A simple constrained-scope python utility to automate relative quantification of mRNA from thermocycler cycle threshold (ct) data. Takes as input raw ct values for target and reference genes from experiment and control conditions and returns as output the fold changes in gene expression using the |Dgr| |Dgr| ct method. Useful automation for repeatitive QPCR analyses for life science grad students and postdocs.
Installation:
$ python -m pip install git+https://github.com/pkmklong/pycr.git
Running pycr:
$ pycr -h
usage: pycr [-h] file_path control normalizer target
positional arguments:
file_path The path to ct data (csv) for relative RNA quantification
control The name of your control group
normalizer The name of your normalizing reference transcript
target The name of your target transcript
optional arguments:
-h, --help show this help message and exit
Input data dictionary:
{column: type description}
"group": str Names of comparison groups
user defined normalizing column: float ct values of normalizing reference transcript
user defined target column: float ct values of target transcript
Fold change:
Demo:
$ pycr ./data/demo_data_extended.csv control rpl19 egf1r INFO:pycr: Loading table: ./data/demo_data_extended.csv INFO:pycr: Calculating delta delta ct INFO:pycr: Saving output table: data/demo_data_extended_processed.csv | | group | rpl19 | egf1r | delta_ct | delta_delta_ct | fold_change | |---:|:--------|--------:|--------:|-----------:|-----------------:|--------------:| | 1 | control | 16.9 | 25.8 | 8.9 | 0.3335 | 0.793609 | | 3 | control | 17.7 | 25.4 | 7.7 | -0.8665 | 1.82323 | | 2 | control | 17.4 | 26 | 8.6 | 0.0335 | 0.977047 | | 6 | control | 17.7 | 25.908 | 8.208 | -0.3585 | 1.28209 | | 4 | control | 17.2 | 25.45 | 8.25 | -0.3165 | 1.24531 | | 17 | trt_a | 17.4 | 24.786 | 7.386 | -1.1805 | 2.26655 | | 20 | trt_b | 17.487 | 25.029 | 7.542 | -1.0245 | 2.03425 | | 23 | trt_b | 17.3865 | 25.647 | 8.2605 | -0.306 | 1.23628 | | 18 | trt_b | 17.9895 | 25.9498 | 7.96032 | -0.60618 | 1.52222 | | 22 | trt_b | 17.9895 | 25.441 | 7.4515 | -1.115 | 2.16595 | .... INFO:pycr: Saving output figure: data/demo_data_extended_processed.png
Note
Currently assumes perfect amplification efficiency and unpaired samples.
.. toctree:: :maxdepth: 2 :caption: Contents: license