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GoSemSim - function mgeneSim() is resulting in similarity matrix without 1s on diagonal
GOSim GOSemSim
updated 14 months ago by ▴ 730 • written 14 months ago by ▴ 10
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I want to convert the go enrichment result to a data frame (tidy data)with two column which one is the gene symbol and the other is go term. Any one…
GO.db GOfuncR GO GOSim goProfiles
updated 18 months ago by ▴ 760 • written 18 months ago by • 0
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compute similarities of GOTerms with GOSim in non-human species
GOSim
updated 5.5 years ago by ▴ 730 • written 5.5 years ago by ▴ 10
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Normalization of specificity level (level of depth) of GO terms dataset
gosim gosemsim
updated 7.1 years ago by ▴ 730 • written 8.5 years ago by ▴ 10
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GOSim yeast
GO Yeast GOSim GO Yeast GOSim
updated 7.1 years ago by • 0 • written 11.9 years ago by ★ 13k
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GOSim Problem
Yeast Organism GOSim Yeast Organism GOSim
11.5 years ago Pablo Andretta Jaskowiak ▴ 10
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Problem while working with GOSim package
GOSim GOSim
11.6 years ago ANIRBAN BHAR ▴ 60
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1.3k
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Simple GO pie and GOSim install error
GO Organism biomaRt GOSim GO Organism biomaRt GOSim
updated 12.6 years ago by ▴ 40 • written 12.6 years ago by ★ 7.2k
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Simple GO pie and GOSim install error
GO Organism biomaRt GOSim GO Organism biomaRt GOSim
12.6 years ago Olivier Lucas ▴ 40
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1.2k
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Query Gene Ontology
GOSim GOSim
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 10
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1.2k
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Gene ID of yeast in GOSemSim and other GO related package may need update
Annotation GO Yeast biomaRt GOSemSim GOSim Annotation GO Yeast biomaRt GOSemSim GOSim
updated 14.6 years ago by ★ 7.2k • written 14.6 years ago by ▴ 20
11 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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