The ACE Model: Estimating heritability with twin data
Published:
A brief primer on heritability and estimating heritability using phenotype (any observable trait such as height, eye color, or a health condition) data from twins.
Posts by Tags
ACE model
R
Getting Started with Random Forest
Published:
A collection of my notes for getting started with random forest for genomics research.
Data Science Tutorials
Published:
A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.
Rstudio
Using RStudio Server
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
Published:
Disclaimer: This blog post will only be relevant to members of the Brito Lab.
alias
Using Aliases in Bash
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
Metagenomic Analysis 1: From QC to Gene Abundances
Published:
The standard pipeline that we use in the Brito Lab for quality control, alignments, and gene abundance calculations for metagenomic data.
bash
Using Sed
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
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
Metagenomic Analysis 1: From QC to Gene Abundances
Published:
The standard pipeline that we use in the Brito Lab for quality control, alignments, and gene abundance calculations for metagenomic data.
brito lab
Setting up SSH Keys
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
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
Published:
Disclaimer: This blog post will only be relevant to members of the Brito Lab.
command line
Using Sed
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
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
Getting Started with Random Forest
Published:
A collection of my notes for getting started with random forest for genomics research.
Data Science Tutorials
Published:
A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.
genetics
The ACE Model: Estimating heritability with twin data
Published:
A brief primer on heritability and estimating heritability using phenotype (any observable trait such as height, eye color, or a health condition) data from twins.
heritability
The ACE Model: Estimating heritability with twin data
Published:
A brief primer on heritability and estimating heritability using phenotype (any observable trait such as height, eye color, or a health condition) data from twins.
how to exit vim
Getting started with Vim
Published:
How to get started using my favorite text editor.
introduction
Welcome!
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)
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
Getting Started with Random Forest
Published:
A collection of my notes for getting started with random forest for genomics research.
Data Science Tutorials
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)
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
Metagenomic Analysis 1: From QC to Gene Abundances
Published:
The standard pipeline that we use in the Brito Lab for quality control, alignments, and gene abundance calculations for metagenomic data.
Using Latent Strain Analysis (LSA)
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
Metagenomic Analysis 1: From QC to Gene Abundances
Published:
The standard pipeline that we use in the Brito Lab for quality control, alignments, and gene abundance calculations for metagenomic data.
random forest
Getting Started with Random Forest
Published:
A collection of my notes for getting started with random forest for genomics research.
sed
Using Sed
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)
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
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
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
Published:
Disclaimer: This blog post will only be relevant to members of the Brito Lab.
ssh
Setting up SSH Keys
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)
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
Getting started with Vim
Published:
How to get started using my favorite text editor.
tutorial
Getting Started with Random Forest
Published:
A collection of my notes for getting started with random forest for genomics research.
Data Science Tutorials
Published:
A collection of data science, programming, and data visualization tutorials I have found on the internet. Sources referenced.
twins data
The ACE Model: Estimating heritability with twin data
Published:
A brief primer on heritability and estimating heritability using phenotype (any observable trait such as height, eye color, or a health condition) data from twins.
vi
Getting started with Vim
Published:
How to get started using my favorite text editor.
vim
Getting started with Vim
Published:
How to get started using my favorite text editor.
welcome
Welcome!
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.