angelolab / ark-analysis / 5958
94%

DEFAULT BRANCH: master
Ran
Jobs 1
Files 34
Run time 2s
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
5958

push

travis-ci-com

web-flow 
Notebook Reorganization (#648)

* change notebook names

* Update README.md

* Text changes for clustering description

* testbook fix

* Readme adjustements, waiting for Pixie preprint

* Add PIxie preprint

* added pixie to citation section

* added years to citation links

* overview fix

* bolding fix

* Add nuclear filtering functionality to pixel clustering pipeline (#653)

* Add nuclear mask filtering to som_utils

* Add nuclear filtering method to pixel clustering notebook

* Print informative message instead of error if seg_dir is None, and check for valid seg_dir if provided

* Remove extra print statement

* Update ark/phenotyping/som_utils.py

Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>

Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>

* Ensure channel norm and pixel norm files get re-computed if a new set of channels are provided (#654)

* Initial commit of normalization updates

* Remove capsys call

* Provide more robust support by resetting entire pixel_output_dir if new set of channels provided

* readme updates

* readme updates

* improved pairwise spatial enrichment analysis notebook name

* fixed mantis-link in readme

Co-authored-by: Candace Liu <candace.liu94@gmail.com>
Co-authored-by: Sricharan Reddy Varra <srivarra@stanford.edu>
Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>

2792 of 2963 relevant lines covered (94.23%)

0.94 hits per line

Jobs
ID Job ID Ran Files Coverage
1 5958.1 (MPLBACKEND=Agg) 0
94.23
 Travis Job 5958.1
Source Files on build 5958
Detailed source file information is not available for this build.