Bioconductor Ensembl

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ensembl biomaRt R

updated 6 months ago by SE ▴ 10 • written 13 months ago by kieran.short ▴ 30

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ensembl ensembldb plant arabidopsis thaliana annotationhub

updated 4 days ago by Bruno • 0 • written 4.6 years ago by Guido Hooiveld ★ 3.6k

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biomart R ensembl

updated 3 months ago by Kevin Blighe 3.8k • written 2.9 years ago by rykerklie7 • 0

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R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl

updated 7 weeks ago by Shreyash • 0 • written 4.5 years ago by rtwest • 0

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biomaRt ensembldb ensembl

7 months ago • updated 5 months ago jamie.gearing ▴ 60

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biomaRt ensembldb ensembl

written 7 months ago by Louisse ▴ 10

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Ensembl biomaRt

10 months ago Hector • 0

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215

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biomaRt ensembldb RNA ensembl

updated 9 weeks ago by Johannes Rainer ★ 2.0k • written 9 weeks ago by Christopher • 0

8 results • Page 1 of 1

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Answer: Individual DESeq2 runs versus a single DESeq2 run with contrasts produce differe by ATpoint ★ 2.9k

Please see the vignette, spitting samples or keeping together is covered there. This was asked many times before, use google or the search …

Comment: Error in loadFUN(x, seqname, ranges) : trying to load regions beyond the boun by merve.sahn • 0

I guess you are mixing the NCBI and UCSC annotations. If you are using a custom-edited code to load the annotations, I would recommend clon…

Comment: HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb by merve.sahn • 0

Unfortunately, that seems to be your issue. There is a relevant thread [here](https://groups.google.com/g/3d-genomics/c/hVVTxXpPcxs?pli=1).

Comment: HiCDCPlus `construct_features` incompatible with BSgenome.Hsapiens.NCBI.T2T.CHM1 by merve.sahn • 0

Hi @Gemma-Zhang-326 , the package currently runs only on genomes and versions with UCSC annotations. I will need to issue an update to use …

Answer: Affymetrix analysis Chiptype hgu133plus2hsentrezg.db vs hgu133plus2.db by Guido Hooiveld ★ 3.6k

I am not familiar with Chipster, but `hgu133plus2hsentrezg.db` refers to the annotation of the Affymetrix HGU133plus2 GeneChip that is base…

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Answer: How to perform a methylation analyisis from m values

A: Renaming the seqlevels in a transcript database from GenomicFeatures

A: ggbio error: Objects of type OrganismDb not supported by autoplot

Answer: DeSEQ 2 Error: some values in assay are negative

DESeq2 Error from Installing a Package

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