Francesco Patane, MSc's repositories
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.
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...
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
Data-Science-For-Beginners
10 Weeks, 20 Lessons, Data Science for All!
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.
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.
captum
Model interpretability and understanding for PyTorch
DeepFRI
Deep functional residue identification
protein-xAI
protein xAI
eNERVE-GUI
eNERVE graphic user interface via Docker
enerve_code
enerve code repo for docker container
enerve_DeepFRI_data
pre-trained models to run DeepFRI in enerve
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
ESM2_experiments
Repository containing colab sheets for experimenting with ESM2 pre-trained large protein language model.
francescopatane96
Config files for my GitHub profile.
ibm3202
Google Colab Tutorials for IBM3202
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
LinearDesign
The LinearDesign mRNA design software.
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.
pytorch
Tensors and Dynamic neural networks in Python with strong GPU acceleration
teachopenvaxx
Computational vaccinology tutorials