User: vinod.acear

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vinod.acear20
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India
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2 weeks, 4 days ago
Joined:
2 years, 1 month ago
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Posts by vinod.acear

<prev • 46 results • page 1 of 5 • next >
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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 4 months ago by vinod.acear20
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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 4 months ago by vinod.acear20
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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 4 months ago by vinod.acear20 • updated 4 months ago by Martin Morgan ♦♦ 20k
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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 11 months ago by vinod.acear20 • updated 11 months ago by UBodenhofer200
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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 18 months ago by vinod.acear20 • updated 18 months ago by Martin Morgan ♦♦ 20k
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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 18 months ago by vinod.acear20
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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 18 months ago by vinod.acear20 • updated 18 months ago by Martin Morgan ♦♦ 20k
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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 19 months ago by vinod.acear20
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Comment: C: How to get list of E.coli genes wit their details on Genome?
... Thanks Vincent, it worked for me.  ...
written 20 months ago by vinod.acear20
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How to get list of E.coli genes wit their details on Genome?
... Hi, Is there any way to extract a list (grange) of all genes of E.Coli with their details like location, strand  type, name,. ...
biomart granges maketxdbfrombiomart written 20 months ago by vinod.acear20 • updated 20 months ago by Vincent J. Carey, Jr.6.2k

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Popular Question 11 months ago, created a question with more than 1,000 views. For How to remove out of bound rows from granges
Popular Question 11 months ago, created a question with more than 1,000 views. For Non overlapping granges (or opposite of subsetByOverlaps)

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