Bioconductor Gsealm

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Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR

12.9 years ago Malcolm Cook ★ 1.6k

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Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR

updated 12.9 years ago by Malcolm Cook ★ 1.6k • written 12.9 years ago by Josh Kaminker ▴ 20

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biomaRt GSEAlm biomaRt GSEAlm

updated 13.4 years ago by James W. MacDonald 68k • written 13.4 years ago by b1gorsuch@comcast.net ▴ 20

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GSEAlm GSEAlm

16.9 years ago Mark W Kimpel ▴ 830

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1.7k

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GO GSEAlm GO GSEAlm

updated 17.1 years ago by rgentleman ★ 5.5k • written 17.1 years ago by Mark W Kimpel ▴ 830

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GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm

updated 17.1 years ago by Dykema, Karl ▴ 90 • written 17.1 years ago by Mark W Kimpel ▴ 830

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870

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GSEAlm GSEAlm

17.6 years ago Assaf Oron ▴ 40

7 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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