Dataset Open Access

Development, evaluation and application of NicheNet: datasets

Browaeys, Robin; Saelens, Wouter; Saeys, Yvan

Here you can find the datasets used for development, validation and application of NicheNet, a method that links ligands to target genes to model intercellular communictation. The software to use NicheNet (i.e. R package nichenetr) is available at:

https://github.com/saeyslab/nichenetr

Short description of individual files:

* data for development of NicheNet: 

- lr_network.rds: network containing ligand-receptor interactions

- signaling_network.rds: network containing signaling interactions

- gr_network.rds: network containing gene regulatory interactions

- weighted networks.rds: integrated weighted ligand-signaling and gene regulatory network

* data for use of NicheNet:

- ligand_tf_matrix.rds: matrix containing ligand-gene signaling scores

- tf_target_matrix.rds: matrix containing gene-gene regulatory scores

- ligand_target_matrix.rds: matrix containing ligand-target gene regulatory potential scores

* datasets for validation of NicheNet:

- expression_settings.rds: 111 expression datasets profiling the transcriptional response to a ligand

* datasets to demonstrate application possibilities of NicheNet:

- pemt_signature.txt: p-EMT geneset for which upstream regulators will be predicted

- hnscc_expression.rds: single-cell expression data of malignant and non-malignant cells from head and neck squamous cell carcinoma tumors

Files (382.6 MB)
Name Size
expression_settings.rds
md5:f96b847c211ec358ec8a44d96a89b29f
37.4 MB Download
gr_network.rds
md5:abafea29ebf4fabfa0b92ac5410c1d3f
13.2 MB Download
hnscc_expression.rds
md5:fe038ec221b610f4aa4e48898371f785
140.1 MB Download
ligand_target_matrix.rds
md5:f62e1efc681eb85176467eda05502aa0
123.2 MB Download
ligand_tf_matrix.rds
md5:a8803ab0a1a42b74ba3b4ec3794af27b
5.7 MB Download
lr_network.rds
md5:055e0707d0ec059ebfa9d985a1d316ce
26.2 kB Download
pemt_signature.txt
md5:1d84fbd1eb85ea0d62955229d8d52caf
717 Bytes Download
signaling_network.rds
md5:f8647102bfc63cf447e48a64a0c19219
11.3 MB Download
tf_target_matrix.rds
md5:99a1436eb0959c456adc65e731785544
16.3 MB Download
weighted_networks.rds
md5:fca16232fe6cb3629fb966b9df0b6aa0
35.3 MB Download
1,360
15,852
views
downloads
All versions This version
Views 1,360817
Downloads 15,85214,495
Data volume 814.7 GB758.4 GB
Unique views 1,186743
Unique downloads 3,7473,490

Share

Cite as