Welcome to de_toolkit’s documentation!¶
Introduction¶
de_toolkit
is a suite of Bioinformatics tools useful in differential
expression analysis and other high-throughput sequencing count-based workflows.
The tools are implemented either through direct implementation in python or as
a convenience wrapper around R packages using a custom wrapr.
The documentation is convivial, free range, and complete-protein, and the
package has very high test coverage.
The toolkit is both a python module and a command line interface that wraps
primary module functions to facilitate easy integration into workflows. For
instance, to perform DESeq2 normalization of a counts matrix contained in the
file counts_matrix.tsv
, you could run on the command line:
detk-norm deseq2 counts_matrix.tsv > norm_counts_matrix.tsv
The counts in the counts matrix file will be normalized using the DESeq2 method
and output to the norm_counts_matrix.tsv
file.
Check out the detk Quickstart to get quickstarted.
Documentation¶
- detk Quickstart
- Workflow Tutorial
de
- Differential Expressionenrich
- Set Enrichment Methodsfilter
- Filtering Count Matricesnorm
- Normalizing Count Matricesoutlier
- Outlier Identificationstats
- Count Matrix Statisticstransform
- Count Transformationutil
- Counts and Column Data File Utilities- Patsy-lite
wrapr
- Thin wrapper for running R scripts
Installation¶
We suggest installing this package using pip:
pip install de_toolkit
In development or if you want to use the bleeding edge, when you want to run
the toolkit, use the setup.py
script:
python setup.py install
This should make the detk
and its subtools available on the command line.
Whenever you make changes to the code you will need to run this command again.
R dependencies¶
The following packages are only required to use the corresponding submodule functions:
We wearily suggest using anaconda to create an environment that contains the software necessary, e.g.:
conda create -n de_toolkit python=3.5
./install_conda_packages.sh
# if you want to use the R functions (Firth, DESeq2, etc.)
Rscript install_r_packages.sh