Showing : methods • reset
0
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3
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1.5k
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Defining BSgenome -> GRanges S4 coercer without package attaching
BSgenome methods GenomicRanges
5.3 years ago Aditya ▴ 160
0
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1
reply
981
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Why does S4Vectors define three functions for Vector -> data.frame coercion
S4Vectors methods
5.3 years ago Aditya ▴ 160
2
votes
2
replies
1.4k
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SetMethod to dispatch on class in unattached package
s4 methods SummarizedExperiment
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
0
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3
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1.3k
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How to clear a cached S4 method
devtools S4 methods cache
6.1 years ago Michael Steinbaugh ▴ 90
0
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0
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1.1k
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Deconvolute bulk RNA-Seq from human epithelial tissue scrapings with immune/blood cell contamination
deconvolution methods
6.9 years ago casey.rimland ▴ 170
5 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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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