CytePool API reference

Return to the guides and validation.

Arrays of counts and expression values are samples x features: rows are samples, columns are features such as genes. Where an argument accepts missing values, NaN marks them in numbers and None in text. numpy masked arrays, and array-likes that convert to one, are refused with a TypeError, because numpy drops the mask when it converts one and the masked entries would be read as data; the message names the argument and says how to mark its missing values instead. The quick start shows how the pieces fit together in a differential-expression analysis.

• Pseudobulk cubes and tables
• Cube files
• AnnData and MuData
• Designs and contrasts
• Normalization and filtering
• Linear models
• Mixed models
• Precision weights for counts
• dream
• Sample quality weights
• Negative binomial models
• Quasi-likelihood F-tests
• DESeq2
• Empirical Bayes moderation
• Gene-set tests
• Rotation gene-set tests
• Multiple testing
• Differential expression
• Cell-type composition
• Meta-analysis
• Figures
• Distributions and special functions
• Smoothing and spline bases