Pinned Repositories
MetaGOflow
MGnify oriented implementation for the Marine Genomic Observatories oriented pipeline, developed in the framework of an EOSC-Life funded project
dingo
A python library for metabolic networks sampling and analysis
darn
Dark mAtteR iNvestigator: diving into the dark matter of your COI sequences
fluxpy
metabolic modelling toolkit
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.
microbetag
annotating microbial co-occurrence networks
pema
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
presentations
Here is a repo for my presentations
microbetagApp-public
microbetag web service
hariszaf's Repositories
hariszaf/pema
PEMA: a flexible Pipeline for Environmental DNA Metabarcoding Analysis of the 16S/18S rRNA, ITS and COI marker genes
hariszaf/darn
Dark mAtteR iNvestigator: diving into the dark matter of your COI sequences
hariszaf/microbetag
annotating microbial co-occurrence networks
hariszaf/gsoc2021
A repo for my proposal for a GSoC2021 project in the framework of GeomScale group and hopefully for the project's implementation.
hariszaf/presentations
Here is a repo for my presentations
hariszaf/bacteria-archaea-traits
A synthesis of bacterial and archaeal phenotypic trait data
hariszaf/bacterial_growth
This repository contains the script developed for my Master Thesis in gut bacterial growth curves.
hariszaf/cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
hariszaf/coi_dark_matter
Dark matter on COI marker gene project
hariszaf/fluxpy
metabolic modelling toolkit
hariszaf/deepnog
Protein orthologous group assignment with deep learning
hariszaf/dingo
A python library for metabolic networks sampling and analysis
hariszaf/DNNGIOR
Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling
hariszaf/FastNNGapfiller
Gapfill GSMMs with costs. Compatible with the ModelSEED db and aplicable to GapSeq draft reconstructions.
hariszaf/fetch_tool
Tool which allows you to fetch RAW read files from the European Nucleotide Archive (ENA)
hariszaf/FlashWeave.jl
Inference of microbial interaction networks from large-scale heterogeneous abundance data
hariszaf/hariszaf.github.io
my personal site
hariszaf/karpathos-swamp
Here is the code and supplementary files for the Karpathos swamp project
hariszaf/manta
microbial association network clustering algorithm
hariszaf/metabolic_toy_model
A repo for building a metabolic toy model to demonstrate various types of analysis
hariszaf/metaGOflow-use-case
In this repo, we present a full example of the metaGOflow pipeline using actual EMO BON sequence data.
hariszaf/MGG
Gui for Microbetag based on scNetViz
hariszaf/my_cv
hariszaf/notes-on-met-mod-analysis
This repo hosts the JBook: "Notes on metabolic modelling analysis"
hariszaf/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.
hariszaf/pema_documentation
a site for how to run PEMA and some emperical hints from metabarcoding studies+9
hariszaf/phd_dissertation
On this repository I will have all related text, figures and code for figures regarding my PhD dissertation
hariszaf/phenotrex
Microbial Phenotype Prediction, successor to PICA, implemented with Python 3.7 and scikit-learn
hariszaf/PhyloMint
Pathway-based and phylogenetically adjusted quantification of competition and cooperation between microbial species
hariszaf/Salmonella-infantis-GEM
Genome scale metabolic reconstruction of S. infantis