API#
Import infercnvpy together with scanpy as
import scanpy as sc
import infercnvpy as cnv
For consistency, the infercnvpy API tries to follow the scanpy API as closely as possible.
Input/Output: io
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Get genomic gene positions from a GTF file. |
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Load results from SCEVAN [FCS+21] for downstream analysis with infercnvpy. |
Preprocessing: pp
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Compute the neighborhood graph based on the result from |
Tools: tl
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Tools add an interpretable annotation to the AnnData
object
which usually can be visualized by a corresponding plotting function.
The tools for embeddings and clustering mirror the scanpy API. However, while the scanpy tools operate on transcriptomics data, the infercnvpy equivalent operates on CNV data.
InferCNV#
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Infer Copy Number Variation (CNV) by averaging gene expression over genomic regions. |
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Inference of genomic copy number and subclonal structure. |
CNV scores#
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Assign each cnv cluster a CNV score. |
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Compute the ITHCNA diversity score based on copy number variation [WFH+21]. |
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Compute the ITHGEX diversity score based on gene expression cite: |
Embeddings#
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Compute the PCA on the result of |
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Compute the UMAP on the result of |
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Compute the t-SNE on the result of |
Clustering#
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Perform leiden clustering on the CNV neighborhood graph. |
Plotting: pl
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InferCNV#
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Plot a heatmap of smoothed gene expression by chromosome. |
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Plot a heatmap of average of the smoothed gene expression by chromosome per category in groupby. |
Embeddings#
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Plot the CNV UMAP. |
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Plot the CNV t-SNE. |
Datasets: datasets
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Return the dataset from [MMR+20] as AnnData object, downsampled to 3000 cells. |
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The original inferCNV example dataset. |