Posts by Tags

ACE model

R

Data Science Tutorials

8 minute read

Published:

A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.

Rstudio

Using RStudio Server

less than 1 minute read

Published:

We now have RStudio Server installed on all CBSU machines! This means that you can run a hosted RStudio session in your browser and not worry about copying over files from the server, or running out of memory on your own machine. Here are the steps you need to follow to use it.

SGE

Getting started on CBSUBrito

3 minute read

Published:

Disclaimer: This blog post will only be relevant to members of the Brito Lab.

alias

Using Aliases in Bash

2 minute read

Published:

What are aliases in bash?

If you are tired of typing out the same long command over and over again, it’s time to set up a few bash aliases. Aliases allow you to create shortcut commands for longer ones. For example, instead of typing out ls -l, you could type ll + Enter to save time.

alignments

bash

Using Sed

1 minute read

Published:

Get to know sed: The basics

I want to introduce sed in a quick and informal way for anyone who just wants to get a taste of what sed can do.

Using Aliases in Bash

2 minute read

Published:

What are aliases in bash?

If you are tired of typing out the same long command over and over again, it’s time to set up a few bash aliases. Aliases allow you to create shortcut commands for longer ones. For example, instead of typing out ls -l, you could type ll + Enter to save time.

bioinformatics

brito lab

Setting up SSH Keys

3 minute read

Published:

Are you tired of typing in a password every time you log into the lab’s server? Follow this tutorial to set up SSH keys so that you never have to type in your password again while logging in!

Using RStudio Server

less than 1 minute read

Published:

We now have RStudio Server installed on all CBSU machines! This means that you can run a hosted RStudio session in your browser and not worry about copying over files from the server, or running out of memory on your own machine. Here are the steps you need to follow to use it.

Getting started on CBSUBrito

3 minute read

Published:

Disclaimer: This blog post will only be relevant to members of the Brito Lab.

command line

Using Sed

1 minute read

Published:

Get to know sed: The basics

I want to introduce sed in a quick and informal way for anyone who just wants to get a taste of what sed can do.

Using Aliases in Bash

2 minute read

Published:

What are aliases in bash?

If you are tired of typing out the same long command over and over again, it’s time to set up a few bash aliases. Aliases allow you to create shortcut commands for longer ones. For example, instead of typing out ls -l, you could type ll + Enter to save time.

data science

Data Science Tutorials

8 minute read

Published:

A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.

genetics

heritability

how to exit vim

introduction

Welcome!

less than 1 minute read

Published:

Welcome to my academic page. While working as a computational geneticist in graduate school, I’ve collected a lot of notes about how various programs/methods/fun little tricks work. I want to use this blog to share those insights, frustrations, and solutions. Some of them may only be useful to members of the Brito Lab, but my hope is that most will be general enough that anyone in the bioinformatics world could find them interesting.

latent strain analysis

Using Latent Strain Analysis (LSA)

10 minute read

Published:

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment. For resources on LSA, see the following: Manual Github Useful Tips Reference

learning

Data Science Tutorials

8 minute read

Published:

A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.

lsa

Using Latent Strain Analysis (LSA)

10 minute read

Published:

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment. For resources on LSA, see the following: Manual Github Useful Tips Reference

metagenomics

Using Latent Strain Analysis (LSA)

10 minute read

Published:

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment. For resources on LSA, see the following: Manual Github Useful Tips Reference

microbiome

random forest

sed

Using Sed

1 minute read

Published:

Get to know sed: The basics

I want to introduce sed in a quick and informal way for anyone who just wants to get a taste of what sed can do.

server

Using Latent Strain Analysis (LSA)

10 minute read

Published:

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment. For resources on LSA, see the following: Manual Github Useful Tips Reference

Setting up SSH Keys

3 minute read

Published:

Are you tired of typing in a password every time you log into the lab’s server? Follow this tutorial to set up SSH keys so that you never have to type in your password again while logging in!

Using RStudio Server

less than 1 minute read

Published:

We now have RStudio Server installed on all CBSU machines! This means that you can run a hosted RStudio session in your browser and not worry about copying over files from the server, or running out of memory on your own machine. Here are the steps you need to follow to use it.

Getting started on CBSUBrito

3 minute read

Published:

Disclaimer: This blog post will only be relevant to members of the Brito Lab.

ssh

Setting up SSH Keys

3 minute read

Published:

Are you tired of typing in a password every time you log into the lab’s server? Follow this tutorial to set up SSH keys so that you never have to type in your password again while logging in!

strain

Using Latent Strain Analysis (LSA)

10 minute read

Published:

LSA was developed as a pre-assembly tool for partitioning metagenomic reads. It uses a hyperplane hashing function and streaming SVD in order to find covariance relations between k-mers. The code, and the process outline in LSFScripts in particular, have been optimized to scale to massive data sets in fixed memory with a highly distributed computing environment. For resources on LSA, see the following: Manual Github Useful Tips Reference

text editor

tutorial

Data Science Tutorials

8 minute read

Published:

A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.

twins data

vi

vim

welcome

Welcome!

less than 1 minute read

Published:

Welcome to my academic page. While working as a computational geneticist in graduate school, I’ve collected a lot of notes about how various programs/methods/fun little tricks work. I want to use this blog to share those insights, frustrations, and solutions. Some of them may only be useful to members of the Brito Lab, but my hope is that most will be general enough that anyone in the bioinformatics world could find them interesting.