User: Pariksheet Nanda

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70
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Location:
University of Connecticut
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2 years, 1 month ago
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Posts by Pariksheet Nanda

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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 6 weeks ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... 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 10 months ago by Pariksheet Nanda70
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... Can you post the full log, please?  Also point out where what particular line in the log has the unexpected number.   ...
written 10 months ago by Pariksheet Nanda70
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... There are several select() functions to subset by columns. One is defined by tidyverse, but in your case select() you need the ones defined by the AnnotationDbi and biomaRt packages. You can check which select() function is first recognized in your environment by calling it without arguments: ## ...
written 10 months ago by Pariksheet Nanda70
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