microbialman

Matt Jackson-Wood's repositories

Simple counting of bacterial colonies from pictures of plates.

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A metagenomics pipeline using the CGAT framework.

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Analyses and code associated with https://doi.org/10.1038/s41591-021-01520-5

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Package to calculate IgA binding scores from IgA-Seq data in R.

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Pipeline to filter rRNA and host contaminant reads from metaomic data sets. Complements MetaAssemblyKit

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A Snakemake pipeline to run many different machine learning algorithms in parallel using the Caret package.

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cgat-flow repository

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Pipelines to run select BioBakery tools within the CGAT pipelines framework.

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Code for analyses presented in the IgAScores paper.

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An assembly based metagenomic pipeline using the Snakemake workflow.

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Pipeline to carryout ORF prediction and annotation from input contigs. Complements MetaAssemblyKit.

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Pipeline to enumerate metagenomic samples from annotated ORFs. Complements MetaAssemblyKit

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Pipeline to pool reads across fasta/q files, ensure unique read names, and dereplicate using BBMap. Complements MetaAssemblyKit.

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R API and htmlwidget for Vitessce

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