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salmon edgeR tximport nf-core gene_counts

updated 6 days ago by i.atanasoai • 0 • written 14 months ago by mohammedtoufiq91 ▴ 10

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328

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edgeR

7 days ago • updated 2 days ago Jonathan ▴ 10

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117

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limma edgeR RNASeq

updated 6 days ago by Gordon Smyth 50k • written 7 days ago by Shaimaa Gamal • 0

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286

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rna-seq edgeR

updated 4 days ago by Gordon Smyth 50k • written 17 days ago by Netanel • 0

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edgeR

updated 1 day ago by Gordon Smyth 50k • written 1 day ago by k___ ▴ 30

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DGEList edgeR

6 days ago prity6459 • 0

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128

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subsettingdata edgeR designmatrix

updated 6 days ago by Gordon Smyth 50k • written 6 days ago by prity6459 • 0

7 results • Page 1 of 1

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Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…

Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0

Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0