similar to: BLAST output parsing

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

Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla.

hello if there is a package can do blast in R? [[alternative HTML version deleted]]

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

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, I'm helping out with a political campaign and would like to use asterisk to blast out about 200,000 calls with a short message from the candidate. Provider: I'm thinking voipjet may be a good solution? Hardware setup: I will have access to several T-1 lines so I would just want to set up the dialers to limit the number of concurrent calls and so forth. I found teleyapper on

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())

Can anyone recommend software that will allow me to utilize my VoIP provider and send fax over IP? I use Asterisk now for my phone system. Thanks! Wiley E. Siler Director of Information Technology Education 2020 4110 N. Scottsdale Rd. Ste 110 Scottsdale, Arizona 85251 (480) 296.0260 (866) 320.2083 ext. 1003 mailto:wsiler@education2020.com <mailto:wsiler@education2020.com>

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

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

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

(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,

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

----- 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 > >

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Hi, I wanted to download a file and did the following: --------------------------------------------------------- > fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > download.file(fileLink,'/geoDat') trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made,

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

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

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,