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FnPCA()
- Creating PCA plots with logit(fn) estimates
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Heatmap_kdeg()
- Creating a L2FC(kdeg) matrix that can be passed to heatmap functions
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NSSHeat()
- Construct heatmap for non-steady state (NSS) analysis
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NSSHeat2()
- Construct heatmap for non-steady state (NSS) analysis with improved mechanism score
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QC_checks()
- Check data quality and make suggestions to user about what analyses to run.
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Simulate_bakRData()
- Simulating nucleotide recoding data
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TL_stan()
- Fit 'Stan' models to nucleotide recoding RNA-seq data analysis
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bakR-package bakR
- The 'bakR' package.
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bakRData()
- bakR Data object helper function for users
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bakRFit()
- Estimating kinetic parameters from nucleotide recoding RNA-seq data
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cB_small
- Example cB data frame
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cBprocess()
- Curate data in bakRData object for statistical modeling
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fast_analysis()
- Efficiently analyze nucleotide recoding data
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metadf
- Example meatdf data frame
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new_bakRData()
- bakRData object constructor for internal use
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plotMA()
- Creating L2FC(kdeg) MA plot from fit objects
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plotVolcano()
- Creating L2FC(kdeg) volcano plot from fit objects
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reliableFeatures()
- Identify features (e.g., transcripts) with high quality data
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validate_bakRData()
- bakR Data object validator
