API
Import CHESSBOARD as:
import chessboard.api as cb
Read and Write: io
Functions for reading and writing data. Users need to read input data into a CHESSBOARD io.Data
object to perform all downstream operations, data manipulation and analysis. CHESSBOARD currently accept 2 input data
types.
MAJIQ builder
.majiq
files. These files contain junction spanning read counts from MAJIQ [Vaquero-Garcia16].Equivalent data processed through another junction mapping software in the form of
.tsv
files.
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CHESSBOARD object for storing and manipulating data. |
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Process and save MAJIQ generated data. |
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Load MAJIQ generated data. |
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Load data from |
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Save the current state of a CHESSBOARD object. |
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Load saved CHESSBOARD object. |
Data Preprocessing: prefilter
Functions for prefiltering informative LSVs as described in Wang et al. 2022.
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Variance filter |
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PBS KS Filter |
Prior Estimation: priors
Functions for estimating priors.
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Posterior Summary: postsum
Functions for summarizing posterior samples.
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Generate a clustering point estimate from MCMC samples. |
Downstream Analysis: analysis
Functions for summarizing posterior samples.
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Output Excel |
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Compute likelihood on held out test data. |
Visualization: vis
Visualization tools.
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ECDF plot |
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Heatmap cluster plot |
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Heatmap cluster plot |
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Heatmap plot |
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LSV Histogram |