Showing : fgsea • reset
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Problem with fgsea
fgsea
updated 7 weeks ago by ▴ 200 • written 7 weeks ago by • 0
2
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3
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360
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fgsea not downloading due to new r version. Is there a way around this?
r fgsea
3 months ago amir.khan • 0
0
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1
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444
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Tied Ranks in fgsea
fgsea
updated 12 months ago by ★ 3.2k • written 12 months ago by • 0
2
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3
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355
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Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 12 months ago by ▴ 200 • written 12 months ago by • 0
3
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3
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641
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Warning with the example of GSEA
fgsea fgse
13 months ago • updated 12 months ago julie.hardy • 0
2
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2
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667
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fgsea usage question - what gene set to use?
fgsea
14 months ago alexandr.gopanenko ▴ 20
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2
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549
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Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 14 months ago by 3.5k • written 14 months ago by ▴ 10
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3
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507
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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 15 months ago by ★ 1.2k • written 15 months ago by ▴ 20
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1
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349
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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 23 months ago by ▴ 200 • written 23 months ago by ▴ 20
1
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2
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446
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what does gseaparam argument in fgsea() means?
fgsea
updated 23 months ago by ▴ 200 • written 23 months ago by ▴ 20
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2
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515
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 3.0 years ago by 36k • written 3.0 years ago by ▴ 10
8
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5
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1.6k
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How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 3.0 years ago by 45k • written 3.0 years ago by ▴ 90
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3
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1.2k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
3.8 years ago atakanekiz ▴ 30
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2
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1.0k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
3.9 years ago martin.busch • 0
1
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5
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1.3k
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 4.8 years ago by ▴ 200 • written 4.8 years ago by • 0
0
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8
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1.6k
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Does fgsea order the stats argument?
fgsea
4.9 years ago rubi ▴ 100
6
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15
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1.6k
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Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 200
2
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1
reply
923
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Direction aware fgsea test
fgsea gsea
updated 5.3 years ago by ▴ 200 • written 5.3 years ago by ▴ 100
18 results • Page 1 of 1
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Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2 by andrebolerbarros ▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Comment: Transcript-level differential expression using DESeq2 by Michael Love 36k
So the way the p-values are generated (non-parametric) you won't get a ranking among these that are highly significant. You can use logFC. …
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2 by Michael Love 36k
Note sure why it's having difficulty converging. You could use apeglm?
Comment: performing the differential binding in ChIP-seq by ATpoint ★ 1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2 by Ekta • 0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
Votes
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
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