Bioinformatics at Małopolska Centre of Biotechnology's repositories
gisaid-scrapper
Scrapping tool for GISAID data regarding SARS-CoV-2
Metagenomic-DeepFRI
Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
metagenome_assembly
WDL Workflow for metagenome assembly
qiime2-api-tutorials
QIIME 2 tutorials using the Artifact API
BERT-torchserve-quickstart
Serving BERT embeddings via Torchserve
gantt-chart
Python code for easy Gantt chart generation
sra-downloader
A script for batch-downloading data from SRA built on SRA-Toolkit.
DILI-analysis
Analysis of liver toxicity data
phage-protein-modularity-data
Phage project computational pipeline.
sars-cov-2-primers-article-suppl
Supplement for "COVID-19 screening: impact of SARS-CoV-2 genomic variants"
dask-crash-course
Dask crash course for UBG Forum meeting
SARSConsensusCaller
SARSConsensusCaller is a wrapper python script for fast consensus sequence calls based on generated vcf files
bioinf-mcb-rnaseq_arenosa_thaliana_20_22
Source code for the RNA-Seq analysis project in collaboration with Plant-microorganism research group
gut_microbiome_dynamics_project
this repo contains data and code produced during development of project 'Dynamics of interactions within the human gut microbiome using machine learning algorithms'
metagenome_assembly-1
WDL Workflow for metagenome assembly
ncov-ingest
A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
phage-protein-modularity-figures
code related to the paper: Protein mosaicism in bacteriophages is extensive and associated with functions linked to core nucleotide metabolism and host tropism .
proj_koryl
Master's thesis on exploring the relationship between genetic similarity and taxonomy in bacteriophages
spatial_sinus_microbiome
Code for the paper "Determinants of the microbiome spatial variability in chronic rhinosinusitis" by Szaleniec et al. 2022
thaliana_etr_etre
Repository of code for publication of endophyte project with Mycoplanta