This repository contains all files and code to reproduce the results in the publication [add link].
When running the code from scripts, there is no need to change working directories - all paths are relative to the R project file located in this repository.
This folder contains: 1) A file with the names of the FASTQ files of all mocks used, including the kraken2 evaluation mocks, and links to download them; 2) The true abundance of each organism; 3) The detected abundance using each kraken2, specifically for its threshold evaluation.
It contains a separate folder for each figure. Within the folders, subfolders contain the necessary data as well as the script to produce the figures. The figures will be saved within their folder when the script is run.
Contains the raw figures that were used in the publication. They are deposited here for direct comparison to any changes that may occur when adjusting the scripts.
It contains bash scripts used to generate mocks and evaluate kraken2, mostly for archive purposes and distribution. All custom functions have been combined into the honeyDSM-seq-analysis R package that can be found here:
current session info
- Session info -----------------------------------------------------------------------------------------------------------------------------------
setting value
version R version 3.6.3 (2020-02-29)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United Kingdom.1252
ctype English_United Kingdom.1252
tz Europe/Istanbul
date 2020-10-06
- Packages ---------------------------------------------------------------------------------------------------------------------------------------
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