Github has vigilant mode which verifies the commit was made by the user who can be verified by the gpg or ssh keys. By default, if you make any commit from the web interface, they seem to be verified. However, we want to enable it from the command line interface. 1. Go to settings in your GitHub account. 2. Click on the SSH and GPG keys section. You will notice a section on how to generate a gpg…
For data.table install, if you plan on using multiple threads, you have to enable it during installation/compilation. When loading the package, you will see a warning that says data.table 1.x.x using 1 threads (see ?getDTthreads). ******** This installation of data.table has not detected OpenMP support. It should still work but in single-threaded mode. This is a Mac. ******** Just go to this link:…
Python is a very popular programming language. It is somewhat easier to read than other programming languages. Best 2nd choice for many tasks that includes data analysis and plotting. R is amazing for my use case and I feel it is the better choice especially when it comes to statistical test and plotting. Ggplot2 is nearly unrivaled for the ergonomics. However, the whenever I am determined to use…
I have used R for quite some time for data analysis. Especially with the use of Tidyverse package, it has been a very decent experience. Ggplot2 package for plotting is mostly intuitive. Synergy of Tidyverse ecosystem along with availability of bioinformatics and statistical analysis software with the R platform, it is an awesome combination. Recently, I have wondered to try out Python for my…
This post is to document the procedure to run Tarsnap on MacOS. Tarsnap is basically an online service that runs on top of Amazon cloud infrastructure for online backup. If you are reading this than you already know much about it but needless to say it is a cool program. First thing, we need to install it which can be easily accomplished using homebrew. brew install tarsnap It can also be…
Using R packages can be fun but installing them can be difficult sometimes. The problem usually happens when the installation needs dev tools or some from one of the bioconductor repository. Usually the instructions are as below. # Required packages install.packages("devtools") install.packages("BiocManager") # Install package here devtools::install_github("xxxx/xxxx", dependencies = c("Depends",…
Data analysis is a huge topic but any data analysis should begin with simple data summary. It is so easy to overlook this step especially when you are dealing with the data is presented in an overly complicated way. Recently, I was handed longitudinal data collected at a two-time point with 2 years interval between them. The data had about 20 columns including the socio-economic factors, parasite…
Google released Colaboratory as a data science tool for the purpose of providing computational and hosting Jupyter notebooks to experiment. It also provides a good demonstration of Tensorflow machine learning library. It saves files as python notebook (.ipynb extension) within a designated folder inside your Google drive account. I got all excited with this and not to say the least that it…
Recently I had to analyze data with very few data points in the range of 3-15. The data consisted of 3 groups and multiple subgroups. The most obvious choice, in this case, was to use a non-parametric statistical test such as Wilcox test. The problem with the Wilcox test is that we have the problem of losing power/sensitivity. A t-test, on the other hand, may give us false-positive especially with…