JAVA uniform random number [0 , 1]

R tutorial

Install R in linux ============ In CRAN home page, the latest version is not available. So, in fedora, Open the terminal yum list R --> To check the latest available version of r yum install R --> install R version yum update R --> update current version to latest one 0 find help ============ ?exact topic name ( i.e. ?mean ) 0.0 INSTALL 3rd party package ==================== install.packages('mvtnorm' , dependencies = TRUE , lib='/home/alamt/myRlibrary/') # install new package BED file parsing (Always use read.delim it is the best) library(MASS) #library(ggplot2) dirRoot="D:/research/F5shortRNA/TestRIKEN/Rscripts/" dirData="D:/research/F5shortRNA/TestRIKEN/" setwd(dirRoot) getwd() myBed="test.bed" fnmBed=paste(dirData, myBed, sep="") # ccdsHh19.bed tmp.bed ## Read bed use read.delim - it is the best mybed=read.delim(fnmBed, header = FALSE, sep = "\t", quote = ...

MATLAB cross validation

// use built-in function samplesize = size( matrix , 1); c = cvpartition(samplesize, 'kfold' , k); % return the indexes on each fold ///// output in matlab console K-fold cross validation partition N: 10 NumTestSets: 4 TrainSize: 8 7 7 8 TestSize: 2 3 3 2 ////////////////////// for i=1 : k trainIdxs = find(training(c,i) ); %training(c,i); // 1 means in train , 0 means in test testInxs = find(test(c,i) ); % test(c,i); // 1 means in test , 0 means in train trainMatrix = matrix ( matrix(trainIdxs ), : ); testMatrix = matrix ( matrix(testIdxs ), : ); end //// now calculate performance %% calculate performance of a partiti...

SLURM tutorial : Basic commands

Main website for learning SLRUM http://slurm.schedmd.com/tutorials.html Submit a job with name and outputfile name(This will overwrite the parameters in shell file header ) sbatch -J job1 -o job1.out --partition=batch myscript.sh Basic shell script for job #!/bin/sh # #SBATCH --job-name=testJob #SBATCH --time=01:00:00 #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --partition=dragon-default # # Display all variables set by slurm env | grep "^SLURM" | sort # cd /projects/dragon/FANTOM5/processed_data_feature ## All my commands for job will go here date;time; mkdir t1 How to submit a batch job sbatch myscript.sh How to check the list of jobs of a user squeue -u user1 squeue -u user1 -l # it will show in details How to check the whole history and status of a job scontrol show job=JOBID How to use one particular node in interactive mode. Useful when all...

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