Showing : fgsea • reset
0
votes
7
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232
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Problem with fgsea
fgsea
updated 7 weeks ago by ▴ 200 • written 7 weeks ago by • 0
2
votes
3
replies
354
views
fgsea not downloading due to new r version. Is there a way around this?
r fgsea
3 months ago amir.khan • 0
0
votes
1
reply
431
views
Tied Ranks in fgsea
fgsea
updated 12 months ago by ★ 3.2k • written 12 months ago by • 0
2
votes
3
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354
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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
votes
3
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630
views
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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661
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fgsea usage question - what gene set to use?
fgsea
14 months ago alexandr.gopanenko ▴ 20
0
votes
2
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544
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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
0
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3
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500
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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
0
votes
1
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349
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 22 months ago by ▴ 200 • written 22 months ago by ▴ 20
1
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2
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442
views
what does gseaparam argument in fgsea() means?
fgsea
updated 23 months ago by ▴ 200 • written 23 months ago by ▴ 20
0
votes
2
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511
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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
votes
5
replies
1.6k
views
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
0
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3
replies
1.2k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
3.8 years ago atakanekiz ▴ 30
1
vote
2
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1.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
3.9 years ago martin.busch • 0
1
vote
5
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1.3k
views
FGSEA only runs with <1000 permutations
fgsea gsea
updated 4.8 years ago by ▴ 200 • written 4.8 years ago by • 0
0
votes
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
votes
15
replies
1.6k
views
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
votes
1
reply
919
views
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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Answer: Using featureCounts and downloading Rsubread by James W. MacDonald 59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package. ``` BiocManager::install("Rsubread") library(…
Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
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Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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