Bioconductor Girafe

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2.6k

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 11.2 years ago by Dan Tenenbaum ★ 8.2k • written 11.2 years ago by Wim Kreinen ▴ 100

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864

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Annotation girafe Annotation girafe

updated 12.6 years ago by Joern Toedling ▴ 50 • written 12.6 years ago by karlerhard@berkeley.edu ▴ 60

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1.4k

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girafe girafe

updated 12.9 years ago by Sean Davis 21k • written 12.9 years ago by chunjiang he ▴ 80

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936

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girafe girafe

updated 13.0 years ago by Joern Toedling ▴ 10 • written 13.0 years ago by karlerhard@berkeley.edu ▴ 60

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870

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Annotation girafe Annotation girafe

updated 13.1 years ago by Hervé Pagès 16k • written 13.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.4k

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edgeR girafe edgeR girafe

updated 13.1 years ago by Hervé Pagès 16k • written 13.1 years ago by karlerhard@berkeley.edu ▴ 60

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1.3k

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edgeR girafe edgeR girafe

updated 13.1 years ago by Chris Fields ▴ 90 • written 13.1 years ago by karlerhard@berkeley.edu ▴ 60

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857

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Alignment annotate girafe Alignment annotate girafe

updated 13.9 years ago by Joern Toedling ▴ 450 • written 13.9 years ago by Andreia Fonseca ▴ 810

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1.3k

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Annotation annotate biomaRt IRanges girafe Annotation annotate biomaRt IRanges girafe

updated 13.9 years ago by Joern Toedling ▴ 450 • written 13.9 years ago by Andreia Fonseca ▴ 810

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1.1k

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girafe girafe

updated 13.9 years ago by Steve Lianoglou ★ 13k • written 13.9 years ago by Andreia Fonseca ▴ 810

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Comment: Cannot connect to ExperimentHub server by Jiayu • 0

Many thanks and it also resolved the same issue for me!

Comment: Help with running egsea() by Chris • 0

I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…

Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0

Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…

Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k

sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…

Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k

I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?

Votes

Answer: minfi latest update for EPIC V2 chip

A: Error in DESeqDataSet : some values in assay are not integers

Answer: Cannot connect to ExperimentHub server

Answer: confused with tximport counts abundance using salmon input

Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call

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Popular Question to Gyan Prakash Mishra ▴ 10