similar to: DNA

Hi, I am making some DNA distances and I would like to use dist.dna as matrix in R, but this command does not include models like GTR... Is there some command or alternative using dist.dna in ape package for models not included like GTR? I would appreciate any help given Thank you very much, Ignacio Quintero Laboratorio de biología evolutiva de vertebrados (Evolvert) Departamento de Ciencias

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DNA sequence as it is.. and calculate the statistics? Thanks! [[alternative HTML version deleted]]

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

Prof. Javier Cabrera will be giving the online course "DNA Microarray Data Analysis" from Jan. 28 - Feb. 25 at statistics.com. Dr. Cabrera is co-author of "Exploration and Analysis of DNA Microarray and Protein Array Data" (the course text; Wiley) and has published a number of articles on gene expression data analysis, data mining and multivariate methods in leading

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

I have just placed version 0.2 alpha of my library, dna, on my web page at www.luc.ac.be/~jlindsey/rcode.html The R functions in this library cover most of the basic methods of dna and protein sequence analysis. The library includes ports of CLUSTAL W for multiple sequence alignment and flip for finding open reading frames in a dna sequence. There are an enormous number of interesting and

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

Hi all, I am interested in calculating and displaying the distributions of pairwise comparisons between DNA sequences in populations. The comparisons are the number of nucleotide sites that differ between the two sequences (mismatches). My sequences are stored in a vector of strings. There is an additional vector of the same length that provides the indices to the DNA sequences. Finally, I

Hi all, I have been asked to look into using asterisk as part of our setup. The eventual goal is to replace as many parts of the existing setup as possible, but in the interim, I just have to make it bolt on and work with all existing parts. My current setup is as follows: Cisco 7940 (ext 2000) | v Asterisk -> Snom SIP proxy(v2.22) -> Vega100 PSTN gw -> Index PBX |

Dear all, I was wondering how to read DNA sequences in R, is there a specific function and/or a specific package for that? Thank you very much in advance, Gian ** [[alternative HTML version deleted]]

Hi, recently, I got a bunch of DNA sequences (with chromosome coordinate for each sequence), I would like to know the relative distance between these sequences and all the genes (genomic sequences) on human genome, i.e., are these sequences locate at upstream of the genes(5 prime end), downstream of the genes(3 prime end) or within the genes. I have about 8000 sequences. Any package, methods

Hello all, Does anyone know of a function for calculating the permanent of a matrix? I have found only the function for calculating a matrix's determinant, and my beginner attempts to figure out a working script (see below) have failed. (That is, I don't get the same answer as when I calculate the permanent in Maple or Mathematica.) My understanding and experience is that it can be

Hi, I am trying to test the proportional-odds model using the "polr" function in the MASS library with the dataset of "housing" contained in the MASS book ("Sat" (factor: low, medium, high) is the dependent variable, "Infl" (low, medium, high), "Type" (tower, apartment, atrium, terrace) and "Cont" (low, high) are the predictor variables

Hello All, Ipsos is currently hiring a Data Scientist, if this position is of interest, please apply using the link below.?? If you have any questions, please do not hesitate to reach out to me directly. Data Scientist - Culver City, CA Summary: A capable and creative programmer with unrelenting attention to detail, an ability to work well with a small team (including both programmers and

Hello All, Ipsos is currently hiring a Data Scientist, if this position is of interest, please apply using the link below.?? If you have any questions, please do not hesitate to reach out to me directly. Senior Data Scientist - Culver City, CA Summary: A capable and creative leader who is experienced in designing, conducting and selling Data Science analytics.? Role includes sales and

Hi, I found a way to delete these ghost entries. All you need is an LDAP tool like Apache Directory Studio. Then you connect via LDAP to the AD. Inside the LDAP tree is a subtree named msdns (or similiar, I'm not able to access my workstation at the moment). There you can find the buggy entry and delete it. Before deleting something it's perhaps a good idea to make a backup of the samba

Easy job with the right tool! Open Apache Directory Studio, select the LDAP browser -> New Connection Enter the server/hostname: dc1.samdom.com -> next Select simple authentication, user: samdom\administrator, password Check authentication and connect. Browse to the corresponding DNS entry: LDAP-Browser Root DSE DC=DomainDnsZones,DC=samdom,DC=com CN=MicrosoftDNS

I'm doing prediction of the survival cases using gene expression profiles(Affymetrix chips). Can somebody tell me how to use the Cox PH model to select genes and make a prediction of survival? Thanks. Guangchun

On 08/03/15 22:06, Tim wrote: > Anyone checked/reproduced this steps with ADSI Editor? > > Regards > Tim > > Am 8. M?rz 2015 23:00:33 MEZ, schrieb Peter Serbe <peter at serbe.ch>: >> Easy job with the right tool! >> >> Open Apache Directory Studio, select the LDAP browser -> New Connection >> >> Enter the server/hostname: dc1.samdom.com