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225

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scran bluster scater scuttle

updated 4 weeks ago by ATpoint ★ 4.0k • written 4 weeks ago by Dario Strbenac ★ 1.5k

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scuttle scater

updated 7 months ago by ATpoint ★ 4.0k • written 7 months ago by Abbi Edwards • 0

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scuttle scater seurat SpatialExperiment

14 months ago cathalgking ▴ 10

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648

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scuttle scater SpatialExperiment

updated 15 months ago by alan.ocallaghan ▴ 160 • written 15 months ago by cathalgking ▴ 10

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normalizeCounts scran librarySizeFactors scuttle scRNAseq

2.2 years ago behr201 • 0

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scater SingleCellExperiment BiocParallel scuttle scran

2.5 years ago enricoferrero ▴ 660

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scran SingleCellExperiment scuttle scater

updated 3.3 years ago by Aaron Lun ★ 28k • written 3.3 years ago by enricoferrero ▴ 660

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scran scater scuttle

updated 3.7 years ago by Aaron Lun ★ 28k • written 3.7 years ago by enricoferrero ▴ 660

8 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'…

Votes

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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