Bioconductor Refseq

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1.2k

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refseq Bioconductor conversion

5.0 years ago heiko_kin ▴ 60

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881

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RefSeq Chromosome Mutalyzer

5.6 years ago heiko_kin ▴ 60

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2.8k

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tximport Gene IDs txdb RefSeq Salmon

updated 5.8 years ago by Michael Love 43k • written 5.8 years ago by holmkn • 0

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3.4k

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edgeR ENEMBL RefSeq

updated 6.7 years ago by Gordon Smyth 53k • written 6.7 years ago by mzillur • 0

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3.2k

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genomicfeatures maketxdbfromucsc refseq

updated 9.3 years ago by Hervé Pagès 16k • written 9.3 years ago by Sebastien Vigneau ▴ 10

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4.6k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 9.8 years ago by Hervé Pagès 16k • written 9.8 years ago by gokcen.eraslan ▴ 10

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3.6k

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promoter granges refseq ucsc organismdb

updated 10.0 years ago by Robert Castelo ★ 3.4k • written 10.0 years ago by efoss ▴ 10

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4.3k

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refseq annotationhub

updated 10.1 years ago by Martin Morgan 25k • written 10.1 years ago by dalloliogm ▴ 50

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2.1k

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customprodb dbsnp refseq varianttools

updated 10.4 years ago by xiaojing.wang ▴ 50 • written 10.4 years ago by kristenbeck527 • 0

9 results • Page 1 of 1

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Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

Votes

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

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