Python API

Import sincei as:

import sincei

The following modules are available for use directly in python.

• sincei.ReadCounter module

  Compute the coverage from bam files in genomic bins or regions (specified in BED or GTF files) and return a cell x feature count matrix. Can used for genome-wide coverage or for specified regions.

• sincei.ExponentialFamily module

  Implementation of many exponential family distributions to be used with the sincei.GLMPCA module. It can be easily extended to include other distributions.

• sincei.GLMPCA module

  Compute the generalized-linear model principal components (GLM-PCs) of a dataset, given an exponential distribution chosen based on prior knowledge.

• sincei.TopicModels module

  Compute LSA (Latent Semantic Analysis) or LDA (Latent Dirichlet Allocation) for an AnnData object and return the cell x topic matrix.

• sincei.multimodalClustering module

  Performs multi-graph clustering for cells with multi-modal data stored in a MuData object and return clusters and UMAP embeddings.

• sincei.RegionQuery module

  Get overlaps between the features in an AnnData and regions in a BED or GTF file.

• sincei.WriteBedGraph module

  Write a bedgraph or bigwig file from bam files. Can be used for genome-wide coverage or for specified regions.

• sincei.Utilities module

  Utility functions used across the package.