GSA Blog

A Gene Set Analysis blog

GSA Analysis with scRNA-seq Data

Gene set or pathway enrichment analysis is a computational approach that determines whether a priori defined gene sets such as a pathway show statistical significance between two biological states. It is powerful when our single-cell RNA-seq data does not have obvious meaningful high-level expres...

Posted by Xie Zihong on May 6, 2022

Gene set analysis for time-series

There are many tools to perform gene set analysis on time-series data. I have reviewed seven of them and here I share some quick tutorials that I have written as interactive jupyter notebooks. Jupyter tutorials: The tutorials can be found here: STEM GSEA for time series ...

Posted by Xiaowei Huang on March 15, 2022

GSA Classroom

--Slides and videos to learn how to perform GSA--

Announcement: We are pleased to announce the introduction of GSA Classroom, a repository of slides, videos, and animations, to learn Gene Set Analysis: GSA Classroom homepage GSA Classroom contains links to entire online courses, including our own animated course. In addition, it has a databa...

Posted by Antonio Mora on October 29, 2021

Galaxy-GSA

--A set of GSA tools in a Galaxy environment--

Announcement: We are pleased to announce the introduction of Galaxy-GSA, a group of GSA tools for different types of scenarios inside a Galaxy platform: Galaxy-GSA homepage Galaxy-GSA is a group of GSA tools wrapped in a Galaxy platform. Each Galaxy-GSA tool gives visibility to all the softwa...

Posted by Antonio Mora on July 20, 2021

GSA-BenchmarKING

--Tools for GSA benchmarking--

Announcement: We are pleased to announce the introduction of GSA-BenchmarKING, a repository of GSA benchmarking tools: GSA-BenchmarKING homepage GSA-BenchmarKING is a repository of apps/workflows/pipelines that allows benchmarking groups of GSA software in an easy and automated way. Currently...

Posted by Antonio Mora on April 15, 2021

To 'p' or not to 'p' (that is our question)

--On GSA and the p-value controversy--

Like many of you, I am not a statistician but a “p-value user”. Computing p-values has become as common to me as dividing numbers or extracting their square root; however, just as division and square roots, there is usually a machine doing it for me: For some of us, “p-value users”, the p-values ...

Posted by Antonio Mora on July 19, 2020

Show me the database

A mini-review of gene set annotation databases

The core of all GSA methods is the comparison between a query dataset (gene list or gene rank) and an annotated database (pathway database, gene set database, or annotated ontology). Most GSA software give the user one or more options to choose a database, with KEGG and GO being the most common o...

Posted by Antonio Mora on January 15, 2020

GSARefDB (The Gene Set Analysis Reference Database)

Announcement: We are pleased to announce the introduction of GSARefDB (The Gene Set Analysis Reference Database): GSARefDB homepage GSARefDB is the most comprehensive database of GSA methods and tools. It is available as an excel file or as a shiny app, and contains information regarding the ...

Posted by Antonio Mora on October 14, 2019

Hello world

Welcome to the birth of the GSA Blog

(“It’s a blog”, somebody says… Eyes opening slowly… Blurry images…) Today we officially start the GSA Blog, and here is all what we have in mind: We want to share posts that feature discussions about both old and new Gene Set Analysis methods and tools, as well as some useful code. We believe su...

Posted by Antonio Mora on June 14, 2019

ABOUT ME

This blog is written by the GSA Central community.

GSA Central is an educational platform to both learn and get an updated and in-depth view of the Gene Set Analysis field.

Gene Set Analysis (GSA) is arguably the most common functional interpretation procedure, and consists on comparing a query gene set to a reference database using a specific statistical method. Here we dicuss the sources, application, and consequences of such methods.

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