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GenomicRanges RleList

8 months ago story.benjamin ▴ 20

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Views IRanges GRanges RleList

updated 4.2 years ago by Mike Smith ★ 6.6k • written 4.2 years ago by Assa Yeroslaviz ★ 1.5k

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iranges s4vectors rle rlelist

7.5 years ago endrebak85 ▴ 40

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bug genomicranges granges rlelist coverage

updated 7.8 years ago by Hervé Pagès 16k • written 7.8 years ago by xiaotong.yao23 ▴ 10

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delayedarray rlelist rle

updated 8.1 years ago by Peter Hickey ▴ 760 • written 8.1 years ago by davide risso ▴ 980

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genomicranges biocgenerics rlelist genomicvars iranges

updated 8.2 years ago by Hervé Pagès 16k • written 8.2 years ago by Devin King ▴ 20

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rlelist ifelse

updated 8.9 years ago by theobroma22 ▴ 10 • written 8.9 years ago by maltethodberg ▴ 180

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Views genomicalignments IRangesList coverage RleList

updated 9.4 years ago by Hervé Pagès 16k • written 9.4 years ago by ccanchaya • 0

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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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Popular Question to James W. MacDonald 68k