search for: seqinr

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPl...

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPl...

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusi...

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusi...

...omaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem with same commend .  > mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") > seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) Error in length(x) : 'x' is missing I need to use...

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC serv...

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC serv...

Dear R developers I am currently working on the seqinR package. The seqinR package allows a remote access to biological databases via a socket connection. We are using the functions socketConnection, writeLines and readLines to open the socket, send request to the server and receive response from the server respectively. Recently, a new func...

Hi everyone I have got a quick question: I the "seqinr" package: *dist.alignment(x,"identity")* This is calculating the square root of pairwise distances. Does anyone know whether/how gaps are counted in this function? Thank you. Best wishes, Bettina [[alternative HTML version deleted]]

Hi I would like to use 'write.fasta(sequences, names, nbchar = 60, file.out, open = "w")' to convert a DNA sequence in a text file to fasta format. How do I read the the text file to prepare the argument 'sequences' of the function. The DNA sequence in the text file is one line as below: ATCACACAACGACACTCACCCTGGACGCTCATC......... Thank you [[alternative HTML

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

Good afternoon. I am a master student in University of Porto in Portugal. At this moment I’m starting to use R, so I have some doubts. The aim of my analysis is: calculate a pairwise FST matrix from fasta file and creat a principal component analyses with adegenet package (I use seqinr and ape package to read this file, then I convert this file into a genind object with DNA2genind function provide in adegenet package). After convert my file the pairwise.fst function is not found. If you could help me would be great. Greetings: Rui Oliveira -- ---------------------------------...

...df[-ns,] } } return(as.data.frame(df)) } > bam <- read.bam("../../example/SRR389185_vs_SINV_sorted.bam", chr="SINV") > # works! remove the function > rm(read.bam) > # load the package > library(viRome) Loading required package: seqinr Attaching package: ?seqinr? The following object(s) are masked from ?package:Biostrings?: translate Loading required package: plyr Attaching package: ?plyr? The following object(s) are masked from ?package:seqinr?: count The following object(s) are masked from ?package:IRanges?:...

Hello R developers, I am working on the "seqinr" package and I encounter a tricky problem using a C function. We defined a C fonction called "getzlibsock" which is dedicated to compressed socket connections. This function is using the R internal C function called "getConnection(int)" in order to get information ab...

Hello, I have a problem with the hist() function and showing densities. The densities sum to 50 and not to 1! I use R version 2.9.1 (2009-06-26) and I load the seqinR library. My data is the following vector: [1] 0.1400000 0.2000000 0.2200000 0.2828283 0.1600000 0.1600000 0.3600000 [8] 0.1600000 0.2200000 0.2600000 0.2000000 0.3000000 0.2200000 0.2342342 [15] 0.1800000 0.2200000 0.1600000 0.2300000 0.2000000 0.2200000 0.2400000 [22] 0.2000000 0.2200000 0.220000...

...works until the *"write.dna" *command - which is not creating the fasta file. Here is my code: ####Get gene sequence from GenBank and store it as fasta file ####16 June 2017 #1- Set the working directory and make sure the right libraries are installed (make sure 'ape' and 'seqinr' packages are installed) WD <- "~Documents/Scripting/R_Studio/Sequences/" setwd <- (WD) #2- Fetch a sequence ( bellow, "enter manually the desired DNA ID") from GenBank and store it as fasta file. DNAid <- "JF806202" # Store the sequence in...

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as

Hi all, Does anyone know what happened to the dna library or the dotmatrix function? For the life of me, I can't find it anywhere with the exception of this reference: http://rss.acs.unt.edu/Rdoc/library/dna/html/dotmatrix.html Thanks! Jeff. http://www.nd.edu/~jspies/ [[alternative HTML version deleted]]

Dear Sir or Madam, I am very new to R, and I am trying to install seqinr-package. In the manual I read that I need to install ape-package first, and I failed to do it. I had the following error messges: /usr/bin/ld: cannot find -lgfortran collect2: ld returned 1 exit status make: *** [ape.so] ?????? 1 ERROR: compilation failed for package 'ape' ** Removing '...