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fgsea
•
reset
3
votes
3
replies
4.2k
views
Warning with the example of GSEA
fgsea
fgse
3.1 years ago • updated 3.0 years ago
julie.hardy
• 0
8
votes
5
replies
3.5k
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
2
votes
3
replies
3.0k
views
fgsea not downloading due to new r version. Is there a way around this?
r
fgsea
2.3 years ago
amir.khan
• 0
6
votes
15
replies
2.9k
views
Change in pathway IDs scheme in reactome.db
reactome.db
fgsea
updated 7.1 years ago by
willem.ligtenberg
▴ 150 • written 7.1 years ago by
alserg
▴ 260
0
votes
3
replies
2.9k
views
fgsea p-values are mostly the same upon analysis
fgsea
gsea
sc-rnaseq
5.8 years ago
atakanekiz
▴ 30
0
votes
8
replies
2.8k
views
Does fgsea order the stats argument?
fgsea
6.9 years ago
rubi
▴ 110
0
votes
1
reply
2.4k
views
Tied Ranks in fgsea
fgsea
updated 3.0 years ago by
Guido Hooiveld
★ 4.0k • written 3.0 years ago by
zli1
• 0
2
votes
2
replies
2.3k
views
fgsea usage question - what gene set to use?
fgsea
3.2 years ago
alexandr.gopanenko
▴ 50
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler
GSEA
fgsea
updated 16 months ago by
Gordon Smyth
50k • written 17 months ago by
nhaus
▴ 30
0
votes
3
replies
2.2k
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
★ 4.1k • written 3.2 years ago by
kavator
▴ 30
1
vote
5
replies
2.1k
views
FGSEA only runs with <1000 permutations
fgsea
gsea
updated 6.8 years ago by
alserg
▴ 260 • written 6.8 years ago by
shawn.w.foley
• 0
0
votes
7
replies
1.9k
views
Problem with fgsea
fgsea
updated 2.1 years ago by
alserg
▴ 260 • written 2.1 years ago by
Barista
• 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.9 years ago
martin.busch
• 0
2
votes
3
replies
1.8k
views
Compute fgsea with my own database with R version 4.0.2
R
fgsea
updated 3.0 years ago by
alserg
▴ 260 • written 3.0 years ago by
julie.hardy
• 0
0
votes
2
replies
1.7k
views
Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 3.2 years ago by
Kevin Blighe
★ 3.9k • written 3.2 years ago by
yueli7
▴ 20
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea
gsea
updated 7.3 years ago by
alserg
▴ 260 • written 7.3 years ago by
rubi
▴ 110
1
vote
2
replies
1.5k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 3.9 years ago by
alserg
▴ 260 • written 3.9 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 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
coulsonr
▴ 20
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt
GO
ensembldb
fgsea
19 months ago
dario.beraldi
• 0
0
votes
1
reply
1.1k
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 3.9 years ago by
alserg
▴ 260 • written 3.9 years ago by
kavator
▴ 30
0
votes
0
replies
868
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff
clusterProfiler
fgsea
11 months ago
pg45863
▴ 10
0
votes
0
replies
640
views
using fgsea to compare two datasets
GSEA
fgsea
10 months ago
Cen
• 0
4
votes
2
replies
627
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
16 days ago • updated 12 days ago
gene_bioconductor
▴ 10
0
votes
5
replies
532
views
Help with DESeq results to pathways with the fgsea package
fgsea
rna
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Gordon
• 0
3
votes
2
replies
403
views
cant' download fgsea_1.20.0.tar.gz
download
fgsea
9 months ago
luca.s
▴ 50
0
votes
0
replies
382
views
is it possible to limit fgsea to particular tissue type?
fgsea
18 months ago
kavator
▴ 30
0
votes
2
replies
372
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
8 weeks ago • updated 6 weeks ago
Gordon
• 0
1
vote
5
replies
368
views
fgsea fork
fgsea
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
yimjohns
• 0
4
votes
5
replies
327
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
13 days ago • updated 3 days ago
Chris
▴ 10
2
votes
2
replies
236
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago
Chris
▴ 10
2
votes
2
replies
229
views
fgsea significant result
fgsea
14 days ago • updated 13 days ago
Chris
▴ 10
0
votes
4
replies
224
views
FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago
sropri
• 0
0
votes
0
replies
140
views
Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago
Chris
▴ 10
33 results • Page
1 of 1
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Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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