User: vinod.acear
vinod.acear • 30
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- India
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Posts by vinod.acear
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... I want to save a mutation data avalable in df format to a .vcf file, But not getting any way to do this. Please advise
> head(sample.mut.ref)
Sample chr pos ref alt
1 1 chr1 905907 A T
2 1 chr1 1192480 C A
3 1 chr1 1854885 G C
4 1 chr1 9713992 G A ...
written 7 months ago by
vinod.acear • 30
• updated 7 months ago by
shepherl ♦♦ 890
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... I have two R installed
1. on a cluster admin account that has "R" (/home/vs580/R/x86_64-pc-linux-gnu-library/3.4 ) directory in my home to contain some locally installed packages.
2. Because of permission issues, I have installed R locally in "home/vs580/My_R/"
But when I install Bioconductor pac ...
written 8 months ago by
vinod.acear • 30
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... I am trying to run CDHIT , on DNAStringSet object of DNA sequences to get non-redundent set of sequences
library(Biostrings)
library("BioSeqClass")
## flank is DNAStrinSet object of equal length sequences
seq = as.character(flank)
## Homolog reduction of whole-length sequence by cd-hit need c ...
written 17 months ago by
vinod.acear • 30
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... Thanks Martin. I know its inefficient way, but this was required as an input for a already written function. I will try to modify it further.
...
written 18 months ago by
vinod.acear • 30
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... Hi
Please help me to convert the DNA sequences of a "DNAStrinset" object to the list of DNA sequences.
Here is the description below:
Input:
> s1
A DNAStringSet instance of length 5
width seq
[1] 7 AGGCTCT
[2] 6 AGGTCT
[3] 7 AGGGTGT
[4] 7 AGGCTCT
[5] 7 TTCGGTA
I ...
written 18 months ago by
vinod.acear • 30
• updated 18 months ago by
Martin Morgan ♦♦ 22k
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... How to draw phylogeny tree of 1100 genomes belonging to diffrent linages of same spices, Where each sequence consists of ~100000 SNPs locations of genome, I tried 'msa' package with default parameters, but it is taking much longer time. Please suggest me any trick to do this.
...
written 2.0 years ago by
vinod.acear • 30
• updated 2.0 years ago by
UBodenhofer • 250
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... Hi, I tried to install "GeneRfold" package, but there is an incompatibility is present between the version of R and package. It is also showing incompatibility of system in installing "GeneR" which is required package for "GeneRFold" (https://support.bioconductor.org/p/82120/#82161)
Please suggest ...
written 2.6 years ago by
vinod.acear • 30
• updated 2.6 years ago by
Martin Morgan ♦♦ 22k
0
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Comment:
C: GeneR installation error
... Thanks, Martin, Can you please tell me, is it possible to way to install this package. I need this package to install geneRFold package.
...
written 2.6 years ago by
vinod.acear • 30
1
vote
1
answer
415
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... Hi, i am getting following error on installing GeneR package. It is showing incompatibility with my R version. Please suggest me solution
The downloaded source packages are in
‘/tmp/Rtmp0hTDVB/downloaded_packages’
Warning message:
package ‘GeneR’ is not available (for R version 3. ...
written 2.6 years ago by
vinod.acear • 30
• updated 2.6 years ago by
Martin Morgan ♦♦ 22k
0
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... Hi
I have two classes of DNA sequences to classify using hidden Markov model, but I could not found the appropriate package in R., Please tell me about any available package to do my task.
...
written 2.7 years ago by
vinod.acear • 30
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