Bioconductor Seqlevels

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granges seqlevels feature request

updated 2.6 years ago by story.benjamin ▴ 20 • written 7.6 years ago by Charles Plessy ▴ 180

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1.7k

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txdb.hsapiens.ucsc.hg19.knowngene seqlevels bugs

updated 8.0 years ago by Hervé Pagès 16k • written 8.0 years ago by wcstcyx ▴ 30

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1.6k

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txdb threeutrsbytranscript seqlevelsstyle seqlevels

9.2 years ago Robert K. Bradley ▴ 40

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8.0k

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granges seqlevels

9.7 years ago Hermann Norpois ▴ 170

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2.0k

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variantannotation seqlevels error

updated 10.3 years ago by Valerie Obenchain ★ 6.8k • written 10.3 years ago by Asma rabe ▴ 290

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Comment: biomaRt rnorvegicus_gene_ensembl not available anymore by Benjamin ▴ 20

I had access temporarily to the rat genome, but now it looks like ensemble 113 is completely down as I have this error: Error : Your q…

Comment: Deseq2 Design by pm_25 • 0

Thanks James for the prompt answer! your explanation makes more sense. in your example, when creating the interactions: ```r results(dds,…

Answer: Standardization of rlog transformed counts before PCA by Michael Love 43k

VST and rlog contain scaling for sequencing depth.

Answer: Limma - using both array and spot weights in lmFit by Gordon Smyth 52k

Was answered here: https://support.bioconductor.org/p/17028/

Answer: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k

Hi, In version 1.19.4 of `spatialLIBD` @lahuuki re-implemented the `gene_set_enrichment_plot()` function using `ComplexHeatmap::Heatmap(…

Votes

Answer: Deseq2 Design

Answer: Fold change calculation in Diffbind vs. DESEQ2?

Fold change calculation in Diffbind vs. DESEQ2?

FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level

Answer: FeatureCounts Output Counts at Exon Level Using Default Settings, want gene leve

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Scholar to James W. MacDonald 67k