User: Pariksheet Nanda

Reputation:
70
Status:
Trusted
Location:
University of Connecticut
Last seen:
2 months, 1 week ago
Joined:
1 year, 5 months ago
Email:
p***************@uconn.edu

Posts by Pariksheet Nanda

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answers
321
views
1
answers
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 10 weeks ago by Pariksheet Nanda70
0
votes
1
answers
321
views
1
answers
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 10 weeks ago by Pariksheet Nanda70
0
votes
1
answers
321
views
1
answers
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 10 weeks ago by Pariksheet Nanda70
0
votes
2
answers
304
views
2
answers
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 10 weeks ago by Pariksheet Nanda70
0
votes
1
answers
253
views
1
answers
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 11 weeks ago by Pariksheet Nanda70
0
votes
0
answers
253
views
0
answers
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 11 weeks ago by Pariksheet Nanda70
0
votes
0
answers
245
views
0
answers
Comment: C: Why does total unique map not equal to library size?
... Can you post the full log, please?  Also point out where what particular line in the log has the unexpected number.   ...
written 11 weeks ago by Pariksheet Nanda70
0
votes
2
answers
317
views
2
answers
Answer: A: Error when running "locateVariants" function in "VariantAnnotation" package
... 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 11 weeks ago by Pariksheet Nanda70
0
votes
2
answers
304
views
2
answers
Comment: C: SNP location annotation problem in "VariantAnnotation" package
... You need to make your Google Drive links publicly accessible. ...
written 11 weeks ago by Pariksheet Nanda70
0
votes
1
answers
287
views
1
answers
Answer: A: what is this error for TPP package
... The problem is VGAM requires R >= 3.4.0 as shown on the CRAN page, but you are using R 3.3.3 Upgrade your version of R. ...
written 11 weeks ago by Pariksheet Nanda70

Latest awards to Pariksheet Nanda

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 392 users visited in the last hour