InterCom - Reconstruction of functional cell-cell communication networks

Reconstructs functional cell-cell communication networks for a given single cell RNA-seq dataset.

Required software

• R v3.5 or greater
• textshape v1.6.0
• ggplot2 v 3.3.0
• stuRpkg v1.3
• dplyr v0.8.5
• doParallel v1.0.15
• stringr v1.4.0
• plyr 1.8.6
• igraph v1.2.5
• Matrix v1.2-18
• reshape2 v1.4.4
• RSpectra v0.16-0
• snow v0.4-3
• taRifx v1.0.6.2
• gtools v3.8.2
• data.table v1.12.8
• rlist v0.4.6.1

Running InterCom

The complete InterCom workflow can be invoked through a single command after loading the library.

InterCom(data,
         anno.tbl,
         species,
         sighot.cutoff=0.1,
         sighot.percentile=70,
         consv.thrs=0.05,
         ncores=4,
         sig.cutoff=0.9,
         z.score.cutoff=2,
         tissue.name,
         temp.folder.name,
         out.path
        )

InterCom parameters

The main InterCom function comes with a variety of parameters for fine-tuning the output. However, in any case, the standard parameters work well in most of the cases. Below we describe every parameter, their ranges and standard values.

• "data": Matrix or data frame of expression values; rows have to correspond to genes and columns to cells. Row names must be gene symbols while column names can be any identifier for a cell. Raw counts or normalized data is permitted.
• "anno.tbl": Data frame annotating each cell with a cluster/cell type. Cell names have to be provided in the first and cluster/cell type information in the second column.
• "species": The organism from which the data was obtained. Currently, only "MOUSE" and "HUMAN" are supported.
• "sighot.cutoff": Cutoff parameter for SigHotSpotter. Can be between 0 and 1.
• "sighot.percentile": Percentile parameter for SigHotSpotter. Can be between 0 and 100.
• "consv.thrs": Fraction of cells per cluster/cell type that must express a ligand, receptor or TF to be considered.
• "ncores": Number of cores to use. Depending on the machine, can be any integer value greater or equal to 1.
• "sig.cutoff": Significance cutoff between 0 (weakest) and 1 (strictest). Default: 0.9
• "z.score.cutoff": Cutoff parameter to determine significant associations between receptors and interface TFs. Default: 2.
• "tissue.name": A name of the dataset.
• "temp.folder.name": Name of the temporary folder to be created within the output path. Default: "temp"
• "out.path": Path to a folder where the output should be stored. Will be created if it does not exist.

InterCom output

The main output of InterCom is a list object containing the final interactome and auxiliary information