Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Analysis of the human hematopoietic stem cell data set

ER Edroaldo Lummertz da Rocha
RR R. Grant Rowe
VL Vanessa Lundin
MM Mohan Malleshaiah
DJ Deepak Kumar Jha
CR Carlos R. Rambo
HL Hu Li
TN Trista E. North
JC James J. Collins
GD George Q. Daley
request Request a Protocol
ask Ask a question
Favorite

We followed the procedure described in https://git.embl.de/velten/STEMNET/tree/master/vignettes to reproduce the analyses reported in Velten et al.21 (accession number: GSE75478). We used 12,281 genes for trajectory analysis and GRN reconstruction. We built a kNN graph from the low-dimensional embedding identified by STEMNET and set k = 13 for subpopulation identification, to capture major subpopulations, and k = 10 for trajectory detection, as the kNN graph generated by k = 10 was already fully connected.

Copyright and License information: The Author(s) ©2018
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

0/150

tip Tips for asking effective questions

+ Description

Write a detailed description. Include all information that will help others answer your question including experimental processes, conditions, and relevant images.

post Post a Question
0 Q&A