A simple constrained-scope Julia 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:
$ julia -e 'using Pkg; pkg"add https://github.com/pkmklong/MolecBio";'
Entry point:
$ julia runner.jl --h
usage: runner.jl -f FILE_PATH -c CONTROL -t TARGET -n NORMALIZER [-h]
optional arguments:
-f, --file_path FILE_PATH
The path to raw ct data (csv) for relative RNA
quantification
-c, --control CONTROL
The name of your control group (default:
"control")
-t, --target TARGET The name of your target transcript
-n, --normalizer NORMALIZER
The name of your normalizing reference
transcript
-h, --help show this help message and exit
Input data dictionary:
{column: type description}
"group": String Names of comparison groups
user defined target column: Float64 ct values of target transcript
user defined normalizing column: Float64 ct values of normalizing reference transcript
Fold change:
Demo:
$ julia src/runner.jl -f "data/demo_data.csv" -c "control" -t "egf1r" -n "rpl19" Parsed args: normalizer => rpl19 target => egf1r control => control file_path => data/demo_data.csv ┌ Info: Loading CT values table └ args["file_path"] = "data/demo_data.csv" ┌ Info: Computing fold change with delta delta ct │ first(ddct_table, 5) = │ 5×6 DataFrame │ │ Row │ group │ egf1r │ rpl19 │ delta_ct │ delta_delta_ct │ fold_change │ │ │ │ String │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │ │ ├─────┼─────────┼─────────┼─────────┼──────────┼────────────────┼─────────────┤ │ │ 1 │ control │ 25.6 │ 17.5 │ -8.1 │ 0.4665 │ 1.38175 │ │ │ 2 │ control │ 25.8 │ 16.9 │ -8.9 │ -0.3335 │ 0.793609 │ │ │ 3 │ control │ 26.0 │ 17.4 │ -8.6 │ -0.0335 │ 0.977047 │ │ │ 4 │ control │ 25.4 │ 17.7 │ -7.7 │ 0.8665 │ 1.82323 │ └ │ 5 │ control │ 25.45 │ 17.2 │ -8.25 │ 0.3165 │ 1.24531 │ ┌ Info: Saving output table to └ ddct_table_path = "data/demo_data_processed.csv" ┌ Info: Saving output figure to └ ddct_figure_path = "data/demo_data_processed.svg"
Note
Currently assumes perfect amplification efficiency and unpaired samples.
.. toctree:: :maxdepth: 2 :caption: Contents: license