francescopatane96

Bioactivity-prediction-with-ML

Create a bioactivity prediction model using molecular descriptors (PADEL) and supervised machine learning (ML).

biofx_python

Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)

Bioinformatics-tools

simple bioinfomatics tools

biomaRt-from-Ensembl-id-to-entrez-AC

This R script allow you to retrieve entrez gene accession from ensembl gene ids from RNA seq analysis. Entrez symbols can then utilize to perform gene enrichment analysis of up and downregulate genes in platforms like Enrichr.

Biotech-Research-Hub

a comprehensive repository designed to empower researchers, scientists, and enthusiasts in the fields of bioinformatics and biotechnology. This repository serves as a one-stop destination for a myriad of invaluable resources, ranging from insightful guides and cutting-edge research papers to informative podcasts, web tools, and efficient workflows

Computer_aided_drug_discovery_kit

This pipeline provides a way to perform pharmaceutical compounds virtual screening using similarity-based analysis, ligand-based and structure-based techniques. The pipeline contains a collections of modules to perform a variety of analysis.

Data-Science-For-Beginners

10 Weeks, 20 Lessons, Data Science for All!

eNERVE

eNERVE is a dynamic, high-throughput and standalone in silico reverse vaccinology pipeline for eukaryotic protein candidate vaccines (PVCs) discovery from entire proteomes (FASTA file).

protein-xAI

protein xAI

RNA-seq_Pipeline

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

francescopatane96/Computer_aided_drug_discovery_kit

This pipeline provides a way to perform pharmaceutical compounds virtual screening using similarity-based analysis, ligand-based and structure-based techniques. The pipeline contains a collections of modules to perform a variety of analysis.

francescopatane96/eNERVE

eNERVE is a dynamic, high-throughput and standalone in silico reverse vaccinology pipeline for eukaryotic protein candidate vaccines (PVCs) discovery from entire proteomes (FASTA file).

francescopatane96/RNA-seq_Pipeline

Deposited R scripts allow to execute a complete RNA-seq Pipeline, starting from sequence reads (FASTQ files) to mapping/annotate the genome using a reference, to counts the number of reads for every gene. when raw counts are obtained, DESeq2 module permits to find differentially expressed genes (DEG) and to perform statistical analysis. The last module of the project allows you to use clusterprofiler in order to perform ORA and GSEA analysis (over-representation analysis and gene set enrichment analysis) using GeneOntology (GO), disease ontology (DO), KEGG, reactome eg...

francescopatane96/Biotech-Research-Hub

a comprehensive repository designed to empower researchers, scientists, and enthusiasts in the fields of bioinformatics and biotechnology. This repository serves as a one-stop destination for a myriad of invaluable resources, ranging from insightful guides and cutting-edge research papers to informative podcasts, web tools, and efficient workflows

francescopatane96/Data-Science-For-Beginners

10 Weeks, 20 Lessons, Data Science for All!

francescopatane96/NERVE

NERVE is an user-friendly software environment for the in silico identification of the best vaccine candidates from whole proteomes of bacterial pathogens. The purpose of this project is to update it, implementing new modules with machine learning based methods, and improving the performance of the already implemented ones.

francescopatane96/biomaRt-from-Ensembl-id-to-entrez-AC

This R script allow you to retrieve entrez gene accession from ensembl gene ids from RNA seq analysis. Entrez symbols can then utilize to perform gene enrichment analysis of up and downregulate genes in platforms like Enrichr.

francescopatane96/captum

Model interpretability and understanding for PyTorch

francescopatane96/DeepFRI

Deep functional residue identification

francescopatane96/protein-xAI

protein xAI

francescopatane96/biotechub-blog

francescopatane96/codon_usage_optimization

francescopatane96/eNERVE-GUI

eNERVE graphic user interface via Docker

francescopatane96/enerve_code

enerve code repo for docker container

francescopatane96/enerve_DeepFRI_data

pre-trained models to run DeepFRI in enerve

francescopatane96/esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

francescopatane96/ESM2_experiments

Repository containing colab sheets for experimenting with ESM2 pre-trained large protein language model.

francescopatane96/francescopatane96

Config files for my GitHub profile.

francescopatane96/francescopatane96.github.io

francescopatane96/gINTomics

francescopatane96/gINTomics-visualizer

francescopatane96/GPT_API_prompting_course

francescopatane96/ibm3202

Google Colab Tutorials for IBM3202

francescopatane96/iFeatureOmega-CLI

iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versio

francescopatane96/Learn-R

francescopatane96/LinearDesign

The LinearDesign mRNA design software.

francescopatane96/nf-ncov-voc

A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 genomes (Variants of Concern and Variants of Interest). Workflow is developed in collaboration with COVID-MVP (https://github.com/cidgoh/COVID-MVP) which can be used to visualize the mutation profiles and functional annotations.

francescopatane96/pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

francescopatane96/singlecell_library

francescopatane96/teachopenvaxx

Computational vaccinology tutorials