SCYN: Single cell CNV profiling method using dynamic programming efficiently and effectively
Project description
SCYN: Single cell CNV profiling method usingdynamic programming efficiently andeffectively
SCYN: Single cell CNV profiling method usingdynamic programming efficiently andeffectively
Pre-requirements
- python3
- numpy>=1.16.1
- pandas>=0.23.4,<0.24
- tasklogger>=0.4.0
- scipy>=1.3.0
- SCOPE
install requirements
pip install -r requirements.txt
To install R package SCOPE, please refer to the README of SCOPE. SCYN integrates the SCOPE to get the cell-by-bin reads depth matrix and perform the normalization. SCYN mainly focuses on finding the optimal CNV segmentation profiling using dynamic programming.
Installation
Installation with pip
To install with pip, run the following from a terminal:
pip install scyn
Installation from Github
To clone the repository and install manually, run the following from a terminal:
git clone https://github.com/xikanfeng2/SCYN.git
cd SCYN
python setup.py install
Usage
Quick start
The following code runs SCYN.
import scyn
# create SCYN object
scyn_operator = scyn.SCYN()
# call cnv
# bam_dir is the input bam directory and output_dir is the output directory
scyn_operator.call(bam_dir, output_dir)
# store cnv matrix to a csv file
scyn_operator.cnv.to_csv('your file name')
Parameters
SCYN(seq='single-end', bin_len=500, ref='hg19', reg='*.bam', mapq=40, K=10, verbose=1)
Parameters
-
seq : string, optional, default: single-end The reads type: single-end or paired-end
-
bin_len : int, optional, default: 500 The bin length, default is 500K
-
ref : string, optional, default: hg19 The reference genome version: hg19 or hg38
-
reg : string, optional, default: .bam The regular expression to match all BAM files in your input directory. For example, ".bam" will match all BAM files ended with '.bam'
-
mapq : int, optional, default: 40 The mapping quality cutoff when calculating the reads coverage
-
K : int, optional, default: 10 The predifined change points number for all chromosomes
-
verbose :
int
orboolean
, optional, default: 1If
True
or> 0
, print status messages
Cite us
Help
If you have any questions or require assistance using SCYN, please contact us with xikanfeng2@gmail.com.
Project details
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