microbialman
Personal account, mainly previous academic work, currently senior scientist in bioinformatics @ Gilead Oxford (Prev. MiroBio)
GileadOxford, UK
Pinned Repositories
CaretSnakemake
A Snakemake pipeline to run many different machine learning algorithms in parallel using the Caret package.
cgat-flow
cgat-flow repository
CGATBioBakery
Pipelines to run select BioBakery tools within the CGAT pipelines framework.
CGATMetaSequencing
A metagenomics pipeline using the CGAT framework.
DDotCounter
Simple counting of bacterial colonies from pictures of plates.
IBDTherapyResponsePaper
Analyses and code associated with https://doi.org/10.1038/s41591-021-01520-5
IgAScores
Package to calculate IgA binding scores from IgA-Seq data in R.
IgAScoresAnalyses
Code for analyses presented in the IgAScores paper.
MetaFilter
Pipeline to filter rRNA and host contaminant reads from metaomic data sets. Complements MetaAssemblyKit
MetaSequencing
An assembly based metagenomic pipeline using the Snakemake workflow.
microbialman's Repositories
microbialman/DDotCounter
Simple counting of bacterial colonies from pictures of plates.
microbialman/CGATMetaSequencing
A metagenomics pipeline using the CGAT framework.
microbialman/IBDTherapyResponsePaper
Analyses and code associated with https://doi.org/10.1038/s41591-021-01520-5
microbialman/IgAScores
Package to calculate IgA binding scores from IgA-Seq data in R.
microbialman/MetaFilter
Pipeline to filter rRNA and host contaminant reads from metaomic data sets. Complements MetaAssemblyKit
microbialman/CaretSnakemake
A Snakemake pipeline to run many different machine learning algorithms in parallel using the Caret package.
microbialman/cgat-flow
cgat-flow repository
microbialman/CGATBioBakery
Pipelines to run select BioBakery tools within the CGAT pipelines framework.
microbialman/IgAScoresAnalyses
Code for analyses presented in the IgAScores paper.
microbialman/MetaSequencing
An assembly based metagenomic pipeline using the Snakemake workflow.
microbialman/MetaAnnotate
Pipeline to carryout ORF prediction and annotation from input contigs. Complements MetaAssemblyKit.
microbialman/MetaEnumerate
Pipeline to enumerate metagenomic samples from annotated ORFs. Complements MetaAssemblyKit
microbialman/PoolReads
Pipeline to pool reads across fasta/q files, ensure unique read names, and dereplicate using BBMap. Complements MetaAssemblyKit.
microbialman/vitessceR
R API and htmlwidget for Vitessce