This is the standalone version of the EviAnn pipeline

PlantTribes is a collection of automated gene family analysis pipelines for comparative plant genomics

Navigation links (and brief descriptions) to my repositories.

Hone computational biology skills by re-enacting Figure 1 of modern biology papers

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

GENA-LM is a transformer masked language model trained on human DNA sequence.

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

Using Deep Learning to predict gene annotations

BERT fine-tuning for POS tagging task (Keras)

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

PASA software

source code for EVM

AI Journey 2019: Combined Solution

Materials of the AI Journey 2020 competition dedicated to the recognition of Peter the Great's manuscripts, https://ai-journey.ru/contest/task01

Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

Teaching materials for the applied machine learning course at Cornell Tech (online edition)

Proteomics search & quantification so fast that it feels like magic

📖 Paper reading list in conversational AI.

One idea to find sequence similarity

Scripting analyses of genomes in Ensembl Plants

Perl scripts for working with the GFF format

Pipeline for improving BRAKER2 gene predictions with MS/MS data

Genome Assembly and Annotation Service code

Experiments for GeneMark-EP/EP+ and ProtHint projects

Repository with data of eukaryotic species used in BRAKER2 experiments

This repository is a usable, publicly available genome annotation and assembly tutorial.

Construct ab initio gene prediction using only BUSCO augustus models. Add in transcriptome for extra support