a-h-b/Data_availability_study

Data availability study

This repository contains code and data for the assessment of the availability of microbial community sequencing data by Stephanie D. Jurburg, Maximilian Konzack, Nico Eisenhauer, and Anna Heintz-Buschart. The following files are included:

Jupyter notebook to perform the literature research

• pdf2seqs.ipynb
• pdf2seqs.html
• pdf2seqs.md

This uses code from https://github.com/komax/teitocsv and a conda environment: pdf2seq.yaml

R notebooks to visualize the analysis results:

Main figures:

• R_Notebook_Analyses_main.Rmd
• R_Notebook_Analyses_main.nb.html

with input data:

• mining_output.txt
• 191206_simplifiedAll.RDS
• 191206_simplifiedSub.RDS
• accessions_bacteria_cleaner_onlyExtra_AHB.txt
• 200315_simplifiedV4.RDS
• all_study_pie.txt

Analysis of raw and metadata:

• R_Notebook_Analyses_Raw_data_and_metadata.Rmd
• R_Notebook_Analyses_Raw_data_and_metadata.nb.html

with input data:

• Metadata.RDS
• raw_data.txt