Metadata-Version: 2.1
Name: BinToGene
Version: 1.21
Summary: A bin to gene conversion package.
Home-page: https://github.com/ferrocactus/BinToGene
Author: Euxhen Hasanaj
Author-email: ehasanaj@cs.cmu.edu
License: UNKNOWN
Description: <h2>BinToGene</h2>
        Library to convert a cell-by-bin matrix to cell-by-gene.
        This can be useful, for e.g., when one wishes to use existing gene expression
        tools to a sc-ATAC-seq cell-by-bin matrix.</br></br>
        
        The package uses a gencode file (v34) to determine start and end locations
        for protein coding genes. This interval is then extended by fixed or gene-length
        dependent values to get a new interval I=(start-v1, end+v2). Then the bins in
        the provided data matrix are searched to see if they intersect I. An efficient
        binary search implementation is used to determine the first and last bin for
        which such intersection is found. Then the values of the bins are added or
        averaged as specified by the user. The resulting vector is a count vector for
        the gene in consideration. Note, the counts here do not represent expression
        of the gene, but chromatin accessibility counts in the case of sc-ATAC-seq.
        In the end, these vectors are stacked to form a cell-by-gene matrix.
        Tools that are used for analyzing gene expression data can be useful in
        analyzing the cell-by-gene matrix formed this way.
        
        Example
        
        ```python
        import numpy as np
        
        x = np.random.randint(0, 2, (200, 4000)) # your cell by bin matrix
        
        bin_names = ['chr1:0-1000', 'chr1:1001-2000', ...] # your list of bin names
        
        btg = BinToGene()  # Use default interval extension parameters
        counts, ids = btg.convert(x, bin_names, prefix='chr', delim1=':', delim2='-')
        ```
        
        Example of a cell-by-gene matrix obtained via UMAP after running some basic preprocessing
        <img src="https://github.com/ferrocactus/BinToGene/blob/master/src/images/example.png" style="zoom:82%;" />
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
