Metadata-Version: 2.1
Name: inferelator-prior
Version: 0.2.1
Summary: Inferelator-Prior Network Generation Tool
Home-page: https://github.com/flatironinstitute/inferelator-prior
Author: Chris Jackson
Author-email: cj59@nyu.edu
Maintainer: Chris Jackson
Maintainer-email: cj59@nyu.edu
License: UNKNOWN
Description: # inferelator-prior
        
        This is a set of pipelines to create expression and prior matrices for network inference. They are designed to create
        data that is compatible with the [inferelator](https://github.com/flatironinstitute/inferelator) package. 
        
        ### Usage
        
            python -m inferelator_prior.network_from_motifs
            usage: network_from_motifs.py --motif motif_PWM_file.meme
                                          -f genome_fasta_file.fasta
                                          -g genome_annotation_file.gtf
                                          -o ~/output/path/prefix
                                          --species {yeast,fly,mouse,human}
                                          -b constraning_bed_file.bed
                                          --cpu num_cores
                                          
        This requires a motif PWM database (`-m PATH`), 
        a genome to search (both sequence as a FASTA `-f PATH` and annotations `-g PATH`),
        and an output prefix for several files (`-o PATH`).
        In addition, default settings for a specific species can be set with (`--species`).
        A BED file can be provided (`-b PATH`) based on some constraining experiment to restrict searching to specific genomic areas.
        This will use multiple cores to search for motifs and process the resulting data.
        By default, all available processors will be used, but this can be overridden with `--cpu N`.
        
        ### Requirements
        
        In addition to
        python dependencies, this package also requires 
        [STAR](https://github.com/alexdobin/STAR),
        [sra-tools](http://ncbi.github.io/sra-tools/), 
        [bedtools](https://bedtools.readthedocs.io/en/latest/),
        [samtools](http://www.htslib.org/), and
        [fimo](http://meme-suite.org/doc/fimo.html).
        
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
