pySCENIC

pySCENIC copied to clipboard

cisTarget problem on the FeatherRankingDatabase command

5

Hi I just start learning how to work with pyscenic. As a newbie, I was trying to run the tutorial for pyscenic for mice (https://pyscenic.readthedocs.io/en/latest/tutorial.html). However, I received an error...

farhad-zare

Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 6.0.7 to 6.3.0. Commits cefe0bf Release 6.3.0 a534fb9 Release 6.3.0b0 87920c5 Add changelog for 6.3.0 (#1669) dd6d9c7 add slide numbering (#1654) 5d2c5e2 Update state filter (#1664) 11ea593...

dependabot[bot]

Errors with running pySCENIC in conda environment or through docker/singularity images

4

I am having issues running pySCENIC. I have attempted to set up a conda environment to use it, as well as using the Docker and Singularity images. I am still...

fouerghi

Bumps [mistune](https://github.com/lepture/mistune) from 0.8.4 to 2.0.3. Release notes Sourced from mistune's releases. Version 2.0.2 Fix escape_url via lepture/mistune#295 Version 2.0.1 Fix XSS for image link syntax. Version 2.0.0 First release...

dependabot[bot]

Fail to download resources

2

Hi all, I fail to download TF files resources and find I can't open https://resources.aertslab.org/. I'd like to know if there are other ways to download these important feather files?...

FionaMoon

[BUG] an error in pySCENIC grnboost2 in Jupyder

1

2022-07-01 09:52:42,226 - distributed.worker - WARNING - Heartbeat to scheduler failed Traceback (most recent call last): File "/ifs/home/yanteng/.conda/envs/ryt/lib/python3.10/site-packages/distributed/comm/tcp.py", line 229, in read frames_nbytes = await stream.read_bytes(fmt_size) tornado.iostream.StreamClosedError: Stream is closed...

socialtree-yt

OSError: Unable to open file (message not aligned)

1

Hello, when I was running the GRN process in SCENIC, I got the following error: "OSError: Unable to open file (message not aligned)". There are many similar errors in the...

Li-mengjie

grnboost2 limit

3

Hi, grnboost2 use all the cores of our server by default, how to limit it ?

wangjiawen2013

Dependencies and versions critical for successful running of pyscenic

2

Can anyone summarize what are the dependencies and versions critical for successful running of pyscenic. I have tried most of the methods described in the issues section by double checking...

bio-visualisation

GRN step

4

Hello, Thank you for the amazing tool. I am running the GRN step on a huge dataset. It has displayed the below output for a while. Is this normal or...

Sayyam-Shah