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GRNBoost is a library built on top of Apache Spark that implements a scalable strategy for gene regulatory network (GRN) inference. GRNBoost was inspired by GENIE3, a popular algorithm for GRN inference. GRNBoost adopts GENIE3's algorithmic blueprint and aims at improving its runtime performance and data size capability.

References:

• S.Aibar et al. SCENIC: single-cell regulatory network inference and clustering
  Nature Methods, 2017, Vol. 14, p.1083–1086; doi:10.1038/nmeth.4463
  
• Van Anh Huynh-Thu et al. Inferring Regulatory Networks from Expression Data Using Tree-Based Methods
  PLoS ONE, 5(9): e12776. doi:10.1371/journal.pone.0012776
  

• GRNBoost GitHub page

• Module Name: GRNBoost (see the modules page for more information)
• Unusual environment variables set
  • GRNBOOST_HOME   installation directory
  • GRNBOOST_BIN         executable directory
  • GRNBOOST_SRC       source code directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=8g 
[user@cn3199 ~]$ module load grnboost
[+] Loading java 1.8.0_11  ...
[+] Loading scala  2.12.2
[+] Loading Apache Spark 2.1.1  (Hadoop 2.7) ...
[+] Loading grnboost  20191216

Start the spark cluster:

[user@cn3199 ~]$ spark start -t 120 2
INFO: Submitted job for cluster fwPsex

Run a sample GRNBoost command:

[user@cn3199 ~]$ $SPARK_HOME/bin/spark-submit \
    --class org.aertslab.grnboost.GRNBoost \
    --master spark://cn3199:7077 \
    --deploy-mode client \
    --jars $GRNBOOST_SRC/lib_amazon_linux/xgboost4j-0.7.jar \
    $GRNBOOST_SRC/target/scala-2.11/GRNBoost.jar -h

GRNBoost 0.1
Usage: GRNBoost [infer] [options]

  -h | --help

  Prints this usage text.

  -v | --version

  Prints the version number.

Command: infer [options]


  -i <i;file> | --input <i;file>

  REQUIRED. Input file or directory.

  -o <file> | --output <file>

  REQUIRED. Output directory.

  -tf <file> | --regulators <file>

  REQUIRED. Text file containing the regulators (transcription factors), one regulator per line.

  -skip <nr> | --skip-headers <nr>

  The number of input file header lines to skip. Default: 0.

  --delimiter <del>

  The delimiter to use in input and output files. Default: TAB.

  -s <nr> | --sample <nr>

  Use a sample of size <nr> of the observations to infer the GRN.

  --targets <gene1,gene2,gene3...>

  List of genes for which to infer the putative regulators.

  -p:<key>=<value> | --xgb-param:<key>=<value>

  Add or overwrite an XGBoost booster parameter. Default parameters are:
  * eta ->      0.01
  * max_depth   ->      1
  * nthread     ->      1
  * silent      ->      1

  -r <nr> | --nr-boosting-rounds <nr>

  Set the number of boosting rounds. Default: heuristically determined nr of boosting rounds.

  --estimation-genes <gene1,gene2,gene3...>

  List of genes to use for estimating the nr of boosting rounds.

  --nr-estimation-genes <nr>

  Nr of randomly selected genes to use for estimating the nr of boosting rounds. Default: 20.


  --regularized

  Enable regularization (using the triangle method). Default: disabled
  When enabled, only regulations approved by the triangle method will be emitted.
  When disabled, all regulations will be emitted.
  Use the 'include-flags' option to specify whether to output the include flags in the result list.

  --normalized

 Enable normalization by dividing the gain scores of the regulations per target over the sum of gain
 scores.
 Default = disabled.

  --include-flags <true/false>

  Flag whether to output the regularization include flags in the output. Default: false.

  --truncate <nr>

  Only keep the specified number regulations with highest importance score. Default: unlimited.
  (Motivated by the 100.000 regulations limit for the DREAM challenges.)

  -par <nr> | --nr-partitions <nr>


  The number of Spark partitions used to infer the GRN. Default: nr of available processors.

  --dry-run

  Inference nor auto-config will launch if this flag is set. Use for parameters inspection.

  --cfg-run

  Auto-config will launch, inference will not if this flag is set. Use for config testing.

  --report <true/false>

  Set whether to write a report about the inference run to file. Default: true.


GRNBoost
--------
https://github.com/aertslab/GRNBoost/

Stop the spark cluster (here, the name of the cluster is the same as was assigned after the 'start spark cluster' command):

[user@cn3199 ~]$ park stop fwPsex

End the interactive session:

[user@cn3199 ~]$ exit
[user@biowulf ~]$