Bioconductor Gene symbol

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deseq2 dataframe ensembl gene id gene symbol entrezid

updated 5 months ago by Erika • 0 • written 5.7 years ago by jason.williams ▴ 10

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2.8k

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deseq2 gene symbol ensembl

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by thkapell ▴ 10

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1.2k

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GRanges gene symbol IdeoViz

6.8 years ago Arman Shahrisa ▴ 20

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2.2k

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dmrcate gene symbol coordinate

7.2 years ago 574233829 • 0

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1.8k

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transcript_id gene symbol

updated 10.1 years ago by James W. MacDonald 68k • written 10.1 years ago by Jo ▴ 30

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14k

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biomart gene symbol

updated 10.2 years ago by Diego Diez ▴ 760 • written 10.3 years ago by chang02_23 ▴ 30

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4.4k

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Pathview KEGG annotation gene symbol visualization

updated 10.2 years ago by Luo Weijun ★ 1.6k • written 10.2 years ago by alakatos ▴ 130

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3.5k

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biomart homo.sapiens genome regions gene symbol

updated 10.3 years ago by Hervé Pagès 16k • written 10.3 years ago by NS ▴ 60

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26k

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tcga cnv gene symbol coordinate

updated 2.8 years ago by James W. MacDonald 68k • written 10.4 years ago by NS ▴ 60

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3.1k

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probe filter subset gene symbol affy

10.5 years ago alakatos ▴ 130

10 results • Page 1 of 1

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

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