Bioconductor Dna methylation

Showing : dna methylation • reset

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minfi cell proportion estimateCellCounts DNA Methylation

5.7 years ago grayapply2009 • 0

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3.1k

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normalization DNA methylation WGCNA

updated 6.5 years ago by Peter Langfelder ★ 3.0k • written 6.5 years ago by enora.fremy • 0

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1.4k

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medips medip-seq dna methylation dmr analysis

updated 7.0 years ago by Lukas Chavez ▴ 570 • written 7.0 years ago by mtefit • 0

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2.3k

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R gdc rna-seq dna methylation

updated 7.1 years ago by Sean Davis 21k • written 7.1 years ago by RichardJActon ▴ 50

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2.0k

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minfi normalization outliers dna methylation densityplot

7.4 years ago peter.fransquet • 0

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1.0k

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differential variability dna methylation iEVORA DVP

7.6 years ago poojitha.stemcell ▴ 10

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1.4k

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rnbeads methylation methylationepic dna methylation

7.8 years ago gabrielrfries • 0

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1.5k

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dna methylation biseq

updated 7.9 years ago by Gordon Smyth 53k • written 7.9 years ago by ahmad.moousavi • 0

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2.5k

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tcgabiolinks dna methylation

updated 8.0 years ago by Marcel Ramos 700 • written 8.0 years ago by michaelwxf2012 • 0

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2.5k

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dna methylation illimina 450k methylation beta M significance

updated 8.2 years ago by James W. MacDonald 68k • written 8.2 years ago by skids121 • 0

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1.7k

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CNV minfi preprocessing dna methylation

8.7 years ago Thomas • 0

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1.4k

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microarray HM450 dna methylation cohcap

updated 8.9 years ago by James W. MacDonald 68k • written 8.9 years ago by poojitha.stemcell ▴ 10

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1.5k

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minfi bumphunter DNA methylation illumina450k

updated 9.5 years ago by James W. MacDonald 68k • written 9.5 years ago by fleur_p90 • 0

13 results • Page 1 of 1

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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150

Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?

Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

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C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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