Metadata-Version: 2.1
Name: celescope
Version: 1.3.1
Summary: GEXSCOPE Single cell analysis
Home-page: https://github.com/zhouyiqi91/CeleScope
Author: zhouyiqi
Author-email: zhouyiqi@singleronbio.com
License: UNKNOWN
Description: 
        # CeleScope
        CeleScope is a collection of bioinfomatics analysis pipelines developed at Singleron to process single cell sequencing data generated with Singleron products. These pipelines take paired-end FASTQ files as input and generate output files which can be used for downstream data analysis as well as a summary of QC criteria.
        
        Detailed docs can be found in [manual](./docs/manual.md).
        
        ## Hardware/Software Requirements
        
        - minimum 32GB RAM(to run STAR aligner)
        - conda
        - git
        
        ## Installation
        
        1. Clone repo
        ```
        git clone https://gitee.com/singleron-rd/celescope.git
        # or 
        git clone https://github.com/singleron-RD/CeleScope.git
        ```
        
        2. Install conda packages
        ```
        cd CeleScope
        conda create -n celescope
        conda activate celescope
        conda install --file conda_pkgs.txt --channel conda-forge --channel bioconda --channel r --channel imperial-college-research-computing
        ```
        
        3. Install celescope
        ```
        pip install celescope
        # Use pypi mirror to accelerate downloading if you are in china
        pip install -i https://pypi.mirrors.ustc.edu.cn/simple/ celescope
        ```
        
        
        ## Reference genome 
        
        ### Homo sapiens
        
        ```
        mkdir hs_ensembl_99
        cd hs_ensembl_99
        
        wget ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
        wget ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz
        
        gunzip Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
        gunzip Homo_sapiens.GRCh38.99.gtf.gz
        
        conda activate celescope
        celescope rna mkref \
         --genome_name Homo_sapiens_ensembl_99 \
         --fasta Homo_sapiens.GRCh38.dna.primary_assembly.fa \
         --gtf Homo_sapiens.GRCh38.99.gtf
        ```
        
        ### Mus musculus
        
        ```
        mkdir mmu_ensembl_99
        cd mmu_ensembl_99
        
        wget ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz
        wget ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz
        
        gunzip Mus_musculus.GRCm38.dna.primary_assembly.fa.gz 
        gunzip Mus_musculus.GRCm38.99.gtf.gz
        
        conda activate celescope
        celescope rna mkref \
         --genome_name Mus_musculus_ensembl_99 \
         --fasta Mus_musculus.GRCm38.dna.primary_assembly.fa \
         --gtf Mus_musculus.GRCm38.99.gtf
        ```
        
        ## [Quick start](./docs/quick_start.md)
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
