valentynbez
MD, PhD student in Bioinformatics. Studying massive genomic datasets and producing software to do it better.
Sunagawa Lab @ ETH ZürichZürich, Switzerland
Pinned Repositories
gantt-chart
Python code for easy Gantt chart generation
metagenome_assembly
WDL Workflow for metagenome assembly
Metagenomic-DeepFRI
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
q2-mOTUs
camda2021-dili
CAMDA 2021 winning solution for "Literature AI for Drug Induced Liver Injury" challenge
metagenome_assembly
WDL Workflow for metagenome assembly
Metagenomic-DeepFRI
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
sinuses_2023
tmvec
valentynbez's Repositories
valentynbez/Metagenomic-DeepFRI
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
valentynbez/sinuses_2023
valentynbez/anndata
Annotated data.
valentynbez/awesome-ai-in-finance
🔬 A curated list of awesome LLMs & deep learning strategies & tools in financial market.
valentynbez/bioconda-recipes
Conda recipes for the bioconda channel.
valentynbez/deblur
Deblur is a greedy deconvolution algorithm based on known read error profiles.
valentynbez/docs
valentynbez/FuncMi
valentynbez/learning-c
valentynbez/learning-rust
valentynbez/llama.cpp
Port of Facebook's LLaMA model in C/C++
valentynbez/metaSNV
MetaSNV, a metagenomic SNV calling pipeline.
valentynbez/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
valentynbez/mOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
valentynbez/ngsreads.align.bwa
An extension for ngsreads, wrapping bwa for aligning short reads.
valentynbez/pharokka
fast phage annotation program
valentynbez/PhaTYP
PhaTYP: Predicting lifestyle for bacteriophages using BERT
valentynbez/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
valentynbez/pyhmmer
Cython bindings and Python interface to HMMER3.
valentynbez/pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
valentynbez/q2-composition
valentynbez/q2-demux
valentynbez/q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data.
valentynbez/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
valentynbez/spatial_sinus_microbiome
Code for the paper "Spatial variability of the microbiome in chronic rhinosinusitis is associated with the patients’ clinical characteristics but not with sinus ostia occlusion" by Szaleniec et al. 2022
valentynbez/thyroid_2023
Code for paper
valentynbez/tm-vec
valentynbez/valentynbez
valentynbez/valentynbez.github.io
Personal website customized from Hugo Academic template
valentynbez/VIBRANT
Virus Identification By iteRative ANnoTation