hariszaf Goto Github PK

bacteria-archaea-traits

A synthesis of bacterial and archaeal phenotypic trait data

bacterial_growth

This repository contains the script developed for my Master Thesis in gut bacterial growth curves.

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

coi_dark_matter

Dark matter on COI marker gene project

darn

Dark mAtteR iNvestigator: diving into the dark matter of your COI sequences

deepnog

Protein orthologous group assignment with deep learning

dingo

A python library for metabolic networks sampling and analysis

dnngior

Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling

fastnngapfiller

Gapfill GSMMs with costs. Compatible with the ModelSEED db and aplicable to GapSeq draft reconstructions.

fetch_tool

Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)

flashweave.jl

Inference of microbial interaction networks from large-scale heterogeneous abundance data

gsoc2020

High dimensional sampling with applications to structural biology

gsoc2021

A repo for my proposal for a GSoC2021 project in the framework of GeomScale group and hopefully for the project's implementation.

hariszaf.github.io

my personal site

karpathos-swamp

Here is the code and supplementary files for the Karpathos swamp project

manta

microbial association network clustering algorithm

metabolic_toy_model

A repo for building a metabolic toy model to demonstrate various types of analysis

metagoflow-use-case

In this repo, we present a full example of the metaGOflow pipeline using actual EMO BON sequence data.

mgg

Gui for Microbetag based on scNetViz

microbetag

annotating microbial co-occurrence networks

my_cv

notes-on-met-mod-analysis

This repo hosts the JBook: "Notes on metabolic modelling analysis"

pema

PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes

pema-tutorials

This repo was built in the framework of the "Microbiome Data Analyses Workshop" from 20 to 23 April 2021. PEMA was presented there and here you can find all the related material.

pema_documentation

a site for how to run PEMA and some emperical hints from metabarcoding studies+9

phd_dissertation

On this repository I will have all related text, figures and code for figures regarding my PhD dissertation

phenotrex

Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn

phylomint

Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species

presentations

Here is a repo for my presentations

salmonella-infantis-gem

Genome scale metabolic reconstruction of S. infantis