Bioconductor Girafe

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2.8k

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 12.2 years ago by Dan Tenenbaum ★ 8.2k • written 12.2 years ago by Wim Kreinen ▴ 100

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1.0k

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Annotation girafe Annotation girafe

updated 13.6 years ago by Joern Toedling ▴ 50 • written 13.6 years ago by karlerhard@berkeley.edu ▴ 60

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1.7k

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girafe girafe

updated 13.9 years ago by Sean Davis 21k • written 13.9 years ago by chunjiang he ▴ 80

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1.1k

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girafe girafe

updated 14.1 years ago by Joern Toedling ▴ 10 • written 14.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.0k

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Annotation girafe Annotation girafe

updated 14.1 years ago by Hervé Pagès 16k • written 14.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.9k

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edgeR girafe edgeR girafe

updated 14.1 years ago by Hervé Pagès 16k • written 14.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.5k

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edgeR girafe edgeR girafe

updated 14.1 years ago by Chris Fields ▴ 90 • written 14.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.0k

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Alignment annotate girafe Alignment annotate girafe

updated 14.9 years ago by Joern Toedling ▴ 450 • written 14.9 years ago by Andreia Fonseca ▴ 810

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1.6k

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Annotation annotate biomaRt IRanges girafe Annotation annotate biomaRt IRanges girafe

updated 14.9 years ago by Joern Toedling ▴ 450 • written 14.9 years ago by Andreia Fonseca ▴ 810

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1.3k

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girafe girafe

updated 14.9 years ago by Steve Lianoglou ★ 13k • written 14.9 years ago by Andreia Fonseca ▴ 810

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Answer: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Hervé Pagès 16k

This should be fast: ```r library(GenomicAlignments) extractMismatchesFromGAlignments <- function(ga) { stopifnot(is(ga, "GAlign…

Answer: GAlignments Cigar to GRanges by Hervé Pagès 16k

```r > as(gal, "GRangesList") GRangesList object of length 2: [[1]] GRanges object with 2 ranges and 0 metadata columns: seqnames …

Comment: DESEq2 comparison with mulitple cell types under 2 conditions by boczniak767 ▴ 740

Dear @mikelove , this method is very appealing but does it avoid making not meaningful comparisons like "1KO" vs "2WT" (using example fro…

Comment: AnnotationHub/ExperimentHub resources backup by James W. MacDonald 68k

You can always grab things from the cache if you want to save or share, but that's not part of the paradigm, so there aren't direct facilit…

Comment: AnnotationHub/ExperimentHub resources backup by igor ▴ 50

Yes, it is cached on your machine, but it wouldn't be cached for your colleagues or for your future self on a different machine. I agree t…

Votes

When running contrasts, does it use normalized read counts?

Importing Salmon counts with tximport with host and virus genomes

Normalization / size factors of samples with high expression of few genes (viral infection)

A: Mult-way interaction design in limma

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