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Questions related from Lon W. R. Fong
I am running an R script that downloads and preprocesses all the available methylation data sets from TCGA. I'm using the Bioconductor package MethylMix for this. However, when I try to process...
04 September 2018 10,016 4 View
I have a gene, let's say p300, and I have a list of genes that are co-expressed with it. I want to find which of these genes have the most similar function to p300. What would be the best tool for...
23 July 2018 5,701 3 View
I have an SDF of docking results generated in smina (spin-off of AutoDock VINA with the ability to handle SDFs). Each compound has five poses that were generated, but I need to get rid of all but...
30 June 2018 2,218 2 View
I'm doing some preliminary analysis on a list of genes of interest, and I was using a data set that contains RNA-seq data from patients and the corresponding clinical information, including...
22 May 2018 8,031 4 View
Specifically, for a virtual screen of 50,000~200,000 compounds, how many binding modes (poses) per compound do you usually ask VINA to generate? And how do you analyze these results? Visually...
20 April 2018 7,586 5 View
I'm a student in computational drug design, but I'm going to move to the bench soon to test some compounds we've designed. I've been reading the methods sections of some papers describing novel...
29 March 2018 5,661 5 View
I know that blind docking is most often used to determine an unknown binding site, but can it be used to determine whether a ligand is thermodynamically more likely to bind a given (known) binding...
10 October 2017 9,904 6 View
I have some HL60 and U937 cells I'm growing in 50mL of media in T75 flasks, and I was wondering if it would be okay to do a 1:2 split by just adding 50mL more media to the same flask instead of...
14 March 2017 3,977 3 View
Hello all, I have a matrix of gene-expression data from 50 samples whose rows are the probes and whose columns are the samples. There is an additional column consisting of the Entrez gene IDs for...
29 September 2015 6,316 8 View