Bioconductor FastMNN

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802

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scanpy scRNAseq fastmnn r

14 months ago Madiha • 0

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866

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batchelor fastMNN scRNAseq

16 months ago • updated 15 months ago Guandong Shang ▴ 40

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1.6k

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scater batchelor scRNAseq fastMNN

updated 16 months ago by Aaron Lun ★ 28k • written 16 months ago by Guandong Shang ▴ 40

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781

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fastmnn batchelor BatchEffect

2.2 years ago p.joshi ▴ 40

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929

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fastmnn scater batchelor

updated 3.4 years ago by Aaron Lun ★ 28k • written 3.5 years ago by ATpoint ★ 3.6k

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428

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fastMNN Interpretation

3.5 years ago mloza ▴ 10

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850

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batchelor batch-correction mnncorrect fastmnn rna-seq

updated 3.6 years ago by Aaron Lun ★ 28k • written 4.3 years ago by rmf ▴ 20

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1.1k

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fastMNN CITE-seq ADT-seq batchelor REAP-seq

updated 3.7 years ago by Aaron Lun ★ 28k • written 3.7 years ago by sorjuelal • 0

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1.3k

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SCRAN fastMNN mnnCorrect

updated 5.4 years ago by Aaron Lun ★ 28k • written 5.4 years ago by tobi • 0

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Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 48k

Reitering James' answer, there is no reason not to use `voomLmFit` if you were planning to follow `voom` by `lmFit`. The reason why `voomLm…

Answer: EdgeR: Exact test and glmQLFTest produce very different results by James W. MacDonald 64k

You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.

Answer: limma::voom vs edgeR::voomLmFit - when to use? by James W. MacDonald 64k

The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…

Comment: 'Subtracting' counts on basis of Negative control media and water samples by Karthik • 0

I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…

Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k

It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…

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Answer: limma::voom vs edgeR::voomLmFit - when to use?

A: DSS understanding delta option and posterior probability

Comment: Ensembl down???

Answer: How should I run ssGSEA Hallmark Enrichment Analysis?

Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default

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