Metadata-Version: 2.1
Name: rnaseqc
Version: 0.0.2
Summary: Multi-sample visualization of metrics from RNA-SeQC
Home-page: UNKNOWN
License: UNKNOWN
Description: # RNA-SeQC Python utilities
        
        This module contains utility code for RNA-SeQC
        
        ## Installing
        
        * From pip: `pip install rnaseqc`
        * From the git repo: `pip install -e python` (Invoke from root of git repo)
        
        ## Usage
        
        This does not install a console entrypoint. You can invoke the utilities in one of three ways:
        
        * From the main module: `python3 -m rnaseqc ...`
        * Calling the target module: `python3 -m rnaseqc.example ...`
        * Calling scripts directly: `python3 python/rnaseqc/example.py`
        
        ## Utilities
        
        The `rnaseqc` module contains 5 main utilities. To get more help with each utility,
        invoke the utility with the `-h` or `--help` option
        
        ### Aggregation
        
        Aggregates RNA-SeQC outputs from multiple samples
        
        ```
        python3 -m rnaseqc aggregate [-h] [--parquet] [-o OUTPUT_DIR] results_dir prefix
        ```
        
        ### Jupyter Notebooks
        
        Creates a jupyter notebook with several figures for comparing samples
        
        ```
        python3 -m rnaseqc notebook [-h] [-t TPM] [-i INSERT_SIZE] [-c COHORT] [-d DATE] metrics output
        ```
        
        ### Figures
        
        Generates figures from an aggregated RNA-SeQC metrics table
        
        ```
        python3 -m rnaseqc report [-h] [--tpm TPM] [--insert-size INSERT_SIZE] [--cohort COHORT] [--output-dir OUTPUT_DIR] [--dpi DPI] metrics prefix
        ```
        
        ### Insert Size distributions
        
        Generates a BED file with intervals used by RNA-SeQC for estimating a sample's insert size distribution
        
        ```
        python3 -m rnaseqc insert-size [-h] [--min-length MIN_LENGTH] [--min-mappability MIN_MAPPABILITY] [--output-dir OUTPUT_DIR] gtf_path mappability_bigwig prefix
        ```
        
        ### Exon remapping
        
        Convert exon names in an `*.exon_reads.gct` file from RNA-SeQC 2.X.X to match names
        as reported by RNA-SeQC 1.1.9
        
        ```
        python3 -m rnaseqc legacy-exons gct gtf
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
