Dongze He

`pr.read_gtf` returns error if some GTF records end with a semicolon

2

Hello, Thanks so much for providing such an excellent tool! I got a GTF file that is concatenated from two separated GTF files, one has a semicolon at the end...

introns() function in pyranges/genomicfeatures.py uses `inplace=True`

5

In the introns() function, the `inplace=True` argument used in the following line will trigger a pandas FutureWarning. https://github.com/biocore-ntnu/pyranges/blob/122e9d458fd3fa2c8e2ec225d1c4410f0a959a46/pyranges/genomicfeatures.py?plain=1#L607 > python3.7/site-packages/pandas/core/arrays/categorical.py:2631: FutureWarning: The `inplace` parameter in pandas.Categorical.add_categories is deprecated and will...

buzzer cannot run because of missing qanta/buzzer/test.py

8

I cannot run buzzer because of the missing file

Question: Does well separated color in the dendrogram mean that the items are distinct?

1

Hello, Thanks for providing this interesting cell clustering method. I am using this method to analyze the similarity between the spliced and unspliced count matrix from the same single-cell RNA-seq...

Update to the latest simpleaf

5

### Description of feature Dear scrnaseq team, Thank you very much for including simpleaf in `scrnaseq`. Recently, we made major changes to simpleaf, including adding new features and fixing bugs....

1. remove pyranges related functions to avoid this dependency 2. update readme and doc to reflect the changes

Upgrade simpleaf and alevinqc

4

Dear scrnaseq developers (and @rob-p, of course ;P ), This PR is related to #312. I did the following things: 1. Update simpleaf version from 0.10.0 to 0.17.2 2. Update...