nousiaso
PhD in genomics/population genetics Biology Dep of University of Crete, post-doc in University of Copenhagen on cancer -omics
BRICCopenhagen
Pinned Repositories
adaptiPhy
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_orthofinder_cafe
Analyses pipelines that I use for my work
ARMOR
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
batch_4DTV_calculation
Calculate
betse
Bio Electric Tissue Simulation Engine.
bin
scripts
bio-pipeline-tang-haibao
haibao scripts
cacaoSV
Scripts for analyzing SVs in cacao
nousiaso's Repositories
nousiaso/batch_4DTV_calculation
Calculate
nousiaso/cacaoSV
Scripts for analyzing SVs in cacao
nousiaso/adaptiPhy
This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"
nousiaso/ARMOR
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
nousiaso/betse
Bio Electric Tissue Simulation Engine.
nousiaso/bioinfokit
Bioinformatics data analysis and visualization toolkit
nousiaso/CellularCompetency
Are cells too cool?
nousiaso/ColabFold
Making Protein folding accessible to all via Google Colab!
nousiaso/Conservation_analysis_using_phylop
Conservation analysis using phyloP
nousiaso/doubledeepms
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)
nousiaso/Dsuite
Fast calculation of Paterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species
nousiaso/evolution
This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
nousiaso/FA-nf
Functional annotation pipeline for proteins from non-model organisms implemented in Nextflow
nousiaso/FastDTLmapper
Genome-wide gene gain/loss mapping tool using DTL(Duplication-Transfer-Loss) reconciliation method
nousiaso/foldseek
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.
nousiaso/genome-analysis
script
nousiaso/GenomeAnnotation
Various scripts that I have created that are useful for genome annotation (repeats & proteins)
nousiaso/GONE
GONE: Scripts, programs and an example data set
nousiaso/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
nousiaso/mutation_bias_analysis
Monroe et al. 2021. Nature
nousiaso/nousiaso
Config files for my GitHub profile.
nousiaso/PASApipeline
PASA software
nousiaso/polymorphology
Analyze genome-wide distributions of polymorphisms in relation to gene features
nousiaso/Precision-projections-of-the-delay-of-resistance-mutations-in-non-small-cell-lung-cancer-via-APOBEC3
The code that was used for the analyses of the Precision projections of the delay of resistance mutations in non-small cell lung cancer via APOBEC3A suppression, using cancereffectsizeR a software package developed from the Townsend group at Department of Biostatistics, Yale School of Public Health.
nousiaso/scalefreecognition
The scaling of goals from cellular to anatomical homeostasis: an evolutionary simulation
nousiaso/seqtk
Toolkit for processing sequences in FASTA/Q formats
nousiaso/SINATRA-Pro
Topological data analytic approach for discovering biophysical signatures in protein dynamics
nousiaso/stat_rethinking_2022
Statistical Rethinking course winter 2022
nousiaso/TOGA
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
nousiaso/vcfstats
Powerful statistics for VCF files