User: Georg Otto

gravatar for Georg Otto
Georg Otto120
Reputation:
120
Status:
Trusted
Location:
United Kingdom
Last seen:
1 week, 6 days ago
Joined:
3 years, 10 months ago
Email:
g*****@ucl.ac.uk

Posts by Georg Otto

<prev • 19 results • page 1 of 2 • next >
0
votes
2
answers
93
views
2
answers
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 15 days ago by Georg Otto120
0
votes
2
answers
93
views
2
answers
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 22 days ago by Georg Otto120
4
votes
2
answers
93
views
2
answers
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 28 days ago by Georg Otto120
3
votes
1
answer
1.7k
views
1
answer
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 3.0 years ago by Georg Otto120 • updated 3.0 years ago by Rory Stark2.1k
2
votes
1
answer
555
views
1
answer
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 3.0 years ago by Georg Otto120 • updated 3.0 years ago by Rory Stark2.1k
0
votes
1
answers
1.1k
views
1
answers
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 3.1 years ago by Georg Otto120
0
votes
1
answers
1.1k
views
1
answers
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 3.1 years ago by Georg Otto120
0
votes
1
answer
1.1k
views
1
answer
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 3.1 years ago by Georg Otto120 • updated 3.1 years ago by James W. MacDonald45k
0
votes
2
answers
673
views
2
answers
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 3.3 years ago by Georg Otto120
0
votes
2
answers
673
views
2
answers
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 3.3 years ago by Georg Otto120

Latest awards to Georg Otto

Popular Question 20 months ago, created a question with more than 1,000 views. For DiffBind dba.peakset() and consensus peaks

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 186 users visited in the last hour