LRBase
and scTensor
scTensor 2.12.0
This vignette has been changed in BioC 3.14, when each data package (LRBase.XXX.eg.db) is deprecated and the way to provide LRBase data has changed to AnnotationHub-style.
LRBase
and scTensor
from BioC 3.14 (Nov. 2021)This section is for the users of previous LRBase.XXX.eg.db-type packages and scTensor. The specifications of the LRBase.XXX.eg.db and scTensor have changed significantly since BioC 3.14. Specifically, the distribution of all LRBase.XXX.eg.db-type packages will be abolished, and the policy has been switched to one where the data is placed on a cloud server called AnnotationHub, and users are allowed to retrieve the data only when they really need it. The following are the advantages of this AnnotationHub-style.
Due to the rapid development of single-cell RNA-Seq (scRNA-Seq) technologies, wide variety of cell types such as multiple organs of a healthy person, stem cell niche and cancer stem cell have been found. Such complex systems are composed of communication between cells (cell-cell interaction or CCI).
Many CCI studies are based on the ligand-receptor (L-R)-pair list of FANTOM5 project1 Jordan A. Ramilowski, A draft network of ligand-receptor-mediated multicellular signaling in human, Nature Communications, 2015 as the evidence of CCI (http://fantom.gsc.riken.jp/5/suppl/Ramilowski_et_al_2015/data/PairsLigRec.txt). The project proposed the L-R-candidate genes by following two basises.
The project also merged the data with previous L-R database such as IUPHAR/DLRP/HPMR and filter out the list without PMIDs. The recent L-R databases such as CellPhoneDB and SingleCellSignalR also manually curated L-R pairs, which are not listed in IUPHAR/DLRP/HPMR. In Bader Laboratory, many putative L-R databases are predicted by their standards. In our framework, we expanded such L-R databases for 134 organisms based on the ortholog relationships. For the details, check the summary of rikenbit/lrbase-workflow2 https://github.com/rikenbit/lrbase-workflow#summary, which is the Snakemake workflow to create LRBase data in each bi-annual update of Bioconductor.
LRBase
and scTensor
frameworkOur L-R databases (LRBase
) are provided a cloud server called AnnotationHub, and users are allowed to retrieve the data only when they really need it. Downloaded data is stored as a cache file on our local machines by the BiocFileCache mechanism. Then, the data is converted to LRBase object by LRBaseDbi. We also developed scTensor, which is a method to detect CCI and the CCI-related L-R pairs simultaneously. This document provides the way to use LRBaseDbi, LRBase objects, and scTensor (Figure 1).