User: vinod.acear

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vinod.acear40
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40
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New User
Location:
India
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5 months, 1 week ago
Joined:
4 years ago
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v**********@gmail.com

Posts by vinod.acear

<prev • 48 results • page 1 of 5 • next >
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Is there any way to write my mutation dataframe to vcf file?
... 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 ...
writevcf deconstructsigs vcfr mutationalpattern synbreed written 17 months ago by vinod.acear40 • updated 17 months ago by shepherl ♦♦ 1.6k
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installation of Biocunductor packages in My home directory.
... 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 ...
biocinstaller installr package installation written 18 months ago by vinod.acear40
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How to run a CDHIT command of "BioSeqClass" package on DNAStringSet object of DNA sequences to get non-redundent set of sequences?
... 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 ...
biostrings bioseqclass cd-hit cdhit written 2.2 years ago by vinod.acear40
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Comment: C: How to convert a DnaStringSet object to list of seq?
... 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 2.3 years ago by vinod.acear40
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How to convert a DnaStringSet object to list of seq?
... 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 ...
list dnastringset stringset written 2.3 years ago by vinod.acear40 • updated 2.3 years ago by Martin Morgan ♦♦ 23k
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How to draw phylogeny tree for long genomes? ('msa' taking much time)
... 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. ...
phylogenetic msa written 2.9 years ago by vinod.acear40 • updated 2.9 years ago by UBodenhofer250
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Installation error GeneRFold and GeneR.
... 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 ...
gener generfold written 3.5 years ago by vinod.acear40 • updated 3.5 years ago by Martin Morgan ♦♦ 23k
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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 3.5 years ago by vinod.acear40
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GeneR installation error
... 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. ...
gener written 3.5 years ago by vinod.acear40 • updated 3.5 years ago by Martin Morgan ♦♦ 23k
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Package for classifying two classes of sequences using hidden markov models?
... 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. ...
classification hmm written 3.5 years ago by vinod.acear40

Latest awards to vinod.acear

Popular Question 14 months ago, created a question with more than 1,000 views. For Extract three types of intergenic regions
Popular Question 14 months ago, created a question with more than 1,000 views. For Extract three types of intergenic regions
Popular Question 14 months ago, created a question with more than 1,000 views. For How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to remove out of bound rows from granges
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Extract three types of intergenic regions
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to remove out of bound rows from granges
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Non overlapping granges (or opposite of subsetByOverlaps)

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