Biostar Metatranscriptomics

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Metagenomics DESeq2 Metatranscriptomics

updated 16 months ago by Michael Love 37k • written 16 months ago by Tom • 0

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cpm filtering transcriptomics rnaseq edgeR metatranscriptomics

updated 2.9 years ago by Gordon Smyth 46k • written 2.9 years ago by vm.higareda ▴ 10

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Comment: OPLS-DA: confidence interval for accuracy metric by etienne.thevenot ▴ 20

- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …

Comment: Data input for aracne2regulon function in viper package by xlal • 0

You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…

Comment: unable to install.packages("spatialLIBD") by Leonardo Collado Torres ▴ 1000

All the solutions Lori proposed are valid. The `STexampleData` package I think has only 1 of our samples (see https://bioconductor.org/pack…

Answer: how to use Rsamtools to parse extra fields from STAR alignment by Martin Morgan 25k

The 'extra columns' are called 'tags' in the SAM specification. Following the documentation `?ScanBamParam` you should add `tag = "NH"`. Se…

Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip by Delta._.43 ▴ 10

Yes, indeed it is the same error. Here are the first few lines of my count file. ``` "ENSG00000000003":"001" 0 "ENSG00000000003":"002" 1032…

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Answer: spot- vs cell-level data access

Answer: unable to install.packages("spatialLIBD")

Comment: unable to install.packages("spatialLIBD")

error running UniProt.ws

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