User: lech.kaczmarczyk

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Posts by lech.kaczmarczyk

<prev • 20 results • page 1 of 2 • next >
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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 2 days 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 4 days ago by lech.kaczmarczyk20 • updated 23 hours 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 6 days 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 12 days 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 14 days ago by lech.kaczmarczyk20
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Comment: C: ENSEMBL IDs 2 Entrez Gene IDs - what to do if no match?
... not all as it seems: > IP_toptreatRT0$entrez <- genemap$entrezgene[match(rownames(IP_toptreatRT0), genemap$ensembl_gene_id)] > IP_toptreatRT0$biotype <- genemap$gene_biotype[match(rownames(IP_toptreatRT0), genemap$ensembl_gene_id)] > IP_toptreatRT0[is.na(IP_toptreatRT0$en ...
written 19 days ago by lech.kaczmarczyk20
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Comment: C: ENSEMBL IDs 2 Entrez Gene IDs - what to do if no match?
... Hi, thanks for quick reply. I did add the examples. Since I get most of the records, I would assume it's just missing records in the database (see NAs after retriving biomaRt annotations). ...
written 19 days ago by lech.kaczmarczyk20
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ENSEMBL IDs 2 Entrez Gene IDs - what to do if no match?
... Hi All, I have gene expression data with ENSEMBL Ids (ENSG00000XXXXXXX). I tried 3 different packages to convert them to ENTREZ IDs (bitr, biomatRt, AnnotationDb), but I consistently get no match for about 5-6% of the genes. I would like to do GO and GSEA, but most GO and GSEA tools require gene sym ...
annotation biomart entrez ensembl written 19 days ago by lech.kaczmarczyk20 • updated 18 days ago by Emily_Ensembl13k
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miRNA annotation package / converting mature_mirna_ids into ENTREZ symbols
... Hi All, How can I convert mature miRNA ID like the ones below into Entrez. I failed to find an annotation package that can handle such names. Of course it is possible to edit the names with regular expressions, but I would like to avoid that if possible. mmu-miR-22-3p mmu-miR-22-3p mm ...
mirna annotation rna-seq written 21 days ago by lech.kaczmarczyk20
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Comment: C: cell type-specific miRNA analysis and miRNA-mRNA expression correlation
... Thanks! Will get to it. Right now still struggling to find a way to analyze the data. Though it's slowly clarifying. One possibility might be to use tools for performing something similar to WGCNA. Got the idea from here: [LINK][1] In my understanding, that should help to delineate pathways, some of ...
written 24 days ago by lech.kaczmarczyk20

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