Differential testing

We grouped tutorials by differential expression concepts:

Introduction to differential expression testing.

Differential expression analysis with continuous covariates such time, concentratino, pseudotime or space.

How to run multiple tests per gene.

Additionally, we also provide links to tutorials that discuss specific concepts as a subset of the tutorial:

Single tests per gene

How to perform likelihood-ratio tests lrt.

How to perform wald tests for a single parameter.

How to perform Wald tests for multiple parameters.

How to perform t-tests.

How to perform wilcoxon (rank sum) tests.

Map single tests across partitions of data set

Diffxpy allows you to define a data set partition and to conduct test on each gene in each partition. This is shown`here <https://nbviewer.jupyter.org/github/theislab/diffxpy_tutorials/tree/master/diffxpy_tutorials/test/multiple_tests_per_gene.ipynb>`__.

Multiple tests per gene

How to perform pairwise tests.

How to perform group tests versus all other groups (versus rest).

Gene set enrichment: enrich

How to conduct a gene set enrichment workflow enrich.

Example work-flows on real data sets

Will be added soon.