minsiksudo/lai_lab_host_depletion

Host DNA depletion experiment

lai_lab_host_depletion

Host DNA depletion experiment

This repository contains all the codes written to wrangle, process, test, and visualize data for a manuscript entitled

Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies

Descriptions of each code were listed as follows:

1. Data wrangling

COD_20221129_MGK_host_1_wrangle.Rmd

3. Exploratory analysis

COD_20230427_MGK_host_3_analysis_figure_table.html

3. CLR + LMER DA calculation

COD_20231022_MGK_HOST_DAanalysis_CLR_LME4.R

4. Tinyvamp pipelines

20230821_amy/benzonase.R

20230821_amy/hostzero.R

20230821_amy/lypma.R

20230821_amy/molysis.R

20230821_amy/qiaamp.R

20230821_amy/untreated.R

5. Analysis used for figures and table generation

COD_20230427_MGK_host_4_analysis_figure_table_with_output.Rmd

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