similar to: The aphid package for analysis with profile hidden Markov models

Dear all, I'd like to introduce a new R package called *phylogram,* for working with evolutionary trees as deeply-nested lists known as "dendrogram" objects. The package provides functions for importing and exporting phylogenetic trees in the Newick parenthetic text format, as well as several functions for command-line tree manipulation. With an emphasis on speed and computational

library(sos) (mp <- findFn('{molecular properties}')) ????? ** found 7 matches in 4 packages and opened two web pages in my default browser with (a) the 7 matches and (b) the 4 packages. The first function was something for amino acids, like you suggested.? Two others returned compound and substance information from PubChem. ????? Does this help? ????? Spencer On

All Is there a package or library that will, given a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be

... In addition, you may wish to also post on the Bioconductor list for this sort of thing. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, May 3, 2018 at 12:58 AM, Spencer Graves <spencer.graves at effectivedefense.org>

Hi all, I am using a discrete Hidden Markov Model with discrete observations in order to detect a sequence of integers. I am using the "hmm.discnp" package. I am using the following code: signature <- c(-89, -98, -90, -84, -77, -75, -64, -60, -58, -55, -56, -57, -57, -63, -77, -81, -82, -91, -85, -89, -93) quant <- length(-110:-6) # Initialize and train the hmm with the

R Community - I am attempting to fit a model as described in Hampton, Bossaerts, and O'doherty (J. Neuroscience) 2006. They use a bayesian hidden markov model to model the Reversal Learning data. I have tried using HMM and depmixS4 with no success. My data is a Reversal Learning Task in which there are 3 sets of patterns over 3 blocks. The participant receives incorrect or correct

Dear group, I tried to run a Repeated Mesures Anova for Mixed effects model and I got a warnning after entering the model specification saying: "Reached total allocation of 254Mb: see help(memory.size)". here is part of the log: *********************************************************** > aphids<-read.table("aphid.txt",header=T) > attach(aphids) > names(aphids)

Hi I am running some linear and non-linear mixed effect models and would like to do some planned contrasts (a priori contrasts) I have looked in the help and in many forums and it seems possible to do so but don't understand how to write the function and I couldn't find an example in Pinheiro and Bates. lme {nlme} has a contrasts argument but I can't understand how to code it.

Hello, I have two tab-delimited files which I would like to combine. In the first one I have gene IDs (Unique) on column 1 and than various experimental results from microarray analysis (see attached files list1 ) the second arrays have the same genes IDs (more and in a different order, some are double) (see attached files list2 ) What I would like to do is to search in the second list for gene

Dear list, This question is about Hidden Markov Model. Given a transition matrix, an emission matrix and a sequence of observed symbols (actually, nucleotide sequences, A, T, C and G), I hope to predict the sequence of state by Viterbi algorithm. I searched R repository for related packages. msm package has function viterbi.msm (as well as very good document), but it only works for

Hi, I am performing a repeated measures 2-way ANOVA to assess the influence of plant and leaf on aphid fecundity. Fecundity is measured for each aphid on a single leaf. Here is what I typed. wingless <- reshape(Wingless, varying =

Is it just me, or is the bio3d package no longer available? Is there another way to do a reasonable nucleic acid sequence alignment in R? Thanks, Jonathan [[alternative HTML version deleted]]

(I think) I'd like to use the hmm.discnp package for a simple discrete, two-state HMM, but my training data is irregularly shaped (i.e. the observation chains are of varying length). Additionally, I do not see how to label the state of the observations given to the hmm() function. Ultimately, I'd like to 1) train the hmm on labeled data, 2) use viterbi() to calculate optimal labeling of

I have two large arrays of strings array1 with 180000 names and array2 with 24000 names ,I want to find the common names in both of them. My arrays are for example Array1 Array2 GAP4 HIST1B-histamine.... MFG12 SNRPD-signal induced... CFH1A

Hello, I am interested in using the capscale function of vegan package of R. I already have a dissimilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to

Hello R-Community, we are running aprogram to fit Non-linear differential equations to Aphid population Data and to estimate the birth and death parameters, here is the code: dat<-data.frame(Time=c(0:60),Cur=c(5,6.2,59,39,38,44,20.4,19.4,34.2,35.4,38.2,48.2,55.4,113.2, 97,112,115,126,136.6,140.6,147.2,151.6,157.8,170,202,210.4,221.2,224.4,248.2,266,

Greetings. I'm a Master's student working on an analysis of herbivore damage on plants. I have a tried running a glm with one categorical predictor (aphid abundance) and a binomial response (presence/absence of herbivore damage). My predictor has four categories: high, medium, low, and none. I used the "ordered" function to sort my categories for a glm. ah <-

Post-hoc test for a zero inflated continuous data set with a tweedie distribution? I have a zero inflated continuous data set of aphid feeding duration on 10+ species of plant. I have fitted a glm model with a tweedie distribution and used anova() function to show that there is significance between the plant species. However, I would now like to perform of post-hoc test, ideally a Tukey-Kramer

Dear R users, I am looking for the source code of the implementation of ppr (Projection Pursuit Regression) in R. It will be great if citations of the source papers on which the implementation is based, are also provided. Thank you, Arvind Iyer, Grad student, Deptt. of Biomedical Engineering Viterbi School of Engineering University of Southern California, Los Angeles [[alternative HTML

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 dotPlot() is now available.