Showing : fgsea • reset
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
8 months ago GT • 0
2
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2
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1.2k
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
15 months ago Assa Yeroslaviz ★ 1.5k
4
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4
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1.7k
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NAs in fgseaMultilevel
fgsea
updated 16 months ago by ▴ 280 • written 16 months ago by • 0
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13
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2.4k
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Ranking the GSEA Results
fgsea log2FC
17 months ago V_Vibes • 0
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0
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561
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Filtering the genesets for fgseaMultiLevel
msigdb fgsea msig
17 months ago Tanvi • 0
4
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5
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2.0k
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Method to find pathways different between 2 groups
fgsea GSVA CAMERA
19 months ago Chris ▴ 20
2
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2
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1.6k
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fgsea significant result
fgsea
19 months ago Chris ▴ 20
4
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2
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
19 months ago gene_bioconductor ▴ 10
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544
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Empty table plot using plotGseaTable()
fgsea
19 months ago Chris ▴ 20
2
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4
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2.1k
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Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
written 19 months ago by ▴ 20
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8
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2.7k
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FGSEA pre-ranked input in increasing order or decreasing
fgsea
updated 18 months ago by ▴ 280 • written 20 months ago by • 0
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5
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1.2k
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fgsea fork
fgsea
updated 20 months ago by 68k • written 20 months ago by • 0
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2
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1.9k
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
20 months ago Gordon • 0
0
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5
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1.8k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 22 months ago by 68k • written 22 months ago by • 0
3
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2
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859
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cant' download fgsea_1.20.0.tar.gz
download fgsea
2.3 years ago luca.s ▴ 50
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1.2k
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using fgsea to compare two datasets
GSEA fgsea
2.4 years ago Cen • 0
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0
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2.1k
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fgsea/clusterProfiler Packages for nCounter data enrichment analysis
NanoStringDiff clusterProfiler fgsea
2.5 years ago pg45863 ▴ 10
7
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6
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4.8k
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Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.9 years ago by 53k • written 3.0 years ago by ▴ 70
0
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0
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733
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is it possible to limit fgsea to particular tissue type?
fgsea
3.1 years ago kavator ▴ 30
0
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4
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1.8k
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GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
3.2 years ago dario.beraldi • 0
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8
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3.8k
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Problem with fgsea
fgsea
updated 17 months ago by 68k • written 3.7 years ago by • 0
2
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3
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5.9k
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fgsea not downloading due to new r version. Is there a way around this?
r fgsea
3.9 years ago amir.khan • 0
0
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1
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3.7k
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Tied Ranks in fgsea
fgsea
updated 4.6 years ago by ★ 4.1k • written 4.6 years ago by • 0
2
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3
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2.7k
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Compute fgsea with my own database with R version 4.0.2
R fgsea
updated 4.6 years ago by ▴ 280 • written 4.6 years ago by • 0
3
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3
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6.5k
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Warning with the example of GSEA
fgsea fgse
4.7 years ago • updated 4.6 years ago julie.hardy • 0
2
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2
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4.0k
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fgsea usage question - what gene set to use?
fgsea
4.8 years ago alexandr.gopanenko ▴ 50
0
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2
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2.2k
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Error: Aesthetics must be either length 1 or the same as the data (1): x and xend
fgsea
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 20
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3
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3.7k
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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 4.8 years ago by ★ 5.0k • written 4.8 years ago by ▴ 30
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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 5.4 years ago by ▴ 280 • written 5.4 years ago by ▴ 30
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2
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2.3k
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what does gseaparam argument in fgsea() means?
fgsea
updated 5.5 years ago by ▴ 280 • written 5.5 years ago by ▴ 30
3
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2
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2.2k
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Calculate S/N ratios from apeglm for GSEA
apeglm fgsea Signal-To-Noise Ratio
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
8
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5
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5.1k
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How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 120
0
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3
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4.5k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
7.4 years ago atakanekiz ▴ 30
1
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2
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2.4k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
7.5 years ago martin.busch • 0
1
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5
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2.9k
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FGSEA only runs with <1000 permutations
fgsea gsea
updated 8.4 years ago by ▴ 280 • written 8.4 years ago by • 0
0
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8
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3.8k
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Does fgsea order the stats argument?
fgsea
8.5 years ago rubi ▴ 110
6
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15
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4.3k
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Change in pathway IDs scheme in reactome.db
reactome.db fgsea
updated 8.6 years ago by ▴ 150 • written 8.6 years ago by ▴ 280
2
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1
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2.2k
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Direction aware fgsea test
fgsea gsea
updated 8.9 years ago by ▴ 280 • written 8.9 years ago by ▴ 110
38 results • Page 1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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