SCRIP

SCRIP (Single Cell Regulatory network Inference using ChIP-seq & motif) is a toolkit for elucidating the gene regulation pattern based on scATAC-seq leveraing a huge amount of bulk ChIP-seq data. It supports (1) evaluating the TR activities in single-cell based on the integration of the scATAC-seq dataset and curated reference; (2) determining the target genes of TR at single-cell resolution; (3) constructing the GRNs in single-cell and identifying cell-specific regulation.

Documentation

For the detailed usage and examples of SCRIP, please refer to the documentation.
For the analysis codes in the paper, please refer to the Notebook.
For any problems encountered in using, feel free to open an issue.
If SCRIP helps in your work, please cite: Single-cell gene regulation network inference by large-scale data integration.

Installation

Dependency, please install them first:

libpng12-0 tabix

Install SCRIP

git clone git@github.com:wanglabtongji/SCRIP.git
cd SCRIP
python setup.py install

Then, please download the reference files and config them with SCRIP config.

Usage

SCRIP all functions

usage: SCRIP [-h] [--version] {enrich,impute,target,config,index} ...

SCRIP

positional arguments:
  {enrich,impute,target,config,index}
    enrich              Main function.
    impute              Imputation Factor function.
    target              Calculate targets based on factor peak count.
    config              Configuration.
    index               Build index with custom intervals.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

For command line options of each command, type: SCRIP COMMAND -

SCRIP enrich function

usage: SCRIP enrich [-h] -i FEATURE_MATRIX -s {hs,mm} [-p PROJECT] [--min_cells MIN_CELLS] [--min_peaks MIN_PEAKS] [--max_peaks MAX_PEAKS]
                    [-t N_CORES] [-m {max,mean}] [-y] [--clean]

optional arguments:
  -h, --help            show this help message and exit

Input files arguments:
  -i FEATURE_MATRIX, --input_feature_matrix FEATURE_MATRIX
                        A cell by peak matrix . REQUIRED.
  -s {hs,mm}, --species {hs,mm}
                        Species. "hs"(human) or "mm"(mouse). REQUIRED.

Output arguments:
  -p PROJECT, --project PROJECT
                        Project name, which will be used to generate output files folder. DEFAULT: Random generate.

Preprocessing paramater arguments:
  --min_cells MIN_CELLS
                        Minimal cell cutoff for features. Auto will take 0.05% of total cell number.DEFAULT: "auto".
  --min_peaks MIN_PEAKS
                        Minimal peak cutoff for cells. Auto will take the mean-3*std of all feature number (if less than 500 is 500). DEFAULT: "auto".
  --max_peaks MAX_PEAKS
                        Max peak cutoff for cells. This will help you to remove the doublet cells. Auto will take the mean+5*std of all feature
                        number. DEFAULT: "auto".

Other options:
  -t N_CORES, --thread N_CORES
                        Number of cores use to run SCRIP. DEFAULT: 16.
  -m {max,mean}, --mode {max,mean}
                        Deduplicate strategy. DEFAULT: max.
  -y, --yes             Whether ask for confirmation. DEFAULT: False.
  --clean               Whether delete tmp files(including bed and search results) generated by SCRIP. DEFAULT: False.

SCRIP target function

usage: SCRIP target [-h] -i FEATURE_MATRIX -s {hs,mm} [-o OUTPUT] [-d DECAY] [-m MODEL]

optional arguments:
  -h, --help            show this help message and exit

Input files arguments:
  -i FEATURE_MATRIX, --input_feature_matrix FEATURE_MATRIX
                        A cell by peak matrix. h5 or h5ad supported. REQUIRED.
  -s {hs,mm}, --species {hs,mm}
                        Species. "hs"(human) or "mm"(mouse). REQUIRED.

Output arguments:
  -o OUTPUT, --output OUTPUT
                        output h5ad file. DEFAULT: RP.h5ad

Other options:
  -d DECAY, --decay DECAY
                        Range to the effect of peaks. DEFAULT: auto.
  -m MODEL, --model MODEL
                        RP model chosen. DEFAULT: simple.

SCRIP config function

usage: SCRIP config [-h] [--show] [--human_tf_index HUMAN_TF_INDEX] [--human_hm_index HUMAN_HM_INDEX] [--mouse_tf_index MOUSE_TF_INDEX]
                    [--mouse_hm_index MOUSE_HM_INDEX]

optional arguments:
  -h, --help            show this help message and exit
  --show
  --human_tf_index HUMAN_TF_INDEX
  --human_hm_index HUMAN_HM_INDEX
  --mouse_tf_index MOUSE_TF_INDEX
  --mouse_hm_index MOUSE_HM_INDEX

SCRIP index function

usage: SCRIP index [-h] -i INPUT -o OUTPUT

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Path to the folder that includes all your bed files. The bed files should be named in "TRName_ID.bed", e.g. "AR_1.bed".
  -o OUTPUT, --output OUTPUT
                        Path to the output folder.

Manually install GIGGLE

SCRIP fast searching is based on GIGGLE. Please install GIGGLE manually first.

git clone git@github.com:ryanlayer/giggle.git
cd giggle
make
export PATH=$PATH:`pwd` # or cp bin/giggle to your environment
cd ..

Next, validate the installation:

giggle

It should return:

giggle, v0.6.3
usage:   giggle <command> [options]
     index     Create an index
     search    Search an index

Besides manually installation, you can try SCRIP install_giggle too.