## User: bright602

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#### Posts by bright602

<prev • 9 results • page 1 of 1 • next >
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... Recently, I am working on annotating the peak files using ChIPseeker. I am wondering is there away to understand the original genome distribution of each categories (promoter, 1st exon,  other exon, 1st intron, other intron, distal intergenic, etc.) from a species? In that case, I could have a basel ...
written 15 months ago by bright6020
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... Thanks for reply. I will look into that and have a try.   ...
written 16 months ago by bright6020
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... > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS High Sierra 10.13.5 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frame ...
written 16 months ago by bright6020
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... > library(clusterProfiler) > data(geneList, package='DOSE') > de <- names(geneList)[1:100] > yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01) Error in download.KEGG.Path(species) :   'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.h ...
written 16 months ago by bright6020
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... Thanks Guido, I tried to repeat but the same error message still pop out. ...
written 16 months ago by bright6020
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... Hi there, Recently I tried to use enrichMKEGG or enrichKEGG function from clusterProfiler, however, there is an error message stating that Error in download.KEGG.Module(species) :   'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... Even I tried to ...
written 16 months ago by bright6020 • updated 16 months ago by Guido Hooiveld2.5k
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... Hi, I have been trying to use the DiffBind for analyzing my ChIP-seq data; during the dba.contrast step, I came across an error that I show below. > H3K4me3 <- dba.contrast(H3K4me3, H3K4me3$masks$V1, H3K4me3$masks$S1, "V", "S",  minMembers=2) Error in pv.addContrast(pv, group1, group2, name1 ...
written 17 months ago by bright6020 • updated 17 months ago by Rory Stark2.9k
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... Hi, I came across an error when building the TxDb from GFF as follow: txdb <- makeTxDbFromGFF(gfffile, format="gff") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in .get_cds_IDX(type, phase) :   the " ...
written 21 months ago by bright6020
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... Hi there, I was trying to build the txdb file using the makeTxDbFromBiomart, however, I came across with an error. The command I typed was : dicty_txdb <- makeTxDbFromBiomart(biomart="protists_mart", dataset="ddiscoideum_eg_gene", ...
written 21 months ago by bright6020 • updated 21 months ago by Hervé Pagès ♦♦ 14k

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