A publicly available repository of curated receptors, ligands and their interactions. Subunit architecture is included for both ligands and receptors, representing heteromeric complexes accurately.

References:

• Vento-Tormo, Roser, et al. "Single-cell reconstruction of the early maternal–fetal interface in humans." Nature 563.7731 (2018): 347.
• Efremova, Mirjana, et al. "CellPhoneDB v2. 0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes." bioRxiv (2019): 680926.

• cellphonedb Main Site
• cellphonedb GitHub repo

• Module Name: cellphonedb (see the modules page for more information)
• Environment variables set
  • CELLPHONEDB_HOME
• cellphonedb uses the python package "Click" that is very opinionated about locale. If you receive locale related errors try setting your LANG and LC_ALL variables to something like en_US.utf8

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive --cpus-per-task=4 --mem=16G --gres=lscratch:10
salloc.exe: Pending job allocation 41538656
salloc.exe: job 41538656 queued and waiting for resources
salloc.exe: job 41538656 has been allocated resources
salloc.exe: Granted job allocation 41538656
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3114 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn3114 ~]$ cd /data/$USER

[user@cn3114 user]$ git clone https://github.com/ventolab/cellphonedb.git
Cloning into 'cellphonedb'...
remote: Enumerating objects: 15, done.
remote: Counting objects: 100% (15/15), done.
remote: Compressing objects: 100% (14/14), done.
remote: Total 9381 (delta 1), reused 4 (delta 1), pack-reused 9366
Receiving objects: 100% (9381/9381), 61.54 MiB | 24.54 MiB/s, done.
Resolving deltas: 100% (7066/7066), done.
Checking out files: 100% (368/368), done.

[user@cn3114 user]$ cd cellphonedb/in/example_data/

[user@cn3114 user]$ git checkout v3.1.0

[user@cn3114 example_data]$ module load cellphonedb
[-] Unloading cellphonedb  3.1.0  on cn4294
[-] Unloading singularity  4.0.1  on cn4294
[+] Loading cellphonedb  3.1.0  on cn4294
[+] Loading singularity  4.0.1  on cn4294

[user@cn3114 example_data]$ cellphonedb database download --version v3.0.0
[ ][APP][15/11/19-07:54:45][INFO] Downloading release v3.0.0 of CellPhoneDB database
[ ][APP][15/11/19-07:54:46][INFO] Download completed!
[ ][APP][15/11/19-07:54:46][INFO] Copying database to /home/$USER/.cpdb/releases/v3.0.0

[user@cn3114 example_data]$ cellphonedb method statistical_analysis test_meta.txt test_counts.txt
[ ][APP][08/11/19-18:25:15][WARNING] Latest local available version is `v2.0.0`, using it
[ ][APP][08/11/19-18:25:15][WARNING] User selected downloaded database `v2.0.0` is available, using it
[ ][CORE][08/11/19-18:25:15][INFO] Initializing SqlAlchemy CellPhoneDB Core
[...snip...]

Create a batch input file (e.g. cellphonedb.sh). For example:

#!/bin/bash
set -e
module load cellphonedb
cd /data/$USER/cellphonedb/in/example_data/
cellphonedb method statistical_analysis test_meta.txt test_counts.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] cellphonedb.sh

Create a swarmfile (e.g. cellphonedb.swarm). For example:

cellphonedb method analysis 1meta.txt 1counts.txt 
cellphonedb method analysis 2meta.txt 2counts.txt 
cellphonedb method analysis 3meta.txt 3counts.txt 
cellphonedb method analysis 4meta.txt 4counts.txt 

Submit this job using the swarm command.

swarm -f cellphonedb.swarm [-g #] [-t #] --module cellphonedb