R/octad.db.R

In Bin-Chen-Lab/octad.db: Open Cancer TherApeutic Discovery (OCTAD) database

#' Open Cancer TherApeutic Discovery (OCTAD) database package
#'
#' This is a support package for the main package ```octad``` which can be obtained [here](https://bioconductor.org/packages/octad)
#' 
#'Package includes all required data for drug repurposing OCTAD pipeline. 
#'Initialization of the pipeline starts with listing all available samples:
#'
#'```phenoDF=.eh[["EH7274"]]``` #load data.frame with samples included in the OCTAD database. 
#'```head(phenoDF)``` #list all data included within the package
#'
#'Besides, the package includes examples of the output from diffExp and runsRGES functions from the octad package along with desctiption of the data:
#'```res=octad.db::res_example``` #load example res from octad.db
#'```?res_example```
#'```sRGES=octad.db::sRGES_example``` #load example sRGES from octad.db
#'```?sRGES_example```
#'
#'```CCLE.log2.read.count.matrix``` log2-transformed matrix containing expression of 56,318 genes in 1,019 cell lines provided in CCLE database 
#'```CCLE.overlaps```  log2-transformed matrix containing expression of 56,318 genes in 51 cell lines present in both LINCS and CCLE databases
#'```CCLE.sample.meta``` data.frame containing cell lines name and tissue of origin from CCLE database
#'```CTRPv2.sensprof``` Cancer Therapeutics Response Portal (CTRP) data.frame containing AUC and IC50 for every drug-cell line pair
#'```EncoderDF``` a data.frame (64 features by 19127 samples) computed from autoEncoder for every sample in the OCTAD database
#'```cmpd_sets_ChemCluster``` list of compounds and their clusters based on chemical structures
#'```cmpd_sets_mesh``` list of compounds and their associations with 662 pharmacological MeSH Terms provided in PubChem
#'```fda_drugs``` data.frame of FDA approved drugs containing name, target and clinical phase
#'```lincs_sig_info``` data.frame for LINCS signatures including experiment id, cell line used in the experiment, purturbagen name, purturbagen type, dose and time
#'```lincs_signatures``` Differential expression of 978 genes in 416,560 experiments
#'```merged_gene_info``` data.frame with the annotation of 75,078 genes which could be used for identifier mapping
#'```octad.LINCS.counts``` expression matrix of 965 genes and 19127 samples in OCTAD database (965 genes were profiled in LINCS)
#'```phenoDF``` data.frame with samples from the OCTAD database including tissue of origin, sample type (tumor-derived or healthy-derived), cancer, orginal source (e.g. TCGA), mutation and stage data if available
#'```random_gsea_score``` precomputed permutated gsea scores for chembl, mesh and ChemCluster databases that are used for drug enrichment analysis
#'```tsne``` 2 dimension tSNE for every sample in the OCTAD database along with sample.id, cancer type and source of the initial data
#'```octad.counts.and.tpm.h5``` expression (TPM and raw counts) matrix of 60,498 genes and 19,127 samples
#'
#' The code can be viewed at the GitHub repository,
#' which also lists the contributor code of conduct:
#'
#' \url{https://bioconductor.org/packages/octad} or \url{https://github.com/Bin-Chen-Lab/octad} for the pipeline package
#' 
#' 
#' @references
#' Zeng, B., Glicksberg, B.S., Newbury, P., Chekalin, E., Xing, J., Liu, K., Wen, A., Chow, C. and Chen, B., 2021. OCTAD: an open workspace for virtually screening therapeutics targeting precise cancer patient groups using gene expression features. Nature protocols, 16(2), pp.728-753.
#' [https://www.nature.com/articles/s41596-020-00430-z](https://www.nature.com/articles/s41596-020-00430-z)
#' @docType package
#' @name octad.db
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