Bioconductor Htseqtools

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Deprecation chipseq htseqtools Bioconductor

updated 4.8 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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2.3k

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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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Answer: NUPOP usage by shepherl 4.2k

You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…

Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0

In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …

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…

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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