User: Ludwig Geistlinger

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40
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New User
Location:
USA/NYC/CUNY
Last seen:
1 month, 2 weeks ago
Joined:
8 years, 8 months ago
Email:
l*****************@sph.cuny.edu

Posts by Ludwig Geistlinger

<prev • 11 results • page 1 of 2 • next >
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Answer: A: CNV-expression testing with edgeR
... 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 7 weeks ago by Ludwig Geistlinger40
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CNV-expression testing with edgeR
... 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 ...
edger written 7 weeks ago by Ludwig Geistlinger40
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Comment: C: rtracklayer::lifOver one-to-many regions and not match UCSC
... 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 4 months ago by Ludwig Geistlinger40
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Answer: A: RNA-seq data type gets error when using sbea
... 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 22 months ago by Ludwig Geistlinger40
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News: Announcing the EnrichmentBrowser 2.0
... 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 ...
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Answer: A: Gviz: add/change bands in ideogram
... that works. great! thank you! ...
written 3.9 years ago by Ludwig Geistlinger40
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Answer: A: Gviz: add/change bands in ideogram
... 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 3.9 years ago by Ludwig Geistlinger40
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Gviz: add/change bands in ideogram
... 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 <- ...
gviz written 3.9 years ago by Ludwig Geistlinger40
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Answer: A: Differential gene expression of Microarray data
... 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 4.0 years ago by Ludwig Geistlinger40 • updated 4.0 years ago by Gordon Smyth35k
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KEGGgraph: retrieveKGML error (due to wrong ftp path)
... 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 ...
kegggraph written 8.6 years ago by Ludwig Geistlinger40 • updated 8.6 years ago by Cristobal Fresno Rodríguez360

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