Retrive the genes (from your query or from the annotation) in a GO term after enrichment.
Looking for a method to get the upstream sequence (e.g. promoter) of a gene / TSS.
Simple use of KEGG api for getting references and mapping pathways.
PCA is the most commonly used clustering method. Through machine learning some new methods were also reported.
The 8th column of a gff file is critical for extracting protein sequences.
With genome browsers you can view the gene structure but only one at a time. I would like to compare gene models from different methologies and would need a Python/R tool for batch visualisation.
Some self-notes from the book Methods for Computational Gene Prediction by William H. Majoros.
Fragmented notes from the book RNAseq Data Analysis - a Practical Approach