Displaying 20 results from an estimated 200 matches similar to: "statistics"
2012 Aug 31
1
reviews for quality control
Hi,
It might be a trivial question but I just wonder if you could advise good theoretical tutorials, reviews on NGS (different platforms) quality control like nucleotides quality by cycle, nucleotides frequency by cycle, GC content and distribution, K-mer frequency by cycle as well as quality control after alignment and mapping.
Look forward to your reply,
Carol
[[alternative HTML version
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..
2012 Oct 21
1
Changing a for loop to a function using sapply
Apparently there is one or more concepts that I do not fully understand
from the descriptions of a function and the apply material. I have
been reading the mail from this forum and have learned much but, in this
case, what I have been reading here and from the manual isn't enough.
The following code produces what I want with the for loop. From what I
have read from this forum, a for
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
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
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))
{
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 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",
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
2005 Jul 14
0
Plzzzzz tell me how to register users in oh323.conf
Assalam Alaikum
i m using oh323.conf n i m calling netmeeting/SJPhone using
Dial(oh323/IP address of netmeeting or anysoftphone )
how can i call any extension .... first of all tell me how to register a uid n password there .... let's say i've a user
type=friend
username=adeel
secret=adeel
context=incoming
mailbox=31
plz plz plzzzzzz send me just a
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
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]]
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
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,
2004 Dec 08
2
similarity matrix conversion to dissimilarity
I have a matrix of similarity scores that I want to convert into a
matrix of dissimilarity scores so that I can apply some clustering
methods to the data. That is, high values in my matrix signify
similarity and low values (zero being the lowest) signify no
similarity. What functions/options in R or its packages are available
for making this kind of transformation of a matrix?
2018 May 03
1
Package for Molecular Properties
... 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>
2012 Apr 26
2
Memoize and vectorize a custom function
My goal is simple: calcuate GC content of each sequence in a list of
nucleotide
sequences. I have figured out how to vectorize, but all my attempts at
memoization failed.
Can you show me how to properly memoize my function?
There is a StackOverflow post on the subject of memoization, but it does not
help me:
http://stackoverflow.com/questions/7262485/options-for-caching-memoization-hashing-in-r
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