User: octaviamdl

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octaviamdl0
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Posts by octaviamdl

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DNA methylation probe selection for GDAC Firehose
... Hi everyone! I have a quick question and I'm hoping someone can help. I noticed that in the gdac firehose DNA methylation data, there are significantly fewer probes selected from the 450K Illumina methylation arrays than on the TCGA data portal (for example, for HNSC, there are roughly 20K DNA meth ...
dna methylation gdac firehose tcga written 5 weeks ago by octaviamdl0
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Comment: C: cageR: errors when trying to use clusterCTSS
... It looks like it's `CAGEr_1.24.0` . I'll try to update the version and see if the issue goes away. Thanks! :) ...
written 14 months ago by octaviamdl0
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Comment: C: cageR: errors when trying to use clusterCTSS
... Hi lu.ne! No, my input files aren't publicly available. I've edited my post above to update what it looks like right after running `getCTSS`, prior to tpm normalization. ...
written 14 months ago by octaviamdl0
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cageR: errors when trying to use clusterCTSS
... Hi everyone! I'm trying to use the cageR package to analyze some CAGE-seq data (paired-end), however, the clusterCTSS function doesn't seem to work for me. Here is the code that I used: cage_bam <- new("CAGEset", genomeName = "BSgenome.Hsapiens.UCSC.hg19", inputFiles = bam_file, inputFile ...
R cage-seq rna-seq written 14 months ago by octaviamdl0

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