Bioconductor Htseqtools

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Deprecation chipseq htseqtools Bioconductor

updated 4.7 years ago by Basti ▴ 780 • written 4.8 years ago by Mick • 0

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4.3k

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htseqtools deseq2 counts cuffdiff

9.8 years ago Jon Bråte ▴ 270

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2.2k

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Coverage htSeqTools Coverage htSeqTools

updated 13.8 years ago by Valerie Obenchain ★ 6.8k • written 13.8 years ago by Juan L. Mateo ▴ 80

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1.9k

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GenomicRanges htSeqTools GenomicRanges htSeqTools

updated 13.8 years ago by Vincent J. Carey, Jr. 6.7k • written 13.8 years ago by Juan L. Mateo ▴ 80

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1.1k

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IRanges htSeqTools IRanges htSeqTools

updated 13.9 years ago by Michael Lawrence ★ 11k • written 13.9 years ago by Ian D. ▴ 70

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1.2k

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convert htSeqTools convert htSeqTools

13.9 years ago Oscar Reina ▴ 20

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1.6k

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htSeqTools ASSIGN htSeqTools ASSIGN

updated 13.9 years ago by Michael Lawrence ★ 11k • written 13.9 years ago by Ian D. ▴ 70

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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…

Votes

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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Commentator to sina.nassiri ▴ 130