Bioconductor Girafe

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votes

2.8k

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 11.8 years ago by Dan Tenenbaum ★ 8.2k • written 11.8 years ago by Wim Kreinen ▴ 100

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992

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Annotation girafe Annotation girafe

updated 13.2 years ago by Joern Toedling ▴ 50 • written 13.2 years ago by karlerhard@berkeley.edu ▴ 60

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1.6k

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girafe girafe

updated 13.5 years ago by Sean Davis 21k • written 13.5 years ago by chunjiang he ▴ 80

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1.1k

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girafe girafe

updated 13.7 years ago by Joern Toedling ▴ 10 • written 13.7 years ago by karlerhard@berkeley.edu ▴ 60

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970

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Annotation girafe Annotation girafe

updated 13.7 years ago by Hervé Pagès 16k • written 13.7 years ago by karlerhard@berkeley.edu ▴ 60

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1.7k

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edgeR girafe edgeR girafe

updated 13.7 years ago by Hervé Pagès 16k • written 13.7 years ago by karlerhard@berkeley.edu ▴ 60

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1.4k

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edgeR girafe edgeR girafe

updated 13.7 years ago by Chris Fields ▴ 90 • written 13.7 years ago by karlerhard@berkeley.edu ▴ 60

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970

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Alignment annotate girafe Alignment annotate girafe

updated 14.5 years ago by Joern Toedling ▴ 450 • written 14.5 years ago by Andreia Fonseca ▴ 810

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1.5k

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Annotation annotate biomaRt IRanges girafe Annotation annotate biomaRt IRanges girafe

updated 14.5 years ago by Joern Toedling ▴ 450 • written 14.5 years ago by Andreia Fonseca ▴ 810

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1.2k

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girafe girafe

updated 14.5 years ago by Steve Lianoglou ★ 13k • written 14.5 years ago by Andreia Fonseca ▴ 810

10 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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