User: marisa.e.miller

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Posts by marisa.e.miller

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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 3 months ago by marisa.e.miller0 • updated 3 months ago by daniel.vantwisk30
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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 15 months ago by marisa.e.miller0 • updated 15 months ago by Guangchuang Yu1.0k
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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 16 months 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 16 months ago by marisa.e.miller0

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