User: marisa.e.miller

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Posts by marisa.e.miller

<prev • 5 results • page 1 of 1 • next >
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xlim not working with ggbio
... Hello, I'm trying to plot a multi-tracked figure with ggbio, and I'm consistently having issues with a couple of the tracks scaling correctly. Particularly, the repeats gff3 and the VCF file are not properly limited by xlim, and when all tracks are plotted together the xlim I specified is ignored. ...
ggbio written 11 months ago by marisa.e.miller0
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makeTxDbFromGFF error "stop codons that cannot be mapped to an exon"
... Hello, I am trying to use makeTxDbFromGFF to import my GFF3 file as a TxDb. Below is the code used and the links to the relevant files: library(GenomicFeatures) chromlen <- read.delim("Puccinia_coronata_avenae_12SD80.primary.chromlen", header = FALSE) colnames(chromlen) <- c("chrom", "lengt ...
genomicfeatures txdb maketxdbfromgff written 15 months ago by marisa.e.miller0 • updated 15 months ago by daniel.vantwisk50
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ClusterProfiler dotplot formatting
... Hello, I've been using clusterProfiler enrichGO to test for enrichment and make summary dotplots. However, the plots sometimes cut off the bubbles on the right edge (see link below). Do you have any recommendations for fixing this issue? Thanks, Marisa   https://drive.google.com/open?id=0B9ZB8R ...
clusterprofiler written 2.3 years ago by marisa.e.miller0 • updated 2.3 years ago by Guangchuang Yu1.1k
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Comment: C: AnnotationForge makeOrgPackage rsqlite_send_query error
... I realized my issues. 1) I need a column titled "EVIDENCE" for the GO table, and 2) I put a duplicate column in the genelist table so that the dataframe now has two columns. This is the output I saw after running makeOrgPackage and I think it shows a successful DB creation: Populating genes table ...
written 2.3 years ago by marisa.e.miller0
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AnnotationForge makeOrgPackage rsqlite_send_query error
... I am trying to make a custom OrgDB for use with clusterProfiler and am encountering the following error message: > nc29_genes = read.csv("nc29.genelist.txt", sep="\t", header=TRUE) > nc29_genes$GID <- as.character(nc29_genes$GID) > nc29_go = read.csv("nc29.genes.go.txt", sep="\t", head ...
annotationforge makeorgpackage written 2.3 years ago by marisa.e.miller0

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