Bioconductor TranscriptR

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transcriptR

updated 3.5 years ago by shepherl 4.1k • written 3.5 years ago by Alice ▴ 10

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transcriptR predictStrand

5.1 years ago jason.williams ▴ 10

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TranscriptR RNA-seq ChIP-seq

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by jason.williams ▴ 10

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transcriptR

updated 5.2 years ago by James W. MacDonald 67k • written 5.2 years ago by jason.williams ▴ 10

4 results • Page 1 of 1

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Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k

> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…

Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80

Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…

Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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