User: Ludwig Geistlinger
Ludwig Geistlinger • 40
- Reputation:
- 40
- Status:
- New User
- Location:
- USA/NYC/CUNY
- Last seen:
- 3 weeks, 3 days ago
- Joined:
- 8 years, 4 months ago
- Email:
- l*****************@sph.cuny.edu
Posts by Ludwig Geistlinger
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... Not sure whether this is what you are aiming for with rtracklayer::liftOver, but I assume general consistency with the UCSC online liftOver (https://genome.ucsc.edu/cgi-bin/hgLiftOver) to be a desired feature for many users.
I can think of several good use cases, but to give you a specific one:
Co ...
written 25 days ago by
Ludwig Geistlinger • 40
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... Hi Ai Chen,
(1) perhaps you want to change the title of your post to something more precise such as:
"Error when using EnrichmentBrowser's sbea function with RNA-seq data"
(2) You maybe by accident also created another post
https://support.bioconductor.org/p/90490/
reporting on the same error t ...
written 18 months ago by
Ludwig Geistlinger • 40
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Dear Bioconductors,
I am delighted to announce a major re-release of the EnrichmentBrowser
package in line with its recent publication:
Geistlinger L, Csaba G, Zimmer R.
Bio ...
written 2.4 years ago by
Ludwig Geistlinger • 40
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... that works. great! thank you!
...
written 3.6 years ago by
Ludwig Geistlinger • 40
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... Hi Florian,
BTW: great work on the Gviz package, I found it to be the best among its kind and recommend it also to others!
Your suggestion to fill gaps in the bands df with gneg bands indeed resolved the error, however now the plot looks weird.
Please find the dataframe below. I used the code as ...
written 3.6 years ago by
Ludwig Geistlinger • 40
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... Hi,
As other users encountered as well: There is no information available on cytobands for my organism.
Specifically, I'm plotting chr12 of bosTau6 giving me an empty ideogram, which is fine.
gen <- "bosTau6"
chr <- "chr12"
start <- 71959908
end <- 77206892
ideoTrack <- ...
written 3.6 years ago by
Ludwig Geistlinger • 40
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... Hi,
you can use the 'volcano' function from the EnrichmentBrowser package in case you have your data in an ExpressionSet.
Otherwise you can just use these lines:
I assume <fcs> to be a vector of log2 fold changes and <ps> a vector of e.g. t-test derived p-values:
plot(x=fcs,
...
written 3.7 years ago by
Ludwig Geistlinger • 40
• updated 3.7 years ago by
Gordon Smyth ♦ 33k
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... Dear BioC developers,
as I try to use the retrieveKGML function of the KEGGgraph package, I
end up with the following error:
------
retrieveKGML(pathwayid='00010', organism='cel',
destfile="/home/cbio/ludwig/test.txt", method="wget")
--17:06:46--
ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel ...
written 8.2 years ago by
Ludwig Geistlinger • 40
• updated 8.2 years ago by
Cristobal Fresno Rodríguez • 350
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... Dear BioC developers,
I intend to map gene expression data on KEGG pathways.
In more detail, I performed a DE analysis on gene expression data from
a hgu95av2 chip and want to color particular genes in corresponding
pathways.
I found out that the KEGGSOAP package already implemented an awesome
acce ...
written 8.3 years ago by
Ludwig Geistlinger • 40
• updated 8.3 years ago by
Marc Carlson • 7.2k
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