This repository is for the paper "q-mer analysis: a generalized method for analyzing RNA-Seq data."
To use q-mer analysis for the example data (example.sam), conduct the following.
./qmer example.sam example_result 10
To reproduce, follow the jupyter notebook in qmer_cocaine
or qmer_sz
.
Note that you need the gff file for H. sapiens to follow the notebook 1.count_based.ipynb
.
- python (3.7.3)
- anaconda3-5.3.1
- biopython (1.75)
- pandas (0.23.4)
- numpy (1.15.1)
- sklearn (0.24.1)
- bokeh (2.2.3)