Showing : fgsea • reset
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fgsea not downloading due to new r version. Is there a way around this?
r fgsea
2.2 years ago amir.khan • 0
8
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3.4k
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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
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2.7k
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Does fgsea order the stats argument?
fgsea
6.8 years ago rubi ▴ 110
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3
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4.0k
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Warning with the example of GSEA
fgsea fgse
3.0 years ago julie.hardy • 0
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1.5k
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what does gseaparam argument in fgsea() means?
fgsea
updated 3.8 years ago by ▴ 240 • written 3.8 years ago by ▴ 30
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1
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1.0k
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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 3.8 years ago by ▴ 240 • written 3.8 years ago by ▴ 30
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3
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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 ★ 4.0k • written 3.2 years ago by ▴ 30
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2
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Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 20
2
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2
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2.2k
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fgsea usage question - what gene set to use?
fgsea
3.1 years ago alexandr.gopanenko ▴ 50
2
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1
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1.5k
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Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 240 • written 7.3 years ago by ▴ 110
6
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15
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2.9k
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Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 7.0 years ago by ▴ 150 • written 7.0 years ago by ▴ 240
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5
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.7 years ago by ▴ 240 • written 6.7 years ago by • 0
3
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2
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1.4k
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 20
7
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6
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2.1k
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Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 15 months ago by 50k • written 16 months ago by ▴ 30
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4
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1.1k
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GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
18 months ago dario.beraldi • 0
0
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2
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306
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
28 days ago • updated 16 days ago Gordon • 0
0
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4
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76
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
23 hours ago • updated 22 hours ago sropri • 0
2
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3
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1.7k
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Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 3.0 years ago by ▴ 240 • written 3.0 years ago by • 0
0
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5
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430
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 9 weeks ago by 65k • written 10 weeks ago by • 0
3
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371
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cant' download fgsea_1.20.0.tar.gz
download fgsea
8 months ago luca.s ▴ 50
0
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3
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2.8k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.8 years ago atakanekiz ▴ 30
0
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7
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1.8k
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Problem with fgsea
fgsea
updated 2.1 years ago by ▴ 240 • written 2.1 years ago by • 0
0
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1
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2.3k
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Tied Ranks in fgsea
fgsea
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
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0
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358
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is it possible to limit fgsea to particular tissue type?
fgsea
17 months ago kavator ▴ 30
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0
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591
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using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 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
5.8 years ago martin.busch • 0
1
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5
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287
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fgsea fork
fgsea
updated 20 days ago by 65k • written 21 days ago by • 0
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805
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
10 months ago pg45863 ▴ 10
28 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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