Bioconductor Ensembldb

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replies

257

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ensembldb

updated 10 days ago by James W. MacDonald 65k • written 11 days ago by Fara • 0

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171

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ensembldb transcriptome genome coordinateconversion

updated 4 weeks ago by Michael Love 41k • written 5 weeks ago by saadmurtazakhan ▴ 10

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225

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TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus

updated 11 weeks ago by James W. MacDonald 65k • written 12 weeks ago by ramonmassoni ▴ 10

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314

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ensembldb genomei GenomeInfoDb

12 weeks ago Kai Hu ▴ 70

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227

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ensembldb biomaRt

updated 11 weeks ago by Robin • 0 • written 12 weeks ago by Pez ▴ 10

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503

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Rstudio cDNA ensembldb NCBI

5 months ago R_Page • 0

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798

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RStudio convert ensembldb NCBI

6 months ago • updated 5 months ago j_denton • 0

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561

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GO ensembldb

6 months ago Rockbar • 0

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841

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AnnotationHubSoftware ensembldb

updated 7 months ago by James W. MacDonald 65k • written 7 months ago by cjag • 0

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1.4k

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ensembldb

updated 9 months ago by James W. MacDonald 65k • written 9 months ago by Max ▴ 10

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490

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Rsubread ensembldb

updated 9 months ago by James W. MacDonald 65k • written 9 months ago by Ya • 0

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1.5k

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ensembldb biomaRt

updated 9 months ago by Michael Love 41k • written 9 months ago by Benjamin ▴ 30

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4.1k

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biomaRt ensembldb UniProt.ws

updated 6 months ago by Marcel Ramos 690 • written 21 months ago by Recep ▴ 20

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2.6k

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ensembldb SNP SNPData genomes

written 2.2 years ago by Weiqiong • 0

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5.8k

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Ensembl Rstudio ensembldb AnnotationHub ensdb

updated 7 weeks ago by shepherl 3.9k • written 2.3 years ago by jon.klonowski ▴ 40

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966

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Annotation biomaRt ensembldb

written 2.5 years ago by Lillian • 0

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5.6k

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ensembl ensembldb plant arabidopsis thaliana annotationhub

updated 4 weeks ago by Shiva • 0 • written 5.5 years ago by Guido Hooiveld ★ 3.9k

17 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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