User: winstondunnmd

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Posts by winstondunnmd

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Comment: C: Can't install Genesis
... However, I can't load the library and other functions of Genesis. > library(GENESIS) Error: package or namespace load failed for ‘GENESIS’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘RSQLite’ Is there a way to install using administrator pr ...
written 6 days ago by winstondunnmd0
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Can't install Genesis
... I have difficulty installing the Genesis package. Please kindly advise. > BiocManager::install("GENESIS") Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'GENESIS' trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/windows/contrib/3.6/GENESIS_2 ...
installation genesis written 6 days ago by winstondunnmd0 • updated 6 days ago by Mike Smith3.9k
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Comment: C: Can't install TopmedPipeline Package
... Thank you Shepherl, it worked. In summary, the installation code for TopmedPipeline is: install.packages("devtools") install.packages("jomo") devtools::install_github("UW-GAC/analysis_pipeline/TopmedPipeline/") ...
written 6 days ago by winstondunnmd0
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Comment: C: Can't install TopmedPipeline Package
... Thank you again Shepherl, Got a short run with this error message: Installing package into ‘C:/Users/winst/Documents/R/win-library/3.6’ (as ‘lib’ is unspecified) * installing *source* package 'TopmedPipeline' ... ** using staged installation ** R ** data ** inst ** ...
written 6 days ago by winstondunnmd0 • updated 6 days ago by Martin Morgan ♦♦ 23k
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Comment: C: Can't install TopmedPipeline Package
... Thank you for you help Shepherl, With BiocManager I got this error message: Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing github package(s) 'remotes UW-GAC/analysis_pipeline/TopmedPipeline/' Error: Failed to install 'unknown package' from GitHub: attempt to set an ...
written 7 days ago by winstondunnmd0
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SeqVarData Error sample.id in sampleData does not match GDS file
... Illumina did my WES and returned very complex and bizzare sample.id like "Sample_CU-18" and "Sample_24" despite I supplied them with simple 3 digit code 018, 024. When I ran SeqVarData: seqData <- SeqVarData(gds, sampleData=annot) it returned the following error: Error in SeqVarData(gds, sampleD ...
seqvardata sample.id written 7 days ago by winstondunnmd0
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Can't install TopmedPipeline Package
... I am a student of SISG Module 17. We learned about the TopmedPipeline functions during the module. This is an extremely useful package but I have only been able to run this through the DataStage and not my own computer. I am simply not able to install TopmedPipeline. https://cran.rstudio.com/bin/wi ...
topmedpipeline written 7 days ago by winstondunnmd0 • updated 7 days ago by shepherl ♦♦ 1.4k
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Comment: C: seqVCF2GDS Error Converting VCF to GDS file
... Thank you Stephanie! The Illumina Basespace provides 2 apps for making the VCF files: the "Enrichment" and "BWA Enrichment" cost exactly the same. When I generated the VCF files with BWA Enrichment it did not cause the problem. ...
written 7 days ago by winstondunnmd0
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seqVCF2GDS Error Converting VCF to GDS file
... Dear Bioconductor: I am a student of SISG Module 17 and used the code to convert my VCF file to GDS file. vcffile <- "data/72_S1.vcf.gz" gdsfile <- "data/72_S1.gds" seqVCF2GDS(vcffile, gdsfile, fmt.import="GT", storage.option="LZMA_RA", verbose=FALSE) The VCF file is generated from WES of h ...
software error seqarray seqvcf2gds written 9 days ago by winstondunnmd0 • updated 7 days ago by zhengx30

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