Metadata-Version: 2.1
Name: CamoTSS
Version: 0.1.6
Summary: CamoTSS: Detection alternative TSS in single cells
Home-page: https://github.com/StatBiomed/CamoTSS
Author: ['Ruiyan Hou']
Author-email: ruiyan@connect.hku.hk
License: Apache-2.0
Description: ============================================================
        CamoTSS for alternative TSS analysis in single cells
        ============================================================
        |pypi| 
        
        .. |pypi| image:: https://badge.fury.io/py/CamoTSS.svg
               :target: https://pypi.org/project/CamoTSS/
        
        
        
        
        Installation
        ============
        
        You can install from this GitHub repository for latest (often development) 
        version by following command line
        
        .. code-block:: bash
        
          pip install -U git+https://github.com/StatBiomed/CamoTSS
        
        In either case, add ``--user`` if you don't have the write permission for your 
        Python environment.
        
        
        Quick start
        ===========
        
        Download test file
        ===================
        
        You can download test file from figshare_.
        
        .. _figshare: https://figshare.com/articles/dataset/CamoTSS_test_data/22641031
        
        Here, you can download some large file include genome.fa, possorted_genome_bam_filtered.bam.
        
        Alternatively, you can also download the reference genome fasta file from Ensembl or Genecode or website of 10x Genomics. 
         
        Run CamoTSS 
        =============
        
        Here are three modes in CamoTSS : **TC+CTSS** , **TC** and **CTSS**.
        
        When you run **TC+CTSS** mode, you will get TC result and then get the CTSS result based on the TC.
        
        When you run **TC** mode, you will only get the TC result.
        
        The **TC+CTSS** and **TC** mode have the same required files.
        
        The --outdir is the only required parameter for **CTSS** mode. But the outdir should include output of TC.  
        
        If you want to run **CTSS** mode, you must based on the output of TC.
        
        You can run CamoTSS **TC+CTSS** mode by using test file according to the following code.
        
        For the remaining modes, you can check this document_.
        
        .. _document: https://camotss.readthedocs.io/en/latest/run_CamoTSS.html
        
        .. code-block:: bash
        
           #!/bin/bash 
           gtfFile= $CamoTSS/test/Homo_sapiens.GRCh38.105.chr_test.gtf
           fastaFile = $download/genome.fa
           bamFile= $download/possorted_genome_bam_filtered.bam
           cellbarcodeFile=$CamoTSS/test/cellbarcode_to_CamoTSS
        
           CamoTSS --gtf gtfFile --refFasta fastaFile --bam bamFile -c cellbarcodeFile -o CamoTSS_out --mode TC+CTSS
        
        
        Alternative TSS or CTSS detecting
        =================================
        
        To identify alternative TSS usage or alternative CTSS usage, Brie2 (Huang & Sanguinetti, 2021) is recommend to be used. 
        
        Here, we provide an example exploiting BRIE2 to detect alterntive TSS/CTSS usage. 
        
        You can check it in our manual_.
        
        .. _manual: https://camotss.readthedocs.io/en/latest/runBRIE.html  
        
        
        Detailed Manual
        ================
        
        The full manual is here_, including:
        
        `Preprocess`_
        
        `Run CamoTSS`_
        
        `Detect alternative TSS/CTSS`_
        
        .. _here: https://camotss.readthedocs.io/en/latest/index.html
        
        .. _Preprocess: https://camotss.readthedocs.io/en/latest/preprocess.html
        
        .. _Run CamoTSS: https://camotss.readthedocs.io/en/latest/run_CamoTSS.html
        
        .. _Detect alternative TSS/CTSS: https://camotss.readthedocs.io/en/latest/runBRIE.html
        
        
        
        Reference
        ===========
        
        Hou, R., Hon, C. C., & Huang, Y. (2023). CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5'scRNA-seq data. bioRxiv, 2023-04.
        
        
        
        
        
        
        
        
        
        
        
        
        
        
Keywords: Transcript Start Site,single-cell RNA-seq
Platform: UNKNOWN
Requires-Python: >=3.5
Provides-Extra: docs
