User: Georg Otto

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Georg Otto120
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4 years, 11 months ago
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g*****@ucl.ac.uk

Posts by Georg Otto

<prev • 19 results • page 1 of 2 • next >
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Answer: A: biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... I can confirm upgrading bioconductor to version 3.6. solved the problem. ...
written 13 months ago by Georg Otto120
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Comment: C: biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... Thanks a lot. I tried both suggested solutions. With the mirror service I got the same error. Installing and using the devel package however made the error go away. Just to clarify: The recommendation not to run querys with more than 500 search values relates to the devel package, not the release pa ...
written 13 months ago by Georg Otto120
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biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... Hi, I have a vector with Ensembl gene IDs > head(gene.id) [1] "ENSG00000223972" "ENSG00000227232" "ENSG00000278267" "ENSG00000243485" [5] "ENSG00000274890" "ENSG00000237613" I am trying to annotate the IDs using biomaRt > library(biomaRt) > ensembl <- useMart("ENSEMBL_MART_ENSEMBL", ...
biomart written 13 months ago by Georg Otto120
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DiffBind dba.peakset() and consensus peaks
... Dear all, I have an issue generating consensus peaks using the DiffBind package. I generate consensus peaks using the dba.peakset() function dbaObj <-  dba(sampleSheet = "samples.csv")   data.peakset <- dba.peakset(dbaObj, consensus = DBA_CONDITION, minOverlap = 2) This generates columns f ...
chipseq diffbind written 4.0 years ago by Georg Otto120 • updated 4.0 years ago by Rory Stark2.6k
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problem with characters in chromosome names in DiffBind dba
... Dear all, I have bed files with ChIP-seq data, with sequence (chromosome) names like this: chr1, chr10, chr11, chr12, chr13, chr13_random, chr14, . . ., chrX I  import the bed file data into a DiffBind DBA object using the command > dbaObj <-  dba(sampleSheet = "samples.csv") The problem ...
diffbind chip-seq written 4.0 years ago by Georg Otto120 • updated 4.0 years ago by Rory Stark2.6k
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Comment: C: heatmap.2 like plot in ggplot
... I take your point that gplots is not a bioconductor package. I am actually looking for something that extends the simple heatmap plot, but allows to include cluster trees, as heatmap.2 does, but in ggplot2. ...
written 4.1 years ago by Georg Otto120
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Comment: C: heatmap.2 like plot in ggplot
... I take your point that gplots is not a bioconductor package. I am actually looking for something that extends the simple heatmap plot, but allows to include cluster trees, as heatmap.2 does, but in ggplot2. ...
written 4.1 years ago by Georg Otto120
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heatmap.2 like plot in ggplot
... Dear all, I am wondering if anybody has implemented a heatmap.2 like functionality (from package gplots) in ggplots2? Best wishes,   Georg ...
plot written 4.1 years ago by Georg Otto120 • updated 4.1 years ago by James W. MacDonald48k
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Answer: A: nearly exact overlaps between GAlignmentPairs and GenomicRanges
... Michael Lawrence writes: > But to get exactly what you want, we need to use type="within" with > findOverlaps() and then filter the hits for cases where the overhang is > below some tolerance (3bp): > > reads <- granges(galp) # simplifies things a bit > hits <- findOverla ...
written 4.3 years ago by Georg Otto120
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nearly exact overlaps between GAlignmentPairs and GenomicRanges
... Dear all, I have a problem finding nerly exact overlaps between read pairs and genomic regions. I try this by using GAlignmentPairs and GenomicRanges: > library(Rsamtools) ex1_file <- system.file("extdata", "ex1.bam", > package="Rsamtools") galp <- readGAlignmentPairs(ex1_file, use.na ...
alignment written 4.3 years ago by Georg Otto120

Latest awards to Georg Otto

Popular Question 13 months ago, created a question with more than 1,000 views. For ggbio error: Objects of type OrganismDb not supported by autoplot
Popular Question 2.5 years ago, created a question with more than 1,000 views. For ggbio error: Objects of type OrganismDb not supported by autoplot
Popular Question 2.5 years ago, created a question with more than 1,000 views. For heatmap.2 like plot in ggplot
Popular Question 2.5 years ago, created a question with more than 1,000 views. For edgeR design matrix, one group vs average of other groups
Popular Question 2.7 years ago, created a question with more than 1,000 views. For DiffBind dba.peakset() and consensus peaks

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