Metadata-Version: 2.1
Name: sciviewer
Version: 0.1
Summary: Tool for interactive exploration of 2D embeddings in Jupyter
Home-page: https://github.com/colabobio/sciviewer
Author: Andres Colubri, Dylan Kotliar
Author-email: andres@broadinstitute.org, dylan_kotliar@hms.harvard.edu
License: MIT
Description: # Single Cell Interactive Viewer
        
        This is an interactive viewer for Jupyter notebooks that allows users exploring an embedding of single-cell RNA-seq data. The user can select directions in the 2D embedding plane (e.g.: UMAP or tSNE), and the viewer will calculate the genes with the highest correlation along those directions. In addition, you can select a group of cells and find the genes that are most differentially expressed.
        
        ## Installation
        
        - Prepare conda environment containing dependencies for py5:
          ```conda env create -n sciviewer -f https://raw.githubusercontent.com/colabobio/sciviewer/master/sciviewer-env.yml```
        - Activate the environment created above:
          ```conda activate sciviewer```
        - Alternatively, if you want to append the needed dependencies to an existing conda environment, you can do the following:
           -  ```conda env update -n your_existing_environment -f https://raw.githubusercontent.com/colabobio/sciviewer/master/sciviewer-env.yml```
           -  ```conda activate your_existing_environment```
        - Install the sciviewer package:
          ```python -m pip install --index-url https://test.pypi.org/simple/ --no-deps sciviewer```
        - To uninstall:
          ```pip uninstall sciviewer```
        - To load the module from a notebook wihtout installing (good for debugging), add the following imports to the notebook:
        
        ```
         import sys
         sys.path.insert(0, '../sciviewer/')
         from sciviewer import SCIViewer
          ```
        - Note, the above won't work if you don't remove the relative imports from the local .py files.
        
        ## Jupyter notebook
        
        This Jupyter notebook demonstrates the use of [py5](http://py5.ixora.io/), a version of Processing for Python, to create an interactive viewer of RNA-seq embedding data. Find it under the notebook folder.
        
        Processing's drawing API and engine can be run from a Jupyter notebook to enable users explore their datasets and then bring the results of their exploration directly into the notebook for further analysis:
        
        ![RNA-seq embed viewer running a Jupyter notebook](extras/images/jupyter_screenshot1.jpg)
        
        The datasets can be quite large, as seen in the next image:
        
        ![RNA-seq embed viewer loading a large dataset](extras/images/jupyter_screenshot2.jpg)
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
