Xiao-Ou Zhang

Not compatible with *.pyx files

3

When I edited [*.pyx files](http://docs.cython.org/src/quickstart/build.html), there was an error information like `No such highlight group name: pythonInclude`. Please help to fix it. Thanks very much!

Support zim

12

## Problem Summary Could zplug support [zim](https://github.com/Eriner/zim) plugins?

I want to run multiple cuffmerge tasks under one directory (such as ./), and each task has its unique output subdirectory (indicating using -o option, such as ./cuffmerge/). However, I...

Better python packaging and uploading to PyPI or bioconda?

3

Cool repo! Would you like to package them better and upload to PyPI or bioconda for more easy usage? Some useful references: - Packaging and uploading to PyPI: [Python Packaging...

Is it possible to use helper function via 'from pytest.helper import ...'?

6

Is it possible to use helper function via `from pytest.helper import ...`?

Incorrect trimming of chromosome name leads to IOError(f"Input .bam file should be chromosome-sorted. (Hint: use `samtools sort {bamfile}`)")

3

I ran velocyto on the rat genome. In rat genome, there are lots of chromosome names with `_`. I noticed that velocyto will trim chromosome name with `_` (https://github.com/velocyto-team/velocyto.py/blob/master/velocyto/counter.py#L275-L283), and...