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@bioinf-mcb Bioinformatics at Małopolska Centre of Biotechnology

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    33 repositories

    • MANIAC

      Public
      Computation of average nucleotide identity with the use of MMseqs2
      Python
      •0•8•0•0•Updated Oct 28, 2024Oct 28, 2024

    • DeepFRI

      Public
      Deep functional residue identification
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •77•6•1•0•Updated Oct 10, 2024Oct 10, 2024

    • Metagenomic-DeepFRI

      Public
      Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.
      genomicsprotein-structureprotein-sequencesmmseqsprotein-function-prediction
      Python
      •
      GNU General Public License v3.0
      •6•32•2•0•Updated Sep 21, 2024Sep 21, 2024

    • q2-predict-dysbiosis

      Public
      Python
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated May 10, 2024May 10, 2024

    • thaliana_etr_etre

      Public
      Repository of code for publication of endophyte project with Mycoplanta
      R
      •
      MIT License
      •0•0•0•0•Updated May 9, 2024May 9, 2024

    • dynamo

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Feb 27, 2024Feb 27, 2024

    • phage-protein-modularity-figures

      Public
      code related to the paper: Protein mosaicism in bacteriophages is extensive and associated with functions linked to core nucleotide metabolism and host tropism .
      R
      •0•0•0•0•Updated Oct 20, 2023Oct 20, 2023

    • phage-protein-modularity-data

      Public
      Phage project computational pipeline.
      Python
      •0•1•0•0•Updated Oct 19, 2023Oct 19, 2023

    • metagenome_assembly

      Public
      WDL Workflow for metagenome assembly
      Python
      •3•9•1•0•Updated Aug 15, 2023Aug 15, 2023

    • q2-dynamo

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 10, 2023Aug 10, 2023

    • q2-health-index

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•2•1•0•Updated Aug 3, 2023Aug 3, 2023

    • gisaid-scrapper

      Public
      Scrapping tool for GISAID data regarding SARS-CoV-2
      scraperseleniumsars-cov-2
      Python
      •
      MIT License
      •16•41•10•1•Updated May 22, 2023May 22, 2023

    • polish-microbiome-project

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • metagenome_assembly-1

      Public
      WDL Workflow for metagenome assembly
      Roff
      •3•0•0•0•Updated Nov 29, 2022Nov 29, 2022

    • spatial_sinus_microbiome

      Public
      Code for the paper "Determinants of the microbiome spatial variability in chronic rhinosinusitis" by Szaleniec et al. 2022
      Jupyter Notebook
      •1•0•0•0•Updated Oct 27, 2022Oct 27, 2022

    • SARSConsensusCaller

      Public
      SARSConsensusCaller is a wrapper python script for fast consensus sequence calls based on generated vcf files
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 19, 2022Oct 19, 2022

    • sra-downloader

      Public
      A script for batch-downloading data from SRA built on SRA-Toolkit.
      Python
      •
      MIT License
      •2•3•0•0•Updated Oct 13, 2022Oct 13, 2022

    • qiime2-api-tutorials

      Public
      QIIME 2 tutorials using the Artifact API
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •6•5•0•1•Updated Sep 4, 2022Sep 4, 2022

    • bioinf-mcb-rnaseq_arenosa_thaliana_20_22

      Public
      Source code for the RNA-Seq analysis project in collaboration with Plant-microorganism research group
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 26, 2022Jul 26, 2022

    • gut_microbiome_dynamics_project

      Public
      this repo contains data and code produced during development of project 'Dynamics of interactions within the human gut microbiome using machine learning algorithms'
      0•0•0•0•Updated Jun 29, 2022Jun 29, 2022

    • pyprimer

      Public
      pyprimer
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Mar 7, 2022Mar 7, 2022

    • proj_koryl

      Public
      Master's thesis on exploring the relationship between genetic similarity and taxonomy in bacteriophages
      Python
      •0•0•0•0•Updated Feb 4, 2022Feb 4, 2022

    • sars-cov-2-primers-article-suppl

      Public
      Supplement for "COVID-19 screening: impact of SARS-CoV-2 genomic variants"
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 9, 2021Nov 9, 2021

    • gantt-chart

      Public
      Python code for easy Gantt chart generation
      pythonjupyter-notebookgantt-chart
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Jul 30, 2021Jul 30, 2021

    • dask-crash-course

      Public
      Dask crash course for UBG Forum meeting
      Jupyter Notebook
      •0•0•0•0•Updated May 25, 2021May 25, 2021

    • BERT-torchserve-quickstart

      Public
      Serving BERT embeddings via Torchserve
      nlppytorchrepresentation-learningbertproduction-servicetorchserve
      Python
      •3•4•0•0•Updated Apr 8, 2021Apr 8, 2021

    • auspice

      Public
      Web app for visualizing pathogen evolution
      JavaScript
      •
      GNU Affero General Public License v3.0
      •161•0•0•0•Updated Mar 12, 2021Mar 12, 2021

    • ribosomal-proteins

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 7, 2021Mar 7, 2021

    • ncov-ingest

      Public
      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.
      Python
      •
      MIT License
      •20•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • DILI-analysis

      Public
      Analysis of liver toxicity data
      Jupyter Notebook
      •1•1•0•0•Updated Mar 6, 2020Mar 6, 2020