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code
data
exploratory
results
submission
.Rprofile
.gitignore
CONTRIBUTING.md
INSTRUCTIONS.md
LICENSE.md
Makefile
README.md
newproject_LICENSE.md

README.md

Download the latest release to the directory and decompress

TITLE OF YOUR PAPER GOES HERE

YOUR PAPER'S ABSTRACT GOES HERE

Overview

project
|- README          # the top level description of content (this doc)
|- CONTRIBUTING    # instructions for how to contribute to your project
|- LICENSE         # the license for this project
|
|- submission/
| |- study.Rmd    # executable Rmarkdown for this study, if applicable
| |- study.md     # Markdown (GitHub) version of the *.Rmd file
| |- study.tex    # TeX version of *.Rmd file
| |- study.pdf    # PDF version of *.Rmd file
| |- header.tex   # LaTeX header file to format pdf version of manuscript
| |- references.bib # BibTeX formatted references
| |- XXXX.csl     # csl file to format references for journal XXX
|
|- data           # raw and primary data, are not changed once created
| |- references/  # reference files to be used in analysis
| |- raw/         # raw data, will not be altered
| |- mothur/      # mothur processed data
| +- process/     # cleaned data, will not be altered once created;
|                 # will be committed to repo
|
|- code/          # any programmatic code
|
|- results        # all output from workflows and analyses
| |- tables/      # text version of tables to be rendered with kable in R
| |- figures/     # graphs, likely designated for manuscript figures
| +- pictures/    # diagrams, images, and other non-graph graphics
|
|- exploratory/   # exploratory data analysis for study
| |- notebook/    # preliminary analyses
| +- scratch/     # temporary files that can be safely deleted or lost
|
+- Makefile       # executable Makefile for this study, if applicable

How to regenerate this repository

Dependencies and locations

  • Gnu Make should be located in the user's PATH
  • mothur (v1.XX.0) should be located in the user's PATH
  • R (v. 3.X.X) should be located in the user's PATH
  • R packages:
    • knitr
    • rmarkdown
  • etc

Running analysis

git clone https://github.com/SchlossLab/LastName_BriefDescription_Journal_Year.git
make write.paper