Displaying 20 results from an estimated 500 matches similar to: "ape 0.1 is released"
2000 May 18
1
tutorial "R pour les débutants" is available on CRAN
Dear R-users,
Thanks to Friedrich Leisch, my document "R pour les d?butants" is available
on CRAN in the contributed documentation section:
http://cran.r-project.org/doc/contrib/Rdebuts.pdf.
It is written in French. "R pour les d?butants" ("R for beginners") gives a
starting point for people with no experience with R (or S). I tried to
explain the basics in the
2000 May 18
1
tutorial "R pour les débutants" is available on CRAN
Dear R-users,
Thanks to Friedrich Leisch, my document "R pour les d?butants" is available
on CRAN in the contributed documentation section:
http://cran.r-project.org/doc/contrib/Rdebuts.pdf.
It is written in French. "R pour les d?butants" ("R for beginners") gives a
starting point for people with no experience with R (or S). I tried to
explain the basics in the
2007 Apr 24
0
new version of seqinR
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 server is released.
Preliminary tests suggest that working with about 100,000
2007 Apr 24
0
new version of seqinR
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 server is released.
Preliminary tests suggest that working with about 100,000
2003 Mar 10
0
ape 1.0 is on CRAN
Dear all,
The version 1.0 of ape (analysis of phylogenetics and evolution) is now on
CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the
initial objectives of the project have been completed. The relevant part of
the Changes file is shown below. All comments, suggestions, or bug reports
are welcome.
Emmanuel Paradis
CHANGES IN APE VERSION 1.0
NEW FEATURES
2002 Nov 29
1
KS for goodness of fit
Dear All,
I have two distributions which I don't their nature. I want to check whether they come from the same distribution. I know that I can use KS test however the standart function ks.test applies only the ks test for testing the difference of two samples (non-parametric). By the way the distribution are of Euclidean distances. One of observed and the other of shuffled data.
Thanks,
Ron
2002 Dec 19
2
More on scan()
Hi,
If I have a CSV file which has several comments at the top, and the data
start immediately after the line:
@DATA
Is it possible to use the scan() command to get the CSV data into R, by
only reading the lines after @DATA? If so, how can I do it?
Cheers,
Kevin
------------------------------------------------------------------------------
/* Time is the greatest teacher, unfortunately it
2006 Aug 21
1
Escaping " ' " character
Dear all:
I have a character object x with ' (single-quote)
character.
x <- c('"hydrolase activity","actin
binding","3',5'-cyclic-nucleotide phosphodiesterase
activity")
I want to write a function that will identify ' and
replaces with \'
myf <- function(term){
if (grep("'",term))
{
2012 Feb 16
1
help with ancestral.pars in phangorn package
Hello, I'm struggling with understanding the output on the ancestral.pars()
command from the phangorn package, I'm new to doing phylogenetic analyses
using R.
I used it on nucleotide data, and it works fine, I'm just not sure how to
read the output.
The output is phyDat class, and outputs a matrix for each node/leaf in the
tree. I figured out that the matrix columns represent the four
2000 Oct 27
1
par(ask=T) in termplot() (PR#711)
At 11:57 25/10/00 +0100, Brian Ripley wrote:
>> Date: mer., 25 oct. 2000 12:38:55 +0200
>> From: Emmanuel Paradis <paradis@isem.univ-montp2.fr>
>
>> I think it would be nice to have par(ask=T) set by default in termplot(),
>> like it is in plot.lm().
>
>Well, it isn't really the default in plot.lm, the default for `ask' being
>
>interactive()
2011 Jan 28
1
Help with ape - read.GenBank()
Hi,
I am trying to work with the ape package, and there is one thing I am
struggling with. When calling the *read.GenBank()* function, I can get it
to work with an object created like this:
*>x <- c("AY395554","AY611035", ...)*
*>read.GenBank(x)*
However, I am trying to use the function to fetch several hundred sequences
at once. So I have been testing with small
2010 Feb 20
0
new package RFLPtools
The new package RFLPtools is available on CRAN.
RFLPtools provides analysis functions for DNA fragment molecular weights
(e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities.
It aims mainly at the identification of similar or identical fragment
patterns to evaluate the amount of different genotypes gained from
environmental samples during diversity studies and at further
2010 Feb 20
0
new package RFLPtools
The new package RFLPtools is available on CRAN.
RFLPtools provides analysis functions for DNA fragment molecular weights
(e.g.\ derived from RFLP-analysis) and nucleotide sequence similarities.
It aims mainly at the identification of similar or identical fragment
patterns to evaluate the amount of different genotypes gained from
environmental samples during diversity studies and at further
2001 Dec 26
3
bug with var(rep(1e30, 3)) (PR#1228)
There seems to be a bug with var() when the argument is a vector with
exactly three values of 1e30 (or close to this value). This does not happen
with twice, four (or more) times this value, or another value.
> var(rep(1e30, 3))
[1] 2.971056e+28
> var(rep(1.2e30, 3))
[1] 2.971056e+28
> var(rep(0.9e30, 3))
[1] 2.971056e+28
> var(rep(0.8e30, 3))
[1] 0
> var(rep(1e29, 3))
[1] 0
>
2017 Aug 04
1
legend and values do not match in ggplot
I have following codes for ggplots. The legends are given in the plot do
not match with the values specified in the codes given below. Your helps
highly appreciated.
Greg
library(ggplot2)
p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+
theme_bw() +theme(panel.border=element_blank()) +
geom_point(size=3)
p2<-p+scale_color_manual(name="Super.Pathway",
2007 Nov 26
1
looking for packages that visualize nucleotide sequence properties
Hi there,
I am looking for R-packages that can help me visualize properties on
nucleotide sequences. I want to display sequences in the 1-100K base range
as lines and plot features above and below those lines.
Any ideas would be welcome.
Thanks,
Bernd
2008 Dec 09
2
motif search
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..
2007 Nov 26
1
visualizing nucleotide sequence properties
Hi there,
I am looking for R-packages that can help me visualize properties on
nucleotide sequences. I want to display sequences in the 1-100K base range
as lines and plot features above and below those lines.
Any ideas would be welcome.
Thanks,
Bernd
[[alternative HTML version deleted]]
2013 Jan 04
0
FW: Index out SNP position
I think you mean between column 1 and 2 of A? Why is 36003918 not
included? It is clearly between 35838396 and 36151202 in the first row of A.
My earlier solution should work fine. Just create a new matrix AX that has
the columns switched so that the start is always column 1 and use that to
identify the ones you want to select. That way you are not modifying B. This
will be faster than checking
2012 Apr 11
0
phangorn and calculation of a rate matrix
Hi, I'm trying to calculate a ratematrix for a RNA aligment (U instead of T)
in order to use it as a ratematrix in Profidst (a phylogenetic program which
takes into account both the primary sequence and the secondary structure of
the RNA, in my case rRNA). The sequence-structure aligment has been made in
4SALE (a java app) and saved as one-letter encoded (using a 12 letters
alphabet,