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txdb granges cds orf R

updated 6.6 years ago by James W. MacDonald 67k • written 6.6 years ago by q.thomas • 0

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Annotatr CDS Exon UTR

updated 6.9 years ago by rcavalca ▴ 140 • written 6.9 years ago by xie186 • 0

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1.8k

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genomeintervals UTRs exons CDS GenomicRanges

updated 7.5 years ago by Michael Lawrence ★ 11k • written 7.5 years ago by rubi ▴ 110

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2.2k

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biomart bioconductor grangeslist cds ribosome profiling

updated 7.7 years ago by Hervé Pagès 16k • written 7.7 years ago by Walter F. Baumann ▴ 10

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genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene cds

8.4 years ago madsheilskov ▴ 10

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cds

9.1 years ago KB ▴ 50

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genomicfeatures genomicranges cds overlap

updated 9.1 years ago by Michael Lawrence ★ 11k • written 9.1 years ago by madsheilskov ▴ 10

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1.6k

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genomicfeatures genomicranges cds overlap

updated 3.2 years ago by balajee • 0 • written 9.1 years ago by madsheilskov ▴ 10

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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0

Michael, Thank you very much!

Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k

Yes, with the knowledge that, it is expected to be underpowered.

Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0

Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?

Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k

The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280

`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…

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Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

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