Bioconductor Methylpipe

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methylation methylPipe

updated 5.6 years ago by mattia pelizzola ▴ 200 • written 5.6 years ago by jonathan.moore • 0

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methylpipe

updated 2.2 years ago by Macarena • 0 • written 7.0 years ago by slbattle ▴ 10

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MethylPipe

updated 7.1 years ago by kamal.fartiyal84 ▴ 10 • written 7.1 years ago by 746458071 • 0

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methylpipe

7.3 years ago pirona • 0

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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…

Votes

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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