BioTools

BioTools is a repository that has many tools and scripts which can be utilized to solve biological problems.

Installation

You can install the BioTools from Github with:

# Run this inside R environment
install.packages("devtools", dependencies = TRUE)
devtools::install_github("Angelovici-Lab/BioTools")

# Run this in your terminal
git clone https://github.com/Angelovici-Lab/BioTools.git
cd BioTools/tools

Usage

1) Hclust Script

Rscript Hclust.R [-h] -i I -o O [-k K] [--clustering_distance CLUSTERING_DISTANCE] [--clustering_method CLUSTERING_METHOD]

mandatory arguments:
  -i I                                          Input file path
  -o O                                          Output folder path

optional arguments:
  -h, --help                                    show this help message and exit
  -k K                                          Number of clusters (optional; default value is 5)
  --clustering_distance CLUSTERING_DISTANCE     Clustering distance
  --clustering_method CLUSTERING_METHOD         Clustering method
  --number_of_tests NUMBER_OF_TESTS             Total number of test cluster size

Hclust Script Example

This is a basic example which shows you how to use Hclust script:

cd /path/to/BioTools/tools
Rscript Hclust.R -i ../data/Hclust.csv -o ../output/07_24_2020

2) PCA Script

Rscript PCA.R [-h] -i I -o O -s S

mandatory arguments:
  -i I        Input file path
  -o O        Output folder path
  -s S        Start column index

optional arguments:
  -h, --help  show this help message and exit

PCA Script Example

This is a basic example which shows you how to use PCA script:

cd /path/to/BioTools/tools
Rscript PCA.R -i ../data/03_22_2020_Arabidopsis_1001_BAA.csv -o ../output/07_25_2020 -s 3

3) Heatmap Script

Rscript Heatmap.R [-h] -i I -o O

mandatory arguments:
  -i I        Input file path
  -o O        Output folder path

optional arguments:
  -h, --help  show this help message and exit

Heatmap Script Example

This is a basic example which shows you how to use Heatmap script:

cd /path/to/BioTools/tools
Rscript Heatmap.R -i ../data/Hclust.csv -o ../output/07_26_2020

4) T-test and FDR Script

Rscript Ttest_and_FDR.R [-h] -i I -o O [--cores CORES] [--fdr_threshold FDR_THRESHOLD]

mandatory arguments:
  -i I                                  Input file path
  -o O                                  Output folder path

optional arguments:
  -h, --help                            show this help message and exit
  --cores CORES                         Number of clusters (optional; default value is 1)
  --fdr_threshold FDR_THRESHOLD         Threshold to filter FDR values

T-test and FDR Script Example

This is a basic example which shows you how to use T-test and FDR script:

cd /path/to/BioTools/tools
Rscript Ttest_and_FDR.R -i ../data/Maize_Drought_proteins_result.csv -o ../output/01_27_2021 --cores 10

5) Heritability Script

Rscript Heritability.R [-h] -i I -o O -s S

mandatory arguments:
  -i I        Input file path
  -o O        Output folder path
  -s S        Start column index

optional arguments:
  -h, --help  show this help message and exit

Heritability Script Example

This is a basic example which shows you how to use Heritability script:

cd /path/to/BioTools/tools

Rscript Heritability.R \
-i /array5/users/Angelovici_lab/GWAS_Project/Arabidopsis_1001/Outlier_removed_raw_data/03_22_2020_Arabidopsis_1001_FAA.csv \
-o /home/ycth8/data/projects/BioTools/output/07_28_2020 \
-s 3

Package Update

To upgrade BioTools to the latest version, please remove the package and re-install the latest BioTools package:

# Run this inside R environment
remove.packages("BioTools")
devtools::install_github("Angelovici-Lab/BioTools")

# Run this in your terminal
cd /path/to/BioTools
git pull