N ratios from apeglm for GSEA
apeglm
fgsea
Signal-To-Noise Ratio
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
coulsonr
▴ 20
8
votes
5
replies
4.9k
views
How to get t-statistic values using edgeR?
r
edger
t-statistic
fgsea
gsea
updated 6.4 years ago by
Gordon Smyth
53k • written 6.4 years ago by
Biologist
▴ 120
0
votes
3
replies
4.4k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
7.2 years ago
atakanekiz
▴ 30
1
vote
2
replies
2.4k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
7.3 years ago
martin.busch
• 0
1
vote
5
replies
2.8k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 8.2 years ago by
alserg
▴ 280 • written 8.2 years ago by
shawn.w.foley
• 0
0
votes
8
replies
3.7k
views
Does fgsea order the stats argument?
fgsea
8.3 years ago
rubi
▴ 110
6
votes
15
replies
4.2k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 8.5 years ago by
willem.ligtenberg
▴ 150 • written 8.5 years ago by
alserg
▴ 280
2
votes
1
reply
2.2k
views
Direction aware fgsea test
fgsea
gsea
updated 8.7 years ago by
alserg
▴ 280 • written 8.7 years ago by
rubi
▴ 110
38 results • Page
1 of 1
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Replies
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20
by
eja.gaasa2e.r.m
• 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error
by
James W. MacDonald
68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins?
by
Gordon Smyth
53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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