User: Ludwig Geistlinger
Ludwig Geistlinger • 50
- Reputation:
- 50
- Status:
- New User
- Location:
- USA/NYC/CUNY
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 9 years, 3 months ago
- Email:
- l*****************@sph.cuny.edu
Posts by Ludwig Geistlinger
<prev
• 11 results •
page 1 of 2 •
next >
0
votes
2
answers
222
views
2
answers
... Thanks a lot for this comprehensive answer and these great suggestions.
Although there are scenarios where a CNV can affect gene expression on a genome-wide
scale (eg by modulating the expression of a coinciding transcription factor, which
in turn regulates distal genes), you rarely have the power t ...
written 8 months ago by
Ludwig Geistlinger • 50
3
votes
2
answers
222
views
2
answers
... Dear edgeR-Team,
I have around 200 samples for which I have
1) CNV data, ie. a matrix X (regions x samples) in which a cell is either 2 (normal diploid), 0/1 (loss), or 3/4/5/... (gain),
2) RNA-seq data, ie. a matrix Y (genes x samples) storing the raw RNA-seq read counts.
Now I want to find for ...
written 9 months ago by
Ludwig Geistlinger • 50
1
vote
1
answer
780
views
1
answers
... 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 11 months ago by
Ludwig Geistlinger • 50
0
votes
1
answer
402
views
1
answers
... 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 2.4 years ago by
Ludwig Geistlinger • 50
1
vote
0
answers
641
views
0
answers
...
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 3.3 years ago by
Ludwig Geistlinger • 50
0
votes
4
answers
956
views
4
answers
... that works. great! thank you!
...
written 4.5 years ago by
Ludwig Geistlinger • 50
0
votes
4
answers
956
views
4
answers
... 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 4.5 years ago by
Ludwig Geistlinger • 50
0
votes
4
answers
956
views
4
answers
... 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 4.5 years ago by
Ludwig Geistlinger • 50
1
vote
2
answers
744
views
2
answers
... 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 4.6 years ago by
Ludwig Geistlinger • 50
• updated
4.6 years ago by
Gordon Smyth ♦ 37k
0
votes
1
answer
884
views
1
answer
... 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 9.2 years ago by
Ludwig Geistlinger • 50
• updated
9.2 years ago by
Cristobal Fresno Rodríguez • 360
Latest awards to Ludwig Geistlinger
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 16.09
Traffic: 176 users visited in the last hour