search for: pubm

Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax...

I''d like to extend bleucloth or redcloth to support custom tags, e.g. I want to use markup like this: [pubmed:18332676] which shall be extended to: <a href="http://www.ncbi.nlm.nih.gov/pubmed/18332676">Behav Pharmacol. 2008 Mar;19(2):121-128.</a> Does anyone know, if this is possible and has some hints how to do this?! I have not decided, wether I want to use redcloth or bluecloth...

Hi: I am trying to search PubMed abstracts which contains BOTH two terms: COL4A1 AND Ocular. I am using the following code: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300", sep="") docId <- xmlT...

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse(" http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXD...

Hi, I actually need to download pdfs through R code. The thing which I want to do is that, search for a paper in pubmed, which is possible by using GetPubMed function in the package "NCBI2R?". GetPubMed(searchterm, file = "", download = TRUE , showurl = FALSE, xldiv = ";", hyper = "HYPERLINK", MaxRet = 30000, sme = FALSE, smt = FALSE, quiet = TRUE, batchsize=500,descHead...

...ternal space (between "Name" and "Major" and the embedded quote marks are defeating me. I can get all the "DescriptorName" tags, but these include both MajroTopicYN = "Y" and "N" variants. Any suggestions? Thanks in advance. Prototype text from PUBMED <MeshHeadingList> <MeshHeading> <DescriptorName MajorTopicYN="Y">Antibodies, Monoclonal</DescriptorName> </MeshHeading> <MeshHeading> <DescriptorName MajorTopicYN="N">Blood Platelets</DescriptorName> <QualifierName MajorTopic...

...al 5874641 6295980 a 13 30 b 36 39 c 0 5 d 40 61 e 16 20 f 13 11 g 3 3 h 9 5 i 12 35 j 157 221 k 17 39 l 6 17 m 666 1387 n 2 5 The significance of digital gene expression profiles. Audic S <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C laverie%20JM%22%5BAuthor%5D&itool=EntrezSystem2.PE...

...efer to stay in the generalized linear model framework and, ideally, maximum likelihood estimators. (A recent review found maximum likelihood estimators using quadrature performed better than penalized likelhood methods, which specifically included glmmPQL in MASS: http://www.ncbi.nlm.nih.gov/pubmed/20949128). The lme4 package apparently supports generalized linear models. The title of the package is "lme4: Linear mixed-effects models using S4 classes" but the brief description is "Fit linear and generalized linear mixed-effects models." Various people, including Do...

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

http://gigamail.rossoalice.alice.it/messages/readMessageFrameset.aspx?DeliveryID=ba40cf18-29db-4404-a3ce-af26f760ecf9 Please, paste the website address above shown in your web browser address field. Make sure the whole string is pasted with no space or any other character. Telecom couldn't generate more clumsy website addresses .... Sorry for that. Thank you in advance, Maura tutti i

...patial statistics, distributed computing, and bioinformatics. Contents: Time Series in R 1.5.0 Naive Time Series Forecasting Methods Rmpi: Parallel Statistical Computing in R The grid Graphics Package Lattice Programmer's Niche geoRglm: A Package for Generalised Linear Spatial Models Querying PubMed evd: Extreme Value Distributions ipred: Improved Predictors Changes in R Changes on CRAN Upcoming Events which makes a total of 44 pages. For the editorial board, Kurt Hornik -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://...

...patial statistics, distributed computing, and bioinformatics. Contents: Time Series in R 1.5.0 Naive Time Series Forecasting Methods Rmpi: Parallel Statistical Computing in R The grid Graphics Package Lattice Programmer's Niche geoRglm: A Package for Generalised Linear Spatial Models Querying PubMed evd: Extreme Value Distributions ipred: Improved Predictors Changes in R Changes on CRAN Upcoming Events which makes a total of 44 pages. For the editorial board, Kurt Hornik -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-announce mailing list -- Read http://...

Hello everyone, I need to do a sample size calculation. The study two arms and two endpoints. The two arms are two different cancer drugs and the two endpoints reflect efficacy (based on progression free survival) and toxicity. Until now, I have been trying to understand this in terms of a one-arm design, where the acceptable rate of efficacy might be 0.40, the unacceptable rate of efficacy

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 https://www.theverge.com/2020/8/6/21355674/human-genes-rename-microsoft-excel-misreading-dates On Tue, Apr 16, 2024 at 3:46?AM jing hua zha...

...ER rrt will switch i with each other! Ultimately I need to update in the db, so I need a list/dataframe with the ID, the original rrt and the adjusted rrt (maybe the first occuring rrt, or the mean of the rrts, doesn't matter). Any ideas about which algorithms can be used? I searched on pubmed, but couldn't find anything Thanks Bart PS: to get the data: dat <- structure(list(ID = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L), rrt = c(0.45, 0.48, 1.24, 0.45, 0.48, 1.22, 0.35, 0.44, 0.46, 1.21, 0.36, 0.45, 0.48, 1.22), Mnd = c(0L, 0L, 0L, 3L, 3L, 3L, 6L, 6...

...of KDD 2009 (I've provided short URLs above because many mailers break the long direct URLs.) Other non-R-specific stories in June covered Simpson's Paradox in polling data, Google Squared, real random numbers, the chances of a meteor bringing down an aircraft, amusing article titles from PubMed, and open-source user interfaces. June was a record-breaking traffic month for the blog. The "Data Mashups" article and the discussion of the Iranian Election were highly visited. Thanks to everyone who provided comments and tips and please keep them coming to david at revolution-compu...

...el-bounces at r-project.org] On Behalf Of Steven McKinney [smckinney at bccrc.ca] Sent: Thursday, November 19, 2009 2:21 PM To: Kevin R. Coombes; r-devel at r-project.org Subject: Re: [Rd] R Usage Statistics Hi Kevin, What a surprising comment from a reviewer for BMC Bioinformatics. I just did a PubMed search for "limma" and "aroma.affymetrix", just two methods for which I use R software regularly. "limma" yields 28 hits, several of which are published in BMC Bioinformatics. Bengtsson's aroma.affymetrix paper "Estimation and assessment of raw copy numbers...

...quot;log"), data = data, method = "REML") pred <- predict.gam (model, type = "response") relative_risk <- exp(pred$fit) However, when I look at the results, it calculates RR for 365 days separately. How can I get a result like the table 4 in this article ( https://pubmed.ncbi.nlm.nih.gov/36161569/)? There is only one RR calculation for each pollutant. I would be very grateful if you could help me. Thank you. Eren YALIN M.D., Research Assistant . University, Medical Faculty, Department of Public Health [[alternative HTML version deleted]]

...rez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <- genSOAPClientInterface(ncbi at operations[[1]], def = ncbi, ncbi at name, verbose=FALSE) > ff at functions$run_eInfo("db=pubmed") Error in toSOAPArray(obj, con, type = type) : no slot of name "elType" for this object of class "SOAPVoidType" what's wrong? I am looking foward to your help. Thanks very much. Tiger

...nt to fit he style of his presentation. Recommendations on other methods are appreciated as well. Hao -- : Hao Chen, Ph.D. : Instructor : Department of Pharmacology : University of Tennessee Health Science Center : Memphis, TN 38163 USA : Office: 901 448 3201 : Mobil: 901 826 1845 : Mining PubMed: http://www.chilibot.net : --