Showing : geneontology • reset
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clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon clusterPro Salmosalar AnnotationHub GeneOntology
updated 7 weeks ago by 41k • written 8 weeks ago by • 0
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 17 months ago by 65k • written 17 months ago by • 0
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4
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RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA gene RNASeqRData edgeR geneontology
18 months ago faiza • 0
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Gene Ontology on Streptococcus Pneumoniae genes sets
GO GeneOntology LocusIDtogeneIDconversion
18 months ago BioinFo.X • 0
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Trouble importing my own Gene Ontology Annotation into topGO
Annotation GeneOntology topGO GO
updated 22 months ago by 65k • written 22 months ago by ▴ 60
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Getting list of genes enriched in each of Biological process terms
GOstats Go.db GeneOntology
3.1 years ago MOHAMMAD • 0
2
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Geno Ontology Analysis using gene symbol
GO.db Annotation Clusterprofile GeneOntology
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
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topGO enrichment analysis, ontology selection.
topGO enrichmentanalysis geneontology
updated 3.2 years ago by ▴ 730 • written 3.2 years ago by • 0
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question on GO analysis using clusterProfiler
clusterprofiler geneontology
updated 6.5 years ago by ▴ 160 • written 6.5 years ago by • 0
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GOSemSim bioconductor package
geneontology R go semantic similarity
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by • 0
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Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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?
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