Showing : fgsea • reset
8
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5
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3.5k
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How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 110
0
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8
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2.8k
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Does fgsea order the stats argument?
fgsea
6.9 years ago rubi ▴ 110
4
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5
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320
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
13 days ago • updated 3 days ago Chris ▴ 10
3
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3
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4.2k
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Warning with the example of GSEA
fgsea fgse
3.1 years ago • updated 3.0 years ago julie.hardy • 0
2
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3
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3.0k
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fgsea not downloading due to new r version. Is there a way around this?
r fgsea
2.3 years ago amir.khan • 0
0
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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 ▴ 260 • written 3.9 years ago by ▴ 30
0
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3
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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 ★ 4.1k • written 3.2 years ago by ▴ 30
0
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2
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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 ★ 3.9k • written 3.2 years ago by ▴ 20
2
votes
2
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2.3k
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fgsea usage question - what gene set to use?
fgsea
3.2 years ago alexandr.gopanenko ▴ 50
4
votes
2
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624
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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
2
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1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 260 • written 7.3 years ago by ▴ 110
6
votes
15
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2.9k
views
Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ▴ 260
1
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5
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2.1k
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.8 years ago by ▴ 260 • written 6.8 years ago by • 0
3
votes
2
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1.4k
views
Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.0 years ago by 42k • written 5.0 years ago by ▴ 20
1
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2
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1.5k
views
what does gseaparam argument in fgsea() means?
fgsea
updated 3.9 years ago by ▴ 260 • written 3.9 years ago by ▴ 30
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 17 months ago by ▴ 30
0
votes
4
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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
2
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372
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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
0
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4
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224
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
4 weeks ago sropri • 0
2
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2
replies
228
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fgsea significant result
fgsea
14 days ago • updated 13 days ago Chris ▴ 10
2
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3
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1.8k
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Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 3.0 years ago by ▴ 260 • written 3.0 years ago by • 0
0
votes
5
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532
views
Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 3 months ago by 65k • written 3 months ago by • 0
3
votes
2
replies
402
views
cant' download fgsea_1.20.0.tar.gz
download fgsea
9 months ago luca.s ▴ 50
2
votes
2
replies
235
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
19 days ago Chris ▴ 10
0
votes
1
reply
2.4k
views
Tied Ranks in fgsea
fgsea
updated 3.0 years ago by ★ 4.0k • written 3.0 years ago by • 0
0
votes
0
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139
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Empty table plot using plotGseaTable()
fgsea
17 days ago • updated 15 days ago Chris ▴ 10
0
votes
0
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382
views
is it possible to limit fgsea to particular tissue type?
fgsea
18 months ago kavator ▴ 30
0
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0
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640
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using fgsea to compare two datasets
GSEA fgsea
10 months ago Cen • 0
0
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3
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2.9k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.8 years ago atakanekiz ▴ 30
1
vote
5
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366
views
fgsea fork
fgsea
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
1
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2
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1.8k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
0
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0
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868
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
0
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7
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1.9k
views
Problem with fgsea
fgsea
updated 2.1 years ago by ▴ 260 • written 2.1 years ago by • 0
33 results • Page 1 of 1
Recent ...
Replies
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!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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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