Bioconductor Coldata

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368

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DESeq2 design coldata

updated 6 weeks ago by swbarnes2 ★ 1.4k • written 6 weeks ago by arfranco ▴ 130

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593

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ColData pheatmap DESeq2

written 11 months ago by dania.khalid • 0

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1.1k

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SingleCellExperiment colData rename

updated 16 months ago by Basti ▴ 780 • written 16 months ago by achoppe ▴ 10

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595

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BiSeq Coldata

4.0 years ago akhaira • 0

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1.5k

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deseq2 levels factor colData

updated 5.3 years ago by Michael Love 42k • written 5.3 years ago by ariel ▴ 20

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43k

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deseq2 coldata

updated 5.6 years ago by swbarnes2 ★ 1.4k • written 5.6 years ago by mjrarcher ▴ 10

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3.2k

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variantannotation coldata

updated 5.7 years ago by Valerie Obenchain ★ 6.8k • written 5.7 years ago by lvclark ▴ 10

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3.6k

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deseq2 coldata NA

updated 5.9 years ago by Michael Love 42k • written 5.9 years ago by t.kuilman ▴ 170

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1.5k

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multiassayexperiment colData

updated 6.5 years ago by Levi Waldron ★ 1.1k • written 6.5 years ago by Lluís Revilla Sancho ▴ 730

9 results • Page 1 of 1

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Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100

Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz

Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k

The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …

Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k

You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.

Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0

In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…

Answer: Design formula, numeric contrast, and lfcshrink in deseq2 by Michael Love 42k

For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…

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Comment: Most enriched pathway is not expressed when modifying universe parameter

Time-course, comparison of two groups

Answer: Behaviour of featureCounts when quantifying multi-mapping reads

Answer: GESA with certain gene list returns no result with human genom, but many result

Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`

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