Bioconductor Workflow

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Bioconductor Workflow

updated 2.3 years ago by Gordon Smyth 50k • written 2.3 years ago by sarastew1994 • 0

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ExperimentData Deprecation Software Release Workflow

2.5 years ago • updated 2.0 years ago shepherl 3.8k

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Workflow Software ExperimentData Deprecation

3.4 years ago • updated 3.0 years ago shepherl 3.8k

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784

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Software annotation experiment workflow

updated 3.7 years ago by shepherl 3.8k • written 3.7 years ago by gnanaprakash.s • 0

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764

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rnaseqGene workflow deseq2

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by Assa Yeroslaviz ★ 1.5k

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3.0k

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software error deseq2 workflow rnaseqGene

updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by pavan-bioconductor • 0

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RNA-Seq Workflow

updated 4.9 years ago by Gordon Smyth 50k • written 4.9 years ago by detroit.drive • 0

7 results • Page 1 of 1

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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

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Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

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