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TCGA GenomicDataCommons

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GenomicDataCommons

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TCGA GenomicDataCommons

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TCGAutils TCGAbiolinks GenomicDataCommons

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Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by Yang Shi • 0

Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.

Comment: HTSeq Counts no longer available by swbarnes2 ★ 1.0k

STAR's output was intended to mimic HTseq-counts.

Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0 by James W. MacDonald 59k

In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…

Comment: DiffBind GreyListChIP error: Error: BiocParallel errors by Rory Stark ★ 4.4k

Could you let me know the versions? Output of `sessionInfo()`.

Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o by Yang Shi • 0

okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.

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Answer: Use MulticoreParam under BatchtoolsParam

Answer: Variance explained (coefficient of determination) in edgeR

HTSeq Counts no longer available

Comment: Problem converting transcript to genomic coordinates with Annotation Hub

Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

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Popular Question to Johannes Rainer ★ 1.9k