Package index • SINBA

Project space

Functions to create project working space, save and reload project.

SINBA.analysis.dir.create(): SINBA.analysis.dir.create

SINBA.loadRData(): SINBA.loadRData

SINBA.saveRData(): SINBA.saveRData

Network object

Functions to clean network output from SJARACNe

get.single.network(): get.single.network

get.combined.network(): get.combined.network

combineNet2target_list(): combineNet2target_list

SINBA object

Functions to create SINBA object.

selectSP_driver_byDB(): selectSP_driver_byDB

cal.SINBA.Activity(): cal.SINBA.Activity

generate.SINBA.eset(): generate.SINBA.eset

combine_names(): combine_names

DA analysis

Functions to compare differential activity between groups and create summary table.

get.SINBA.DE.2G(): get.SINBA.DE.2G

seed2partners_ftest(): seed2partners_ftest

l2l_ftest(): l2l_ftest

ROCTest(): ROCTest

generate.masterTable.SINBA(): generate.masterTable.SINBA

generate.AUCTable(): generate.AUCTable

Combination screening layout

Funtions to optimize Seed-Partner drivers layout

find_max_sum_submatrix(): find_max_sum_submatrix

fitness_function(): fitness_function

convert_deltaZ2_matrix(): convert_deltaZ2_matrix

Build-in Drugdatabases

Funtions to load and filter drug-gene interactions from build-in databases. Wrapper funtion to interact with DGIdb API.

drugdb.preload(): Preload drug database files into R workspace for SINBA

drugdatabase_names(): drugdatabase_names

sourceDatabases(): sourceDatabases

Drugbank_drugphase_levels(): Drugbank_drugphase_levels

Repurposing_HUB_drugphase_levels(): Repurposing_HUB_drugphase_levels

ChEMBL_drugphase_levels(): ChEMBL_drugphase_levels

geneCategories(): geneCategories

interactionTypes(): interactionTypes

queryDgidb_V5_drug(): queryDgidb_V5_drug

queryDgidb_V5_gene(): queryDgidb_V5_gene

queryDgidb_V5_drugAnnotation(): queryDgidb_V5_drugAnnotation

Visulization

Funtions to visulize SINBA results

draw.box_SINBA(): draw.box_SINBA

draw.GSEA_SINBA(): draw.GSEA_SINBA

draw.NetBID_SINBA(): draw.NetBID_SINBA

draw.ROC_SINBA(): draw.ROC_SINBA