pyvalence is a python package for processing data generated from analytical chemistry. pyvalence reads analytical data from native formats into readily accessible pandas DataFrames and supports common analysis techniques (e.g. standard curves regression and utilization) to reduce manual, one-off data processing. Analysis conducted with pyvalence allows researchers to spend less time processing data and more time interpreting results.
pyvalence easily import data from a root directory using pyvalence.build
agi = AgilentGcms.from_root('data-directory')
which provides easily accessible and organized data.
library_ids = agi.results_lib
areas = agi.results_tic
chromatograms = agi.chromatogram
Plotting the chromatogram is now simple with pandas plots based on matplotlib.
chromatgrams.loc['run1'].plot('tme','tic')
For GCMS data pyvalence.analysis will compile data, create regression curves and calculate concentrations in few lines of code.
compiled_data = match_area(lib,area)
curves = std_curves(comp,stnd)
conc = concentrations(compiled_data,curves)
pyvalence depends on scientific python packages that can be tricky to build from source. For that reason, we recommend the Anaconda python distribution which utilizes the conda package management system.
With conda, binary installers for the planning version of pyvalence are accessible via:
conda install -c blakeboswell pyvalencepip install pyvalenceForthcoming
Python>= 3.6
The following dependencies are bundled in the pyvalence install:
Tour the on-rails example notebooks at pyvalence on-rails.