Showing : fgsea • reset
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
11 months ago GT • 0
2
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2
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1.4k
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
18 months ago Assa Yeroslaviz ★ 1.5k
4
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4
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2.2k
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NAs in fgseaMultilevel
fgsea
updated 18 months ago by ▴ 280 • written 19 months ago by • 0
1
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13
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3.1k
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Ranking the GSEA Results
fgsea log2FC
20 months ago • updated 19 months ago V_Vibes • 0
0
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0
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688
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Filtering the genesets for fgseaMultiLevel
msigdb fgsea msig
20 months ago Tanvi • 0
4
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5
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2.2k
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
22 months ago • updated 21 months ago Chris ▴ 20
2
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2
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2.2k
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fgsea significant result
fgsea
22 months ago Chris ▴ 20
4
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2
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2.0k
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
22 months ago gene_bioconductor ▴ 10
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597
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Empty table plot using plotGseaTable()
fgsea
22 months ago Chris ▴ 20
2
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4
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2.5k
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 22 months ago by ▴ 20
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8
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3.8k
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 20 months ago by ▴ 280 • written 22 months ago by • 0
1
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5
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1.5k
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fgsea fork
fgsea
updated 23 months ago by 68k • written 23 months ago by • 0
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2
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2.3k
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
23 months ago Gordon • 0
0
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5
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2.2k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 2.0 years ago by 68k • written 2.1 years ago by • 0
3
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2
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975
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cant' download fgsea_1.20.0.tar.gz
download fgsea
2.5 years ago luca.s ▴ 50
0
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0
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1.3k
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using fgsea to compare two datasets
GSEA fgsea
2.6 years ago Cen • 0
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0
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2.6k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
2.8 years ago pg45863 ▴ 10
7
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6
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5.4k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 70
0
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0
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795
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is it possible to limit fgsea to particular tissue type?
fgsea
3.3 years ago kavator ▴ 30
0
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4
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2.0k
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GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
3.4 years ago dario.beraldi • 0
0
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8
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4.0k
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Problem with fgsea
fgsea
updated 20 months ago by 68k • written 3.9 years ago by • 0
2
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3
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6.3k
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fgsea not downloading due to new r version. Is there a way around this?
r fgsea
4.1 years ago amir.khan • 0
0
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1
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3.9k
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Tied Ranks in fgsea
fgsea
updated 4.8 years ago by ★ 4.1k • written 4.8 years ago by • 0
2
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3
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2.9k
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Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 4.8 years ago by ▴ 280 • written 4.8 years ago by • 0
3
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3
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7.0k
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Warning with the example of GSEA
fgsea fgse
4.9 years ago • updated 4.8 years ago julie.hardy • 0
2
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2
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4.3k
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fgsea usage question - what gene set to use?
fgsea
5.0 years ago alexandr.gopanenko ▴ 50
0
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2
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2.4k
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Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 20
0
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3
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3.9k
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 5.0 years ago by ★ 5.0k • written 5.0 years ago by ▴ 30
0
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1
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1.9k
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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 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 30
1
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2
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2.5k
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what does gseaparam argument in fgsea() means?
fgsea
updated 5.7 years ago by ▴ 280 • written 5.7 years ago by ▴ 30
3
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2
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2.4k
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 20
8
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5
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5.4k
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How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 120
0
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3
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4.8k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
7.6 years ago atakanekiz ▴ 30
1
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2
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2.5k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
7.7 years ago martin.busch • 0
1
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5
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3.1k
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 8.6 years ago by ▴ 280 • written 8.6 years ago by • 0
0
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8
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4.0k
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Does fgsea order the stats argument?
fgsea
8.7 years ago rubi ▴ 110
6
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15
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4.7k
views
Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 8.9 years ago by ▴ 150 • written 8.9 years ago by ▴ 280
2
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1
reply
2.4k
views
Direction aware fgsea test
fgsea gsea
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by ▴ 110
38 results • Page 1 of 1
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Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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