orthos

orthos decomposes RNA-seq contrasts into unspecific and experiment-specific components using conditional variational auto-encoders.

Key Features:

• Contrast Decomposition: Decomposes RNA-seq contrasts from experiments such as gene knock-out or compound treatment into unspecific and experiment-specific components.
• Database Querying: Enables efficient querying of original and decomposed contrasts against a large database of contrasts derived from ARCHS4 to identify similar experiments.
• Visualization: Provides plotting functions to visualize the results of searches for similar contrasts.

Scientific Applications:

• Functional Interpretation of RNA-seq Experiments: Identifies similar experiments by comparing decomposed contrast components, aiding interpretation of gene knock-out and compound treatment studies.

Methodology:

Conditional variational auto-encoders are used for variance decomposition of RNA-seq contrasts.