User: vinod.acear

gravatar for vinod.acear
vinod.acear20
Reputation:
20
Status:
New User
Location:
India
Last seen:
3 weeks, 5 days ago
Joined:
2 years, 9 months ago
Email:
v**********@gmail.com

Posts by vinod.acear

<prev • 48 results • page 1 of 5 • next >
0
votes
1
answer
84
views
1
answer
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 9 weeks ago by vinod.acear20 • updated 8 weeks ago by shepherl ♦♦ 640
0
votes
0
answers
92
views
0
answers
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 3 months ago by vinod.acear20
0
votes
0
answers
187
views
0
answers
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 12 months ago by vinod.acear20
0
votes
2
answers
369
views
2
answers
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 12 months ago by vinod.acear20
3
votes
2
answers
369
views
2
answers
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 12 months ago by vinod.acear20 • updated 12 months ago by Martin Morgan ♦♦ 22k
0
votes
1
answer
338
views
1
answer
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 19 months ago by vinod.acear20 • updated 19 months ago by UBodenhofer250
0
votes
1
answer
355
views
1
answer
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 2.2 years ago by vinod.acear20 • updated 2.2 years ago by Martin Morgan ♦♦ 22k
0
votes
1
answers
351
views
1
answers
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 2.2 years ago by vinod.acear20
1
vote
1
answer
351
views
1
answer
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 2.2 years ago by vinod.acear20 • updated 2.2 years ago by Martin Morgan ♦♦ 22k
0
votes
0
answers
243
views
0
answers
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 2.3 years ago by vinod.acear20

Latest awards to vinod.acear

Popular Question 12 months ago, created a question with more than 1,000 views. For Extract three types of intergenic regions
Popular Question 19 months ago, created a question with more than 1,000 views. For How to remove out of bound rows from granges
Popular Question 19 months ago, created a question with more than 1,000 views. For Non overlapping granges (or opposite of subsetByOverlaps)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 203 users visited in the last hour