User: ረ

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Posts by ረ

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Protein pathway analysis -- Classify, organize, and cluster a list of proteins / discovering relations between a set of proteins and linking them to disease
... I have  a list of proteins (only Uniprot IDs) and I am interested in discovering relations between them.   Most importantly I want to focus on disease pathways and find out whether the proteins I am looking at are part of particular disease(s). Additionally, functional relations, pathway analysis, ...
pathways pathway analysis disease protein written 8 months ago by 0
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Using 'BSgenome::export' to write each chromosome of an organism into separate files
... PROBLEM I have the following script where I am using the export function from BSgenome package to write only the first seven chromosomes of an object (of class BSgenome) into separate files. source("https://bioconductor.org/biocLite.R") biocLite("BSgenome.Scerevisiae.UCSC.sacCer3") library(BSgeno ...
bsgenome biocgenerics export bsapply written 13 months ago by 0 • updated 12 months ago by James W. MacDonald49k
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Kernel Ridge Regression in R for Drug-Target Interaction
... I want to run Kernel Ridge Regression on a set of kernels I have computed, but I do not know how to do this in R. I found the constructKRRLearner function from CVST package, but the manual is not clear at all, especially for me being a complete beginner in Machine Learning. The function needs and x ...
regression R kernel ridge written 2.9 years ago by 0 • updated 2.5 years ago by Guido Kraemer0
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ChemmineR package - fpSim and cmp.similarity - Tanimoto kernels
... I have a text file containing 100 drug compounds (rows) and 100 protein kinase targets (columns). Values reflect how tightly a compound binds to a target. I also have the drug SMILES of the drugs. I converted SMILES to SDF. Then I used "fingerprintOB" function to generate fingerprints from that SDF ...
chemminer written 2.9 years ago by 0 • updated 2.9 years ago by Thomas Girke1.7k
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GOSemSim Package - mgeneSim() function / In is.na(go) : is.na() applied to non-(list or vector) of type 'NULL'
... I have the entrez IDs of 100 proteins and I have put them in a list and been trying to use R's mgeneSim function from the GOSemSim package, but I am getting the following error:   > mgeneSim(protein_id_list, organism="human")     <0 x 0 matrix>     There were 50 or more warnings (use war ...
gosemsim mgenesim written 2.9 years ago by 0 • updated 2.9 years ago by Guangchuang Yu1.1k

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Popular Question 2.8 years ago, created a question with more than 1,000 views. For Kernel Ridge Regression in R for Drug-Target Interaction

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