How to use topgo. Different test statistics and different methods for eliminating local similarities and depen-dencies between GO terms can be implemented and applied. Jan 27, 2021 · We will use the „weight01“ method which is also the default method used by TopGO. Jun 14, 2024 · Use GOBU and its FastInput plugin to enter the gene list. In this tutorial, I will use the sequencing data from E-MTAB-8411 to demonstrate how to use topGO, clusterProfiler and Enrichr via its R interface enrichR to perform GO enrichment analysis. Feb 12, 2024 · So, if you must use topGO, you could try and make one of these packages, or use orthologs between your species and one of the model organisms that have an org. The alternative is to use a different tool. One of the main advantages of topGO is the uni ed gene set testing framework it o ers. Jun 23, 2025 · topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Nov 22, 2024 · This article aims to simplify the process of choosing an appropriate R package for GO enrichment analysis by introducing two popular Bioconductor packages: topGO and globaltest. This guide compares these packages, highlights their differences, and Nov 18, 2018 · Specificaly for topGO, the way in which you can perform enrichment against a custom 'database' is described in the manual: Gene set enrichment analysis with topGO (see 4. qafwr nd7ckc ebcq gor vui uqr0r 8ei fbyqs uevuapa o3p