Displaying 20 results from an estimated 100 matches similar to: "looking for packages that visualize nucleotide sequence properties"
2009 Jul 28
2
Looking for example of usage of function unz
I would greatly appreciate some example of correct usage of function unz.
I have to download and uncompress the following web compressef file:
ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip
I tried the following command that does not work:
Targets.rec <- readLines(zz <- unz("ftp://ftp.sanger.ac.uk/pub/mirbase/targets/v5/arch.v5.txt.homo_sapiens.zip"))
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]]
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))
{
2007 Oct 25
4
ploting labels on barplot
Again me.
I want to plot the numbers on the bars of a barplot.
This can be done using hist function when setting the label argument true
(i.e.
data <- c(1,2,3,4)
hist(data, labels=T)
When I try this using barplot I get an error:
> barplot(summary(data), labels=T)
Error in axis(if (horiz) 2 else 1, at = at.l, labels = names.arg, lty =
axis.lty, :
formal
2007 Dec 01
3
compare strings
Sorry for the question, but I really cannot find the right search terms to
find an answer..
I have a data frame with strings in some of the columns.
I want to know all the rows where the strings in both columns are equal.
How do I do this?
Thanks,
Bernd
[[alternative HTML version deleted]]
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
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",
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..
2018 May 03
3
Package for Molecular Properties
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
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
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
2007 Oct 25
2
data frame usage
Hi,
I am new to R and couldn't find any information on how to handle my table
data that I just read in the way I want to use it..
I read in a table from a file:
x <- read.delim("filenam", header=TRUE)
one column (x$label) hold the class labels. Another holds some values
(x$val).
I want to calculate summary statistics for different classes.
How would I do this?
Thanks,
Bernd
2006 Mar 22
2
R package for computing state path using Viterbi algorithm
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
2018 May 03
0
Package for Molecular Properties
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
2012 Nov 03
2
reorder() in the latticeExtra library
Hello all, thanks for your time and help. Below are my commands, and it
generates a really nice plot, however I am not happy with the reorder()
function. I would like the order to be the same as they appear in the
genotype variable "genotype <- c("CJ1450 NW 4/25/12","CJ1450 BAL
4/25/12","CJ1450 NW 4/27/12","CJ1450 BAL 4/27/12","CJ1721 NW
2007 Oct 29
2
Qsub - unable to open connection to X11 display
Hi there,
I want to run an R script on a cluster with qsub. Obviously I don't want to
display any X window, but I want use png() or something else to write out
images.
Unfortunately I get the following error message:
> png(filename = " ALL.png", width = 480, height = 480, pointsize = 12, bg =
"white", res = NA)
Error in X11(paste("png::", filename,
2002 Sep 05
0
ape 0.1 is released
Ape is an R package for "analyses of phylogenetics and evolution". The
first version (0.1) has been released on 27 August 2002 and is available on
CRAN.
>From the 'Description' file of version 0.1:
Ape provides functions for reading, and plotting
phylogenetic trees in parenthetic format (standard Newick
format), analyses of comparative data in a
2009 Apr 08
1
Colour each letter of a text string in a plot
I am inserting a DNA sequence into a plot, and hope to colourize each
of the four nucleotide of the DNA sequence with a unique colour i.e.,
A ("red"), C ("green"), G ("blue", and T ("yellow"). I use the
following codes, but the DNA sequence only shows as "red"
DNA <- "ACGT"
plot(1, xlim = c(0,1), ylim = c(0,1), axes=F,