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cazy_webscraper Public
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
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cazomevolve Public
`cazomevolve` ('cazome-evolve') investigates the evolution of CAZomes, and identifies CAZy families that co-occur within the genomes of candidate species, more frequently than would be expected by …
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Supplementary information for the annotation of 634 fungal and oomycete CAZomes using pyrewton
Jupyter Notebook MIT License UpdatedMar 30, 2024 -
SI_Hobbs_et_al_2024_Pecto Public
Supplementary information for analyses reported in Hobbs et al. (2024), describing the evolution of the CAZome
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Supplementary Information for the independent benchmarking of CAZyme classifiers dbCAN, eCAMI and Hotpep
HTML MIT License UpdatedDec 23, 2023 -
pyrewton Public
Python package for the identification of comprehensive CAZyomes of candidate species
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Supplementary information on the exploration of the CAZome and carbohydrate processing enzyme activities in soft rot Pectobacteriaceae
Jupyter Notebook MIT License UpdatedNov 1, 2023 -
bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedJul 28, 2023 -
SI_Foltanyi_et_al_2023 Public
Bioinformatics work for the paper Foltanyi et al., 2022
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carpentries_materials Public
Repo containing data and teaching materials for carpentries workshops
Jupyter Notebook MIT License UpdatedMay 10, 2023 -
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saintBioutils Public
Repository of utility and miscellaneous functions for using in bioinformatics pipelines, primarily in Python
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SI_CE_PL_exploration Public
Explore the sequence, structure and function of CAZymes containing a CE and PL9 domain.
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Supplementary information for analyses reported in Hobbs et al. (2023), for presenting the software package `cazy_webscraper`
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Materials for the SIPBS CompBio workshop
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kaggle_ML Public
Repo for storing code and notebooks for competing in kaggle machine-learning and data science competitions.
Jupyter Notebook MIT License UpdatedJun 13, 2022 -
template_bioinformatics_project Public template
Forked from sipbs-compbiol/template_bioinformatics_projectStarting template for UG/PG bioinformatics projects using git
Creative Commons Attribution Share Alike 4.0 International UpdatedJun 1, 2022 -
ncfp Public
Forked from widdowquinn/ncfpProgram and package that retrieves nucleotide coding sequences from NCBI that correspond to a set of input protein sequences.
Python MIT License UpdatedMay 17, 2022 -
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SequenceTools Public
Forked from Computational-conSequences/SequenceToolsPrograms used in the lab for various tasks
Perl GNU General Public License v3.0 UpdatedJun 11, 2021 -
ten_great_papers Public
Forked from widdowquinn/ten_great_papersTen great papers for wet lab biologists starting out in computational biology
MIT License UpdatedJan 12, 2021 -
SI_Holmes_etal_2020 Public
Forked from widdowquinn/SI_Holmes_etal_2020Supplementary information for Holmes et al. (2020)
HTML MIT License UpdatedMay 27, 2020 -
eCAMI Public
Forked from zhanglabNKU/eCAMISimultaneous Classification and Motif Identification(eCAMI)
Python UpdatedApr 28, 2020 -
pyani Public
Forked from widdowquinn/pyaniPython module for average nucleotide identity analyses
Python MIT License UpdatedApr 6, 2020 -
Rosalind_Python_Problems Public
Store of Python files containing solutions to problems from Rosalind
Python UpdatedMar 3, 2020 -
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