similar to: how to save an updated dataset

I'm trying to read some web tables directly into R. These are both genome sequencing projects (eukaryotes and metagenomes) from NCBI and look very similar; however, only the first one works. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi I added ?dump=selected to the end of the url string to get a tab- delimited file (which is what happens

Hi, > url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL

----- Original Message ----- > From: "Uwe Ligges" <ligges at statistik.tu-dortmund.de> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "R-devel at r-project.org" <r-devel at r-project.org> > Sent: Saturday, August 8, 2015 3:57:34 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default download method > >

We were also able to reproduce the issue on Windows Server 2012. If there's anything we can do to help please let me know; Elliot Waingold (CC'd here) can provide access to the VM we used for testing if that's of any help. # David Smith -- David M Smith <davidsmi at microsoft.com> R Community Lead, Revolution Analytics (a Microsoft company)? Tel: +1 (312) 9205766 (Chicago IL,

Hi, I am trying to use a CGI service (Pubchem PUG) via RCurl and am running into a problem where the data must be supplied via POST - but I don't know the keyword for the argument. The data to be sent is an XML fragment. I can do this via the command line using curl: I save the XML string to a file called query.xml and then do curl -d @query.xml

On 08.08.2015 01:11, Dan Tenenbaum wrote: > Hi, > >> url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" >> download.file(url, tempfile()) > trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' > Error in download.file(url, tempfile()) : > cannot open URL

Hi David, ----- Original Message ----- > From: "David Smith" <davidsmi at microsoft.com> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Uwe Ligges" <ligges at statistik.tu-dortmund.de>, "Elliot Waingold" > <Elliot.Waingold at microsoft.com> > Cc: "R-devel at r-project.org" <r-devel at r-project.org>

----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at fredhutch.org> > To: "Uwe Ligges" <ligges at statistik.tu-dortmund.de> > Cc: "R-devel at r-project.org" <r-devel at r-project.org> > Sent: Saturday, August 8, 2015 4:02:54 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default download method

Hi all, I'm new to Centos, just moved here from Gentoo Linux. I have to install a server for bioinformatics purposes and I see that default yum repositories do not include any bioinformatics software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't find a valuable solution: which is (or which are) the best repository I should add to have a satisfying list

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f <- url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r") download.file("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", destfile=tempfile())

I want to get the count matrix of genes from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146049. Is it possible for GSE146049? After getting counts, I want to do TMM normalization. [[alternative HTML version deleted]]

Is there anyway to plot a matrix using a 3d bar plot. Something like bar3 in matlab? The example in demo hist3d does a 3d barplot for binned data, but has anyone tried something for a simple matrix with spaces betwen bars and axis labels using matrix dimnames or 1,2,3? stages<-letters[1:3] A<-matrix(c( 0.21, 0.21,0.03, 0.55, 0.58, 0.09, 1.30, 1.35, 0.22), nrow=3, byrow=TRUE,

How can I subscribe to R genomic list? On Sun, 2 Apr 2023, 9:28 pm Peter Langfelder, <peter.langfelder at gmail.com> wrote: > It's a microarray data set, so I don't think you would want to apply > an RNA-seq pipeline. You'd be better off applying a normalization > appropriate for this type of microarray data. > > HTH, > > Peter > > On Sun, Apr 2, 2023

Dear All, The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each

Hi, I would like to construct a transition matrix from a data frame with annual transitions of marked plants. plant<-c(1:6) class<-c("seed","seed", "seed", "veg", "rep", "rep") fate<-c("dead", "veg","veg","rep", "rep", "veg") trans<-data.frame(plant, class, fate)

I wanted to print the first and last rows of some dataframes in Sweave using dots in columns to separate the two parts. Head and tail almost work, but I have problems with factors and row names. z<-data.frame(id=letters[1:26], x=sample(1:26,26)) rbind(head(z,3), ".", tail(z,1)) id x 1 a 18 2 b 8 3 c 14 4 <NA> . 26 z 10 Warning message: invalid

Hi, I need to resample rows in a data frame by subsets L3 <- LETTERS[1:3] d <- data.frame(cbind(x=1, y=1:10), fac=sample(L3, 10, repl=TRUE)) x y fac 1 1 1 A 2 1 2 A 3 1 3 A 4 1 4 A 5 1 5 C 6 1 6 C 7 1 7 B 8 1 8 A 9 1 9 C 10 1 10 A I have seen this used to sample rows with replacement d[sample(nrow(d), replace=T), ] x y fac 7 1 7 B 2

(Mostly for Roy): I saw this on the SWIG list, and wonder if it might be related to the problems we have been seeing where multi-arg typemaps end up invoking the wrong wrapper methods. (Not the newly-discovered directorout stuff). Perhaps if we switched to "compactdefaultargs" things would start to work more sanely. Looking at this section of the SWIG docs, it looks like it should

Hi all, I am trying to download, decompress and read a csv file. My code: myurl <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE24729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile <- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon <- gzcon(gzfile(myfile,