diffxpy
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theislab
Differential expression analysis for single-cell RNA-seq data.
Pairs with https://github.com/theislab/batchglm/pull/146 This PR aims to upgrade `batchglm`. The main outstanding question mentioned on slack is whether the 5 failing tests in `test_constrained.py` and `test_pairwise_null.py` should be deleted. It...
Hello, currently, I am using diffxpy for my differential analysis and tried using two factors for my `formula_loc = "time_point" and "sample"`. My data consist of 2 time points (juvenile...
Hey, In my Wald tests, lowest non-zero p-value I get is 2.220446049250313e-16. I'm using master branch and default dtype seems float64. I was wondering why it's not lower. Given that...
Hi! I get this error when running a very simple wald test. I saw that you solved the same problem two years ago but didn't publish how exactly. Could you...
Hi I try to use t-test on two specific group of genes stored in adata.obs.I labeled the two groups with symbol 1 and 2,and 0 for the rest of the...
when the lrt model was used to test, this error was occured. in may case, adata.X was used as the input data.
**Describe the bug** `de.test.versus_rest()` returns the wrong comparison for GLM tests (I have tested it with `test=wald`). This is due to the comparison being made on the wrong coefficient, *i.e.*...
Hi David, After using diffxpy for quite some time now, I am using it on a new machine now and I'm running into the following the error when running diffxpy's...
Hi, I'm trying to use `diffxpy` with an AnnData object that has been clustered using the Leiden algorithm. When I run the following command: `wilcox_test = de.test.wilcoxon(data = batches_bbknn, grouping...
When running the example for differential testing from diffxpy_tutorials/test/introduction_differential_testing.ipynb as it is, with 100 genes, de.test.wald raises a ValueError: assignment destination is read-only. When increasing the number of genes to...
