Valentyn Bezshapkin's repositories
Metagenomic-DeepFRI
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
anndata
Annotated data.
awesome-ai-in-finance
🔬 A curated list of awesome LLMs & deep learning strategies & tools in financial market.
bioconda-recipes
Conda recipes for the bioconda channel.
deblur
Deblur is a greedy deconvolution algorithm based on known read error profiles.
llama.cpp
Port of Facebook's LLaMA model in C/C++
metaSNV
MetaSNV, a metagenomic SNV calling pipeline.
MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
mOTUs
motus - a tool for marker gene-based OTU (mOTU) profiling
ngsreads.align.bwa
An extension for ngsreads, wrapping bwa for aligning short reads.
pharokka
fast phage annotation program
PhaTYP
PhaTYP: Predicting lifestyle for bacteriophages using BERT
pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
pyhmmer
Cython bindings and Python interface to HMMER3.
pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data.
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
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
thyroid_2023
Code for paper
valentynbez.github.io
Personal website customized from Hugo Academic template
VIBRANT
Virus Identification By iteRative ANnoTation