Daniel Burkhardt

Check for single group passed for tests

1

Current behavior: ```python import scanpy as sc import numpy as np import diffxpy.api as de adata = sc.AnnData(np.random.normal(size=(100,10))) de.test.rank_sum(adata, grouping=np.tile('a', 100)) ``` raises: ``` --------------------------------------------------------------------------- IndexError Traceback (most recent call...

Fixing two_sample default noise_model

3

default noise_model in the two_sample helper function now matches the docstring and other testing methods

Unexpected / Uninformative Error messages with simple input data and two_sample 'wald' or 'lrt'

1

I came across the following errors while using Splatter simulated data. ### Error 1 - Infs and NaNs ```python import numpy as np import scanpy as sc import diffxpy.api as...

de.test.wilcoxon fails if dataset contains all-zero genes

7

Ran into this while using diffxpy checking DE between all clusters in a sample: Usage looks like: ```python for cluster in np.unique(metadata['clusters']): in_cluster = metadata['clusters'] == cluster curr_data = data.loc[in_cluster]...

Make index_unique boolean for concatenating AnnDatas

2

Hi all, I find `index_unique` being both the indicator for whether or not to concatenate batch labels to the `obs_names` and the option that denotes the delimiter to use to...

Implementing Molecular Cross Validation

2

**Is your feature request related to a problem? Please describe.** Currently, MAGIC tends to oversmooth data when using automatic `t` selection and graph fitting parameters. **Describe the solution you'd like**...

Wrong number of fastqs for 10xv1

1

I have 10X 3' v1 chemistry data with four fastq files: ``` EBT0_1A_S1_L001_I1_001.fastq.gz # 8 nt per read EBT0_1A_S1_L001_R1_001.fastq.gz # 98 nt per read EBT0_1A_S1_L001_R2_001.fastq.gz # 16 nt per read...

Generalize tl.dendrogram function to either axis

4

- [X] Closes #1549 - [X] Tests included or not required because: - Added regression test for subsetting var_names - Added test for when groupby is None - [ ]...

Feature request: highlight on double-click and bounding box outline

18

Hi, I was really excited to see this plugin. I have two questions: First, is it possible to highlight only when the whole word has been highlighted instead of highlighting...

[Question] Why doesn't cisTopicObject inherit from AnnData?

3

I'm looking through the code and documentation for the [cisTopicObject](https://pycistopic.readthedocs.io/en/latest/api.html#module-pycisTopic.cistopic_class), and it seems very similar to the concept of an AnnData object. Why not just inherit from AnnData directly and...