This program allows to combine 3 dimensional architecture and transcriptional activity of a whole genome.
git clone https://github.com/kabhel/3D_transcription_map.git
cd 3D_transcription_map
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A linux distribution.
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The programming langage Python3 and the following standard libraries :
pip3 install -r requirements.txt
# This command will install the following modules:
# docopt==0.6.2
# numpy==1.15.2
# pandas==0.23.4
# schema==0.6.8
# tqdm==4.28.1
# plotly==3.4.2
The program takes in input a file containing the 3D coordinates of a chromosome/genome for each genes and a file containing the gene expression values in different conditions. The generated interactive plot is in html format.
Chromosome 1 of the genome of Plasmodium falciparum
./3d_transcription_map data/toy_example_chr1/coordinates.txt data/toy_example_chr1/expressions.txt -o results/plot_chr1.html
./3d_transcription_map -h
Usage:
./3d_transcription_map COORDINATES EXPRESSIONS [--nb_genes INT] [--cpu INT] [--output PATH]
Arguments:
COORDINATES Path to the file containing informations
about 3D coordinates of the genes.
EXPRESSIONS Path to the file containing the gene expression
values in different conditions.
Options:
-h, --help Show this.
-n INT, --nb_genes INT Indicates the number of genes nearby
to take into account. [default: 10]
-c INT, --cpu INT Number of cpus to use for parallelisation. By default
using all available (0).
[default: 0]
-o PATH, --output Path Path to the generated plot (html format).
[default: results/plot.html]
- Hélène Kabbech ~ Bioinformatics master student at Paris Diderot University
- Costas Bouyioukos ~ Supervisor