系列回顧:
1.RNA velocity分析練習(一)文件下載以及預處理
要獲取我們需要的loom文件,你需要先安裝以下文件:
- 首先要求你的python >=3.6.0
- 安裝依賴軟件:
$ conda install numpy scipy cython numba matplotlib scikit-learn h5py click
當然你也可以選擇用pip進行安裝:
$ pip install numpy scipy cython numba matplotlib scikit-learn h5py click
- 安裝pysam
$ pip install pysam
- 安裝velocyto(這就是我們之后生成loom文件需要的軟件)
$ pip install velocyto
- 測試是否安裝成功:
$ velocyto --help
Usage: velocyto [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
run Runs the velocity analysis outputting a loom file
run10x Runs the velocity analysis for a Chromium Sample
run_dropest Runs the velocity analysis on DropEst preprocessed data
run_smartseq2 Runs the velocity analysis on SmartSeq2 data (independent bam file per cell)
tools helper tools for velocyto