User: Arman Shahrisa

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Posts by Arman Shahrisa

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Comment: C: Obtain GRanges object by gene names
... What I need is genome information in GRanges. Then I need to subset my desired genes. I would really appreciate any suggestions. ...
written 12 months ago by Arman Shahrisa10
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Obtain GRanges object by gene names
... I want to create a plot to show how desired genes are located across the different chromosomes with IdeoViz. How can I create a GRanges object that includes 24 chromosomes but only genes that I want? The plot needs it as input. ...
granges gene symbol ideoviz written 12 months ago by Arman Shahrisa10
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Is there a package that help me draw copy number alteration for each chromosome?
... Hi everyone. Is there any Bioconductor Package that could help me simply draw something like this by using gene locations and numeric copy number values and it doesn't need a complicated class of data as input?   ...
copynumber alteration written 14 months ago by Arman Shahrisa10
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Is there any prerequisites for taking correlation in genomic data?
... I know this question might not be related to Bioconductor but I couldn't think of anywhere else. When I take correlation between two genes, should I exclude genes that their expression is not meaningful? Additionally, should I exclude samples that their z-score is under e.g. z-score = 2? Or should I ...
correlation written 21 months ago by Arman Shahrisa10 • updated 21 months ago by chris86390
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Comment: C: How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
... Exactly! Thank you very much. ...
written 2.2 years ago by Arman Shahrisa10
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How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
... How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)? Is there any package(s) that lets me convert the gene symbol to cytogenetic bands? ...
bioconductor cytogenetics written 2.2 years ago by Arman Shahrisa10 • updated 2.2 years ago by Martin Morgan ♦♦ 24k
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How can I mention separate creator and correspondence in a package?
... I'm developing a Bioconductor package in which I'm a creator, author, and maintainer. But someone else is the corresponding author. Is the following code correct in the package description?   Author: c(person(first = "A****", last = "S*******",                             email = "s*************** ...
package description written 2.6 years ago by Arman Shahrisa10 • updated 2.6 years ago by Martin Morgan ♦♦ 24k
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Comment: C: I'm developing a package. How can I specify a dependent package to be installed
... Hi, My package requires "xlsx" package to export data as excel files. Even with java runtime environment installed, R returns an error during the installation of "xlsx" package. I googled it and found "install.packages("xlsxjars", INSTALL_opts = "--no-multiarch")" in a forum. It fixed the problem f ...
written 2.6 years ago by Arman Shahrisa10
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I'm developing a package. How can I specify a dependent package to be installed with an option?
... I'm developing a package. How can I specify a dependent package to be installed with an option? For example, inside description file: Depends: cgdsr, xlsx, gplots, RColorBrewer, rafalib, Biobase, genefilter, xlsxjars I manually install the "xlsxjars" package as "install.packages("xlsxjars", INSTA ...
package dependency written 2.6 years ago by Arman Shahrisa10 • updated 2.6 years ago by Hervé Pagès ♦♦ 14k
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Comment: C: How to create automated cbind in a for loop
... I fixed the problem. It was a "E" instead of "e". I appreciate for your time. ...
written 3.9 years ago by Arman Shahrisa10

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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Database download ends with error for AnnotationHub

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