search for: qsars

Hello R Users, I am interested in using R to generate quantitative structure-activity relationships (QSARs) for small molecules given a set of molecular descriptors (the X's) and biological data (Y's) (usually tab-delimited data files). Has anyone done this using R ? Would you be willing to share your R scripts (or ideas) for doing this with me ? I am particularly interested in R codes for...

Dear list: I am interested in the following sort of problem, as is found frequently in the field of QSAR. I have biological activity as a function of chemical structure, with structure defined in a categorical manner in that the SUBSTITUENT is the levels of the POSITION factor. For example, data from Kubinyi (http://www.kubinyi.de/dd-12.pdf) for this type of analysis is presented as follows:

Dear all, I am a statistician doing research in QSAR, building regression models where the dependent variable is a numerical expression of some chemical activity and input variables are chemical descriptors, e.g. molecular weight, number of carbon atoms, etc. I am building regression models and I am confronted with a widely a technique called Y-RANDOMIZATION for which I have difficulties in

Dear users I am reposting this and hope it will be accepted this time. I am using copula package to fit my bivariate data and simulation. As explained in package documentation we can use our own data distribution to feed on copula as long as we have d, p and q (pdf, cdf and quantile) functions are available. Hence my code for those are: # Make the functions for data distribution

Sir, This query is related to randomForest regression using R. I have a dataset called qsar.arff which I use as my training set and then I run the following function - rf=randomForest(x=train,y=trainy,xtest=train,ytest=trainy,ntree=500) where train is a matrix of predictors without the column to be predicted(the target column), trainy is the target column.I feed the same data

Hi people! (Especially Johannes, probably =) I recently switched to DSPAM + antispam plugin combination. Mostly I am happy but there is a problem with calling dspam-exec in order to relearn the messages. Moving messages to spam folder does not work, giving the error message 'Failed to call dspam' to client. I tried to add some debug output and here are the results: This is the output of

Hi: I'm starting a research of Support Vector Regression. I want to obtain a model to predict a property A with a set of property B, C, D, ... This problem is very common for example in QSAR models. I want to know some examples and package that could help me in this way. I know about caret and e1071. But I' don't know if this package can work with continues variables.?

Hi all, I would like to do some QSAR analysis (quantitative structure activity relationship). I need to use some Partial Least Squares (PLS) regression, but I have not seen this option on the R-project. Is it possible to do this kind of regression on R? thank you in advance best regards, olivier [[alternate HTML version deleted]]

Error in mvr(Kd_nM ~ qsar, ncomp = 6, data = my, validation = "CV", method = "kernelpls") :   Invalid number of components, ncomp How I can fix this? [[alternative HTML version deleted]]

Dear list, I would like to plot points with two types of labels, one at the data point (the name of the point) and another offset a bit with another factor which is either of the two greek characters alpha or beta. I have tried to get the routine to plot a greek character with expression() or with substitute() and have not yet had any success. The following only plots the word in english in

> > On 2022-11-08 15:49, Orion Poplawski wrote: > > On 11/8/22 13:12, Simon Matter wrote: > > Is anyone else experiencing trouble with > kernel-3.10.0-1160.80.1.el7.x86_64? > > I'm seeing a kernel panics in the kvm module on one of our VM hosts with > > it. > > I did notice a new libvirt

Change it to GRUB_DEFAULT=0 (I encountered the same issue week ago with a workstation booted for three month with an older kernel because of https://bugzilla.redhat.com/show_bug.cgi?id=2143438 , and solved it this way) Regards, Petko On 3/14/23 10:51, Rob Kampen wrote: > Can I edit /etc/default/grub and change > > GRUB_DEFAULT=saved > > to something else? -- Petko Alov

Three more packages will be showing up on your mirror soon. The caret package (short for "Classification And REgression Training") aims to simplify the model building process. The package has functions for - data splitting: balanced train/test splits, cross-validation and bootstrapping sampling functions. There is also a function for maximum dissimilarity sampling. -

I apologize in advance for posting a question not related to R. I need references to papers that use multiple linear regression in an industrial application and also in a biological experiment. This is aimed to biologists/chemists (non-statisticans) so if anyone has written a brilliant paper where the use of multiple regression is important and also understandable to people with little

Three more packages will be showing up on your mirror soon. The caret package (short for "Classification And REgression Training") aims to simplify the model building process. The package has functions for - data splitting: balanced train/test splits, cross-validation and bootstrapping sampling functions. There is also a function for maximum dissimilarity sampling. -

Hello, all experts, My major is computer-aied drug design ( main QSAR). Now, my paper need be reviesed, and one reviewer ask me do genetic algorithm coupled with gaussian process method (GA+GP). my data: training set: 191*106 test set: 73*106 here, I need use GA+GP to do variable selection when building the model. In R, there are not GA package like in matlab

This issue has been around for some months, but other things keep crowding out a fix. uname give me 3.10.0-1160.36.2.el7.x86_64 #1 SMP Wed Jul 21 11:57:15 UTC 2021 yet I have 3.10.0-1160.76.1.el7.x86_64 3.10.0-1160.81.1.el7.x86_64 3.10.0-1160.83.1.el7.x86_64 3.10.0-1160.88.1.el7.x86_64 loaded. The system uses UEFI to boot. sudo ls -l /sys/firmware/efi gives: total 0 -r--r--r--.? 1 root

*//* *//* */Cloud Futures: Hot Topics in Research and Education/* Berkeley, CA | May 7-8, 2012 http://research.microsoft.com/cloudfutures2012/ The Cloud Futures Workshop series brings together thought leaders from academia, industry, and government to discuss the role of cloud computing across a variety of research and educational areas---including computer science, engineering, Earth

*//* *//* */Cloud Futures: Hot Topics in Research and Education/* Berkeley, CA | May 7-8, 2012 http://research.microsoft.com/cloudfutures2012/ The Cloud Futures Workshop series brings together thought leaders from academia, industry, and government to discuss the role of cloud computing across a variety of research and educational areas---including computer science, engineering, Earth

Has this been solved? Is there a bug report I can follow? Thank you for letting me know, Val?re Binet On Wed, Nov 16, 2022 at 2:23 PM Bill Gee <bgee at campercaver.net> wrote: > On the other hand --- I just upgraded one of my CentOS7 systems to > 3.10.0-1160.80.1 today. With that kernel it will not run any KVM guest. > The system hangs - HARD - within one or two seconds of