Orestis Nousias's Projects
This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"
Analyses pipelines that I use for my work
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
Calculate
Bio Electric Tissue Simulation Engine.
scripts
haibao scripts
BWK awk modified for biological data
Code for Mastering Python for Bioinformatics (O'Reilly, 2021, ISBN 9781098100889)
Bioinformatics data analysis and visualization toolkit
This is a basic repository with all the scripts necessary to reconstruct the data analysis from our work on the 200 Genomes
Scripts for analyzing SVs in cacao
A tool for concatenating multiple fasta alignments for supermatrix phylogenetic analyses
Are cells too cool?
fork of cndtools
Making Protein folding accessible to all via Google Colab!
Conservation analysis using phyloP
Bash + AWK script for quick Vlookups using CSV files. Ideal for large data sets
Source code for fitting thermodynamic models (MoCHI), downstream analyses and to reproduce all figures in the following publication: Global mapping of the energetic and allosteric landscapes of protein binding domains (Faure AJ, Domingo J & Schmiedel JM et al., 2021)
Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
A pipeline used to identify different modes of duplicated gene pairs
This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
ExUTR is a practical and powerful tool that enables rapid genome-wide 3'-UTR prediction from massive RNA-Seq data
Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster.
Scripts to functionally annotate genes
script
React
Typescript
Django
Laravel
Facebook
Microsoft
Google
Alibaba
D3
Tencent