This repo contains relevant codebase for CARMEN-RVP and CARMEN-VARIANT analyses.
CARMEN-RVP is a CRISPR/Cas13 based assay detecting 9 respiratory viruses which is run on a Fluidigm Biomark HD instrument. The readout is raw fluorescence data extracted from the Fluidigm RT-PCR software. The exported data can then be further analyzed with this tool.
src folder:
The main script for the analysis is called 'carmen_rvp_analysis.py'. The other scripts contain functions that will be imported during the analysis run.
img folder:
Icons for graphical user interface.
archive-expertversion folder:
For R&D use only. This contains an older version of the tool that provides the user with more flexibility on the input.
Python dependencies:
- pandas==1.0.5
- seaborn==0.10.1
- matplotlib==3.2.2
- Gooey==1.0.7
- numpy==1.18.5
- xlrd==1.1.0
Inputs:
- Fluidigm Biomark raw data file (.csv)
- Sample assignment sheet (.xlsx): Template "assignment-template.xlsx" can be downloaded here.
Clone this github repository to always have the most up-to-date version. An executable version for Windows and Mac will be coming soon.
The assignment sheet can be downloaded from this repository.
Samples controls have to be named 'EC', 'NTC', 'NDC', 'CPC'.
The control assay without crRNA has to be called 'no-crRNA' and the assay for RNaseP has to be called 'RNaseP' or 'RNAseP'.
- If the command line is used, run the the main script with the following command:
$ pythonw ./src/carmen_rvp_analysis.py - Choose an output prefix and an output directory
- Upload the assignment sheet and the raw data file
- Click start run.
CARMEN-VARIANT is a CRISPR/Cas13 based assay detecting COVID-19 variants and SNP mutations of concern which is run on a Fluidigm Biomark HD instrument. The readout is raw fluorescence data extracted from the Fluidigm RT-PCR software. The exported data can then be further analyzed with this tool.
src folder:
The main scripts for the analysis:
- carmen_variant_dataparser.py: will parse the data exported from the Fluidigm RT-PCR software
- carmen_variant_analysis.py: will determine the test positivity for each SNP and the ultimate variant call
Python dependencies:
- pandas==1.0.5
- seaborn==0.10.1
- matplotlib==3.2.2
- numpy==1.18.5
Inputs:
- Fluidigm Biomark raw data file (.csv)
- Sample assignment sheet (.xlsx): Template "assignment-template.xlsx" can be downloaded here.
- FCthresholds (.csv): contains the thresholds for each crRNA guide pairs for a single SNP.
Clone this github repository to always have the most up-to-date version. An executable version for Windows and Mac will be coming soon.
The assignment sheet can be downloaded from this repository.
Samples controls have to be named 'EC', 'NTC', 'NDC', 'CPC'.
The control assay without crRNA has to be called 'no-crRNA' and the assay for RNaseP has to be called 'RNaseP' or 'RNAseP'.
$ python ./src/carmen_variant_dataparser.py *arglist $ python ./src/carmen_variant_analysis.py *arglist