Bioconductor Entrez gene identifiers

Showing : entrez gene identifiers • reset

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1.7k

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biomart entrez gene identifiers ensembl conversion

updated 4.8 years ago by Mike Smith ★ 6.1k • written 4.8 years ago by EdgeR_A_Poe ▴ 10

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2.0k

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biomart ensembl entrez gene identifiers

updated 5.2 years ago by James W. MacDonald 63k • written 5.2 years ago by rina ▴ 20

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11k

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org.hs.eg.db entrez gene identifiers genesymbols

updated 5.6 years ago by mat149 ▴ 70 • written 5.6 years ago by imalumberjack ▴ 10

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2.5k

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bioconductor biomart entrez gene identifiers ensembl ensembl mart

updated 6.5 years ago by Thomas Maurel ▴ 790 • written 6.5 years ago by daniel.carbajo • 0

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1.6k

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org.Hs.eg.db entrez gene identifiers ensemble

updated 6.6 years ago by James W. MacDonald 63k • written 6.6 years ago by Marcus Aurelius • 0

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1.8k

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getBM entrez gene identifiers duplicate rnaseq

6.7 years ago Jose Luis Soto Vázquez • 0

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1.1k

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goseq entrez gene identifiers

updated 7.4 years ago by James W. MacDonald 63k • written 7.4 years ago by Mehmet Ilyas Cosacak • 0

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1.0k

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biomart ensembl ensemble mart entrez gene identifiers

7.6 years ago serpalma.v ▴ 60

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924

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mta10 entrez gene identifiers

updated 7.8 years ago by James W. MacDonald 63k • written 7.8 years ago by jacorvar ▴ 40

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12k

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org.hs.eg.db uniprot accessions entrez gene identifiers

updated 8.1 years ago by James W. MacDonald 63k • written 8.1 years ago by Aditya ▴ 160

10 results • Page 1 of 1

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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.

Comment: collapseReplicates error after tximeta by Michael Love 40k

A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…

Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

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Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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