Showing : pgsea • reset
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Extract info from smc object
PGSEA smc object
6.3 years ago da.de ▴ 30
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PGSEA Steps Using Bioconductor
microarray pgsea
updated 8.2 years ago by ★ 8.2k • written 8.2 years ago by • 0
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 70
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Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.1 years ago by ★ 1.3k • written 10.1 years ago by ▴ 660
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
12.2 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
12.7 years ago Valerie Obenchain ★ 6.8k
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PGSEA and smcPlot
GO hgu133plus2 PGSEA GO hgu133plus2 PGSEA
12.8 years ago Iain Gallagher ▴ 930
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PGSEA and Ruuid
Ruuid PGSEA Ruuid PGSEA
15.3 years ago Daniel Klevebring ▴ 80
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Loading the PGSEA package.
PGSEA PGSEA
updated 15.3 years ago by ▴ 90 • written 15.3 years ago by ▴ 20
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a couple of questions on PGSEA package and GSEA
PGSEA PGSEA
updated 15.6 years ago by ▴ 210 • written 15.6 years ago by ★ 1.2k
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ENTREZ identifiers for PGSEA
GO lumi PGSEA GO lumi PGSEA
updated 15.8 years ago by ▴ 90 • written 15.8 years ago by ▴ 370
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PGSEA question
probe PGSEA probe PGSEA
updated 16.2 years ago by ▴ 210 • written 16.2 years ago by ▴ 70
12 results • Page 1 of 1
Recent ...
Replies
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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