Showing : fgsea • reset
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4
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
6 days ago sropri • 0
1
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5
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298
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fgsea fork
fgsea
updated 26 days ago by 65k • written 27 days ago by • 0
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2
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324
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
4 weeks ago • updated 22 days ago Gordon • 0
0
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5
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449
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 10 weeks ago by 65k • written 11 weeks ago by • 0
3
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2
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375
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cant' download fgsea_1.20.0.tar.gz
download fgsea
8 months ago luca.s ▴ 50
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0
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595
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using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 0
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0
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815
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
11 months ago pg45863 ▴ 10
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 16 months ago by 50k • written 16 months ago by ▴ 30
0
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0
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363
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is it possible to limit fgsea to particular tissue type?
fgsea
17 months ago kavator ▴ 30
0
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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
19 months ago dario.beraldi • 0
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
2
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3
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2.9k
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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
0
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1
reply
2.4k
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Tied Ranks in fgsea
fgsea
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 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
3
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3
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4.1k
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Warning with the example of GSEA
fgsea fgse
3.0 years ago julie.hardy • 0
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
0
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2
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1.6k
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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
0
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3
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2.1k
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 ★ 4.0k • written 3.2 years ago by ▴ 30
0
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1
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1.0k
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 3.8 years ago by ▴ 240 • written 3.8 years ago by ▴ 30
1
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2
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1.5k
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what does gseaparam argument in fgsea() means?
fgsea
updated 3.9 years ago by ▴ 240 • written 3.9 years ago by ▴ 30
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 41k • written 5.0 years ago by ▴ 20
8
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5
replies
3.4k
views
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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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
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
1
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5
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2.0k
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.8 years ago by ▴ 240 • written 6.8 years ago by • 0
0
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8
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2.7k
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Does fgsea order the stats argument?
fgsea
6.8 years ago rubi ▴ 110
6
votes
15
replies
2.9k
views
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
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 240 • written 7.3 years ago by ▴ 110
28 results • Page 1 of 1
Recent ...
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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