gff

A genome visualization python package for comparative genomics

Python programs for processing GFF3 files

convert various features into a GFF-like file for use in genome browsers

Frequently used commands in bioinformatics

Efficiently keep track of changes to genomes

scripts for RNA-Seq analysis

command lines tool to annotate miRNAs with a standard mirna/isomir naming

Convert sequence IDs between ucsc/refseq/genbank

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

🧬 GFFBase — Rust+DuckDB GFF3/GTF engine

LinkML schema for GFF3, the Genome Feature Format

Gff-toolbox is a toolbox of commands that enables one to get the gist of their GFF annotation files, as well as to analyse them in different ways.

A python code to display Player Character (PC) items from a NWN BIC file, to a CSV file. This is meant to be used with ThreeTowns server items (custom 2da files)

Bio-Wrangler is a Python package for bioinformatics data wrangling. It helps load, filter, merge, and summarize bioinformatics datasets from formats like FASTA, FASTQ, VCF, and GFF.

This pipeline infers exon functional annotations using coordinates from a .gff file and derives corresponding intron coordinates along with relevant annotations. Users can optionally specify the length of intronic fragments to extract. The pipeline is suited for splicing code analyses.

Lift annotations from a GTF file to an adata object.

Predicting Transcription Factor Binding Sites from ENCODE data using Machine Learning