Bioconductor GenomicFiles

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GenomicFiles

updated 5 months ago by Hervé Pagès 16k • written 5 months ago by user_bioinfo • 0

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766

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GenomicInteractions Basic4Cseq DNASeq GenomicFiles

3.5 years ago koushik • 0

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1.5k

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GenomicFiles ShortRead Rsamtools

3.8 years ago robmaz77 ▴ 20

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915

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GenomicFiles

updated 5.7 years ago by Martin Morgan 25k • written 5.7 years ago by Qiang ▴ 80

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1.1k

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genomicfiles

updated 7.0 years ago by Martin Morgan 25k • written 7.0 years ago by Qiang ▴ 80

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1.3k

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genomicfiles reduceByRange

updated 7.3 years ago by Valerie Obenchain ★ 6.8k • written 7.3 years ago by maltethodberg ▴ 180

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1.3k

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GenomicFiles BiocParallel

updated 7.5 years ago by shepherl 4.1k • written 7.6 years ago by m.van_iterson ▴ 20

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1.5k

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rsamtools genomicalignments genomicfiles

updated 8.4 years ago by Hervé Pagès 16k • written 8.4 years ago by jfiksel ▴ 30

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1.7k

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genomicfiles rsamtools

updated 8.5 years ago by Martin Morgan 25k • written 8.5 years ago by victoriaccorey ▴ 10

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2.8k

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rsamtools genomicalignments genomicfiles

updated 9.4 years ago by Martin Morgan 25k • written 9.4 years ago by Welliton de Souza ▴ 70

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1.1k

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GO Biostrings rtracklayer GenomicRanges BiocParallel GenomicFiles

10.3 years ago Dan Tenenbaum ★ 8.2k

11 results • Page 1 of 1

Recent ...

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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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