similar to: Analyzing multiple text files

Hi everyone,  I am using bio3d package for some sequence analysis because of its nice integrated MUSCLE execution. However, I have been encountering some errors while I was running seqaln function, which calls for installed MUSCLE program. In my case, I stored the MUSCLE program on the desktop with pathway of "./Desktop/muscle/src/muscle". I had no problem running MUSCLE directly from

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]]

Hello everyone, I would like to parse very large xml files from MS/MS experiments and create R objects from their content. (By very large, I mean going up to 5-10Gb, although I am using a 'small' 40M file to test my code.) My first attempt at parsing the 40M file, using the XML package, took more than 2200 seconds and left me quite disappointed. I managed to cut that down to around 40

Building the current release 2.7 branch on x86_64-apple-darwin10 with r81455 reverted, I get the following Polyhedron 2005 benchmark results (with no test failures)... ================================================================================ Date & Time : 7 Apr 2010 22:24:16 Test Name : llvm_gfortran_lin_p4 Compile Command : llvm-gfortran -ffast-math -funroll-loops -msse3

On Apr 7, 2010, at 8:41 PM, Jack Howarth wrote: > Building the current release 2.7 branch on x86_64-apple-darwin10 > with r81455 reverted, I get the following Polyhedron 2005 benchmark > results (with no test failures)... Very nice! A 14% speedup on a benchmark we don't tune for isn't bad. I imagine that there are several easy wins you could get on it if you were interested

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

for the script, please kindly see the script below. At line 10 and line 13, my problems occurs. The first one is I try to retrieve the gene official name from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated example of matching source (extract the Nnat, sometime it would

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is

Dear R-developers, I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, Gene,SNP,prot,log10p YWHAE,13:62129097_C_T,1433E,7.35 YWHAE,4:72617557_T_TA,1433E,7.73 Both read.cv() and readr::read_csv() consider prot(ein) name as (possibly confused by

On Wed, Apr 07, 2010 at 09:54:36PM -0700, Chris Lattner wrote: > > On Apr 7, 2010, at 8:41 PM, Jack Howarth wrote: > > > Building the current release 2.7 branch on x86_64-apple-darwin10 > > with r81455 reverted, I get the following Polyhedron 2005 benchmark > > results (with no test failures)... > > Very nice! A 14% speedup on a benchmark we don't tune for

[CCing Dale since this was his change, not mine] The change in 81455 fixes a compiler crash. It doesn't happen very often, but I can't imagine we would want to back that out. Fixing it would be a more reasonable solution. From a quick look at it, the problem is that gcc/config/darwin-c.c is registering va_opt for GC. When you build for Fortran, darwin-c.o is not linked so the GC gets

?s 11:46 de 16/04/2024, jing hua zhao escreveu: > Dear R-developers, > > I came to a somewhat unexpected behaviour of read.csv() which is trivial but worthwhile to note -- my data involves a protein named "1433E" but to save space I drop the quote so it becomes, > > Gene,SNP,prot,log10p > YWHAE,13:62129097_C_T,1433E,7.35 > YWHAE,4:72617557_T_TA,1433E,7.73 >

Gene names being misinterpreted by spreadsheet software (read.csv is no different) is a classic issue in bioinformatics. It seems like every practitioner ends up encountering this issue in due time. E.g. https://pubmed.ncbi.nlm.nih.gov/15214961/ https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1044-7 https://www.nature.com/articles/d41586-021-02211-4

What I am trying to do is use GUI function, traitr, and to call for a pdb file and save it and then display it. I want to call for it by taking it from the user and then displaying it on the screen. I am having problems with that. The line pdb <- read.pdb(""ProteinCode) where proteincode should be the name of the protein, for example 1ly2, but it always ends up being protein. My

Hi, Suppose I have the following tabular data: 1729_at | TRADD | TNFRSF1A-associated via death domain | protein-coding 1773_at | FNTB | farnesyltransferase, CAAX box, beta | protein-coding 177_at | PLD1 | phospholipase D1, phosphatidylcholine-specific | protein-coding What is the right separator used for read.table function? I tried this: dat <-

Hello, I am trying to make a plot of the rates of an enzyme against three different protein concentrations (there are 45 rates in total and split up into 3 groups of 15, each receiving one of the 3 protein concentrations). When I enter the following code I instead get 3 separate boxplots for each of the three different protein concentrations ... plot(rate ~ ferm, data=LDH, col=LDH$rate,

Friends, I am a newbie to R. Just installed and started with R. I installed netcdf library (netcdf-4.0.tar.gz) and then ncdf package of R from CRAN with the following command. R CMD INSTALL --configure-args="-with-netcdf_incdir=/usr/local/netcdf/include -with-netcdf_libdir=/usr/local/netcdf/lib" ncdf_1.6.tar.gz The installation was successful. But when i try to use ncdf inside R, i

My laboratory is measuring the abundance of various proteins in the blood from either healthy individuals or from individuals with various diseases. I would like to determine which proteins, if any, have significantly different abundances between the healthy and diseased individuals. Currently, one of my colleagues is performing an ANOVA on each protein with MS Excel. I would like to analyze

On Thu, Apr 08, 2010 at 08:45:48AM -0700, Bob Wilson wrote: > [CCing Dale since this was his change, not mine] > > The change in 81455 fixes a compiler crash. It doesn't happen very often, but I can't imagine we would want to back that out. Fixing it would be a more reasonable solution. From a quick look at it, the problem is that gcc/config/darwin-c.c is registering va_opt

Comparing the Polyhedron 2005 benchmark results for gfortran from llvm-gcc-4.2 of April 7th, 2010 and September 18th, 2010 (from the rc2 2.8 release branch), we seem to be regressing in performance for this release.... ================================================================================ Date & Time : 7 Apr 2010 22:24:16 Test Name : llvm_gfortran_lin_p4 Compile Command :