Metadata-Version: 2.1
Name: scvr
Version: 1.1
Summary: single cell VR preprocess
Home-page: https://github.com/pinellolab/singlecellvr
Author: Huidong Chen
Author-email: huidong.chen@mgh.harvard.edu
License: UNKNOWN
Description: # singlecellvr
        
        <img src="images/SCVR_logo.png" alt="http://www.singlecellvr.com" width="400" height="160">
        
        <img src="images/scvr.jpeg" alt="http://www.singlecellvr.com" width="400" height="40">
        
        Single cell visualization using Virtual Reality (VR)  
        
        http://www.singlecellvr.com/
        
        SingleCellVR can be used with our preprocessed datasets found at the link above or by following the steps below to process your own dataset.
        
        ## SingleCellVR Preprocess:  
        
        Prepare your data for the visualization on Single Cell VR website <https://singlecellvr.com/>
        
        Installation
        ------------
        Install and update using pip:  
        `pip install scvr`
        
        Usage
        -----
        `$ scvr --help`
        
        ```
        usage: scvr [-h] -f FILE -t {scanpy,paga,seurat,stream} -a ANNOTATIONS [-g GENES] [-o OUTPUT]
        
        scvr Parameters
        
        required arguments:
          -f FILE, --filename FILE
                                Analysis result file name (default: None)
          -t {scanpy,paga,seurat,stream}, --toolname {scanpy,paga,seurat,stream}
                                Tool used to generate the analysis result (default: None)
          -a ANNOTATIONS, --annotations ANNOTATIONS
                                Annotation file name. It contains the cell annotation key(s) 
                                to visualize in one column (default: None)
                                
        optional arguments:
        
          -g GENES, --genes GENES
                                Gene list file name. It contains the genes 
                                to visualize in one column (default: None)
          -o OUTPUT, --output OUTPUT
                                Output folder name (default: scvr_report)
          -h, --help            show this help message and exit
        ```
        
        
        Examples:
        ---------
        ### Scanpy:  
        
        To get single cell VR report for Scanpy :  
        ```bash
        scvr -f ./scanpy_result/scanpy_10xpbmc.h5ad -t scanpy -a annotations.txt -g genes.txt -o scanpy_report
        ```
        
        * Input files can be found [here](https://www.dropbox.com/sh/m6u9y38mi5qgf3o/AACe6cgiywaxM7ARtw54sg1Ha?dl=0) 
        * To generate the `scanpy_10xpbmc.h5ad`, check out [Scanpy analysis](https://nbviewer.jupyter.org/github/pinellolab/singlecellvr/blob/master/examples/scanpy_10xpbmc.ipynb?flush_cache=true). *(Make sure set `n_components=3` in `sc.tl.umap(adata,n_components=3)`)*
        
        
        ### PAGA:  
        
        To get single cell VR report for PAGA :  
        ```bash
        scvr -f ./paga_result/paga3d_paul15.h5ad -t paga -a annotations.txt -g genes.txt -o paga_report
        ```
        
        * Input files can be found [here](https://www.dropbox.com/sh/03zpxs9zv7yusi1/AADKVSU8Il1JcjA7lfHjmRpSa?dl=0) 
        * To generate the `paga3d_paul15.h5ad`, check out [PAGA analysis](https://nbviewer.jupyter.org/github/pinellolab/singlecellvr/blob/master/examples/paga_paul15.ipynb?flush_cache=true). *(Make sure set `n_components=3` in `sc.tl.umap(adata,n_components=3)`)*
        
        ### Seurat:  
        To get single cell VR report for Seurat :  
        ```bash
        scvr -f ./seurat_result/seurat3d_10xpbmc.loom -t seurat -a annotations.txt -g genes.txt -o seurat_report
        ```
        * Input files can be found [here](https://www.dropbox.com/sh/tpk4qfm5qsjpffn/AADmKmyDx7rhzKBOpIlAgMEUa?dl=0) 
        * To generate the `seurat3d_10xpbmc.loom`, check out [Seurat analysis](https://nbviewer.jupyter.org/github/pinellolab/singlecellvr/blob/master/examples/seurat_10xpbmc.ipynb?flush_cache=true). *(Make sure set `n.components = 3` in `pbmc <- RunUMAP(pbmc, dims = 1:10, n.components = 3)`)*
        
        ### Velocity:
        To get single cell velocity report for scvelo:
        ``` bash
        scvr -t velocity -f examples/pancrease_velocity.h5ad -a clusters
        ```
        
        ### STREAM:  
        To get single cell VR report for STREAM : 
        ```bash
        scvr -f ./stream_result/stream_nestorowa16.pkl -t stream -a annotations.txt -g genes.txt -o stream_report
        ```
        * Input files can be found [here](https://www.dropbox.com/sh/fg84hfdeihielun/AACRcmuAIg9RMU30ChgAZevza?dl=0) 
        * To generate the `stream_nestorowa16.pkl`, check out [STREAM analysis](https://nbviewer.jupyter.org/github/pinellolab/singlecellvr/blob/master/examples/stream_nestorowa16.ipynb?flush_cache=true).
        
        Or use STREAM package, e.g.:
        ```python
        import stream as st
        st.save_vr_report(adata,
                          ann_list=['label','kmeans','branch_id_alias','S4_pseudotime'],
                          gene_list=['Gata1','Car2','Epx','Mfsd2b','Mpo','Emb','Flt3','Dntt'],
                          file_name='stream_report')
        ```
        
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
