User: lech.kaczmarczyk

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Posts by lech.kaczmarczyk

<prev • 25 results • page 1 of 3 • next >
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Comment: C: QSEA package - Enrichement parameters choice (addEnrichmentParameters)
... Thanks for that. Yes, I read that, but found it somehow not exhausting the topic. Sorry for my lack of understanding. ...
written 7 weeks ago by lech.kaczmarczyk20
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R package (or other software) allowing to save a biological network in GPML format
... I would like to import a custom made pathway into Pathvisio. It only accepts GPML format. Is there any R package containing a relevant export function that I could use? Cheers, Lech ...
gpml cytoscape written 7 weeks ago by lech.kaczmarczyk20 • updated 7 weeks ago by Jean-Karim Heriche13k
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QSEA package - Enrichement parameters choice (addEnrichmentParameters)
... Hi All, I am using QSEA to analyze MeDIP data. I am stuck on the step where enrichment parameters need to be defined (FUN `addEnrichmentParameters`). To get the rough idea about the data, I input the defaults. But now I would like to make sure they are the right choice. To quote the help of the FUN: ...
medips qsea methylation medip written 7 weeks ago by lech.kaczmarczyk20
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Comment: C: Cytoscape - "Ontology and Annotation" import window not opening
... Thanks a bunch, good to know. ...
written 8 weeks ago by lech.kaczmarczyk20
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Peak calling on MeDIP data
... Hi All, I have MeDIP data in the form of Bowtie BAM files. I would like to determine the regions differentially methylated (DMRs) between my samples. How can I extract the information related to the methylation of specific regions of interest, as [on this plot][2]? I would like to correlate this inf ...
medip written 8 weeks ago by lech.kaczmarczyk20
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Pathvisio fails to open .xml files.
... Hi all, I would like to open with `Pathvisio` pathway files downloaded from KEGG website (as .xml files, though web browser). I am getting this error while doing it: [screenshot][1]. Are these file not compatible, or is there a way around? Thank in advance for any help. Cheers, Lech [1]: https:/ ...
pathvisio written 8 weeks ago by lech.kaczmarczyk20
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Cytoscape - "Ontology and Annotation" import window not opening
... Hi All, I try to open the "Ontology and Annotation" import window ( File → Import → Ontology and Annotation...) in Cytoscape (3.5.1) for Ubuntu. Instead of the expected window, only the small thing like [this][1] appears on the screen instead ([full screenshot here][2]). Similar thing happens on M ...
cytoscape written 8 weeks ago by lech.kaczmarczyk20 • updated 8 weeks ago by xanderpico100
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Custom graphNEL object for pathview
... Hi All, I would like to compare miRNA and mRNA sequencing results using `Pathview`. By default, `Pathview` uses a KEGG xml file downloaded using the function `pathview()`. My first problem is how to feed `Pathview` with a custom pathway (for example a reactome pathway converted into graphNEL object ...
rna-seq written 9 weeks ago by lech.kaczmarczyk20
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EdgeR GLMfit issue - only high and negative LFC, please help
... Hi All, I tried to use EdgeR GLM fit function on my data, but I only get some clearly incorrect results. I spent hours trying to spot my error. Limma voom lmFit worked fine on the same data. Here is the script. I figured that something is wrong with how the comparison are set, but don't know how and ...
rna-seq written 10 weeks ago by lech.kaczmarczyk20
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Calculating genomic distances between miRNA clusters
... Hi All, I have a lists of mature miRNAs (in the format `mmu-mir-129-5p`) from different cell types together with expression data (LFC vs Control). I would like to group those genes according to genomic distance (thereby also grouping miRNAs of the same cluster together). Then, I would like to make s ...
rna rna-seq written 10 weeks ago by lech.kaczmarczyk20

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