Chris Baker's repositories
entrez_qiime
A utility to generate input files for taxonomy assignment in QIIME from the NCBI database
permafrost-pathogens
Exploration of pathogens in Alaskan permafrost thaw samples
amplicon-template
Template repo for setting up new amplicon sequencing analyses
centrarium
A simple yet classy theme for your Jekyll website or blog.
snakemake-template
template for snakemake analyses
training-rstudio
Multi-purpose Rstudio binder for training events
imnavait-public
Code for Baker et al. 2023 (doi:10.1088/1748-9326/acc542)
leeches-public
Code for Ji et al. (2022) "Measuring Protected-Area Effectiveness using Vertebrate Distributions from Leech iDNA"
leeches2018-public
ailaoshan-public
phyloseq
phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
R-template
template for R analyses
scIntegral
Highly scalable integration and classification of single-cell RNA sequencing data