User: Pariksheet Nanda

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University of Connecticut
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p***************@uconn.edu

Posts by Pariksheet Nanda

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Rbowtie fails to compile with gcc 9.1.0 with error: reference to Byte is ambiguo
... Fault persists using the same compiler and flags as the Bioconductor malbec2 build server. I found Bioconductor's report for the build server and Rbowtie installation: 1. Build server compiler and compiler flags: https://bioconductor.org/checkResults/3.9/bioc-LATEST/malbec2-NodeInfo.html 2. Rbowti ...
written 4 weeks ago by Pariksheet Nanda110
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Comment: C: Rbowtie fails to compile with gcc 9.1.0 with error: reference to Byte is ambiguo
... Edit: I fixed the md5-* injections by adding newlines between code blocks. I'm not sure why the post has all the md5-* nonsense that wasn't in the preview >_< ...
written 4 weeks ago by Pariksheet Nanda110
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Rbowtie fails to compile using spack with "error: reference to Byte is ambiguous"
... Edit: The fault happens with gcc 7.4.0 that the bioconductor build server uses, in addition to gcc 9.1.0 There appears to be a C++ namespace collision between bowtie's bundled dependency `seqan::Byte` against zlib's `Byte`: ``` > BiocManager::install("Rbowtie") ...
rbowtie software error written 4 weeks ago by Pariksheet Nanda110
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Comment: C: co-evolution analysis for RNA
... I think most phylogeny computation programs (paup*, mrbayes, etc) tend to be run outside of R using nexus files, while R packages are used more for analyzing the trees and plotting (ggtree, ape, etc). For literature searches, you probably need to define the type of interaction between your ncRNA an ...
written 12 months ago by Pariksheet Nanda110
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Comment: C: Problems install R XML package on CentOS 7
... Ah, so you're using Anaconda's R distribution.  Why don'y you use the conda package for CRAN's XML (called r-xml)?  To reproduce your problem I installed Anaconda3 4.4.0 on RedHat 7.4, then: cat 'export PATH=$PATH:~/anaconda3/bin' >> ~/.bashrc source ~/.bashrc conda install -c r r-essentials ...
written 21 months ago by Pariksheet Nanda110
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Comment: C: Problems install R XML package on CentOS 7
... Looks like the new markdown functionality is affecting the last section`# Install XML` with an `a href` tags, but looks normal when I try to edit the post. Rewritten here without markdown: # Install XML R -q --vanilla < devtools::install("./XML", force = TRUE, args = "--configure-args='--with-l ...
written 21 months ago by Pariksheet Nanda110
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Answer: A: Problems install R XML package on CentOS 7
... Generally to troubleshoot a configure problem, you should download the package tarball, run the installation, and inspect the config.log file. The problem in this case is the configure script incorrectly judges you to be using libxml 1 from parsing the include directory. If it detects the directory ...
written 21 months ago by Pariksheet Nanda110
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Answer: A: SNP location annotation problem in "VariantAnnotation" package
... None of those snips fall within transcripts: > intersect(transcripts(txdb), rd_abnorm) GRanges object with 0 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> ------- seqinfo: 47 sequences (1 circular) from 2 genomes (hg38, NA); n ...
written 21 months ago by Pariksheet Nanda110
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Comment: C: Solving error for error of factors
... For us to reproduce the problem, can you share the download link for TCGA as well as any additional steps to get your 5 sample files? ...
written 21 months ago by Pariksheet Nanda110
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Comment: C: subsetting GRanges object based on gene IDs
... Hi Assa, Don't worry about embarrassment.  You asked an excellent question about programming efficiently that's also useful to others reading the support site. As far as resources go, %in% is not discussed in the GenomicRanges  introduction vignette, though it is mentioned in man page examples and ...
written 21 months ago by Pariksheet Nanda110

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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: SNP location annotation problem in "VariantAnnotation" package

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