signatureSearch-package | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis |
addGESSannot | Add Compound Annotation Info to GESS Result Table |
addMOA | Add MOA annotation to drug data frame |
add_pcid | Add PCID to drug data frame |
append2H5 | Append Matrix to HDF5 File |
build_custom_db | build_custom_db |
calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in 'selectedStats' list. |
cellNtestPlot | Number of Tests in Cell Types |
cell_info | LINCS 2017 Cell Type Information |
cell_info2 | LINCS 2020 Cell Type Information |
chembl_moa_list | MOA to Gene Mappings |
clue_moa_list | MOA to Drug Name Mappings |
comp_fea_res | Plot for Comparing Ranking Results of FEA Methods |
create_empty_h5 | Create Empty HDF5 File |
dim | Dimensions of an Object |
dim-method | Dimensions of an Object |
drugs | Extract/Assign Drug Names for feaResult |
drugs-method | Extract/Assign Drug Names for feaResult |
drugs10 | Drug Names Used in Examples |
drugs<- | Extract/Assign Drug Names for feaResult |
drugs<--method | Extract/Assign Drug Names for feaResult |
drug_cell_ranks | Summary ranking statistics across cell types |
dsea_GSEA | FEA Methods |
dsea_hyperG | FEA Methods |
dtnetplot | Drug-Target Network Visualization |
enrichGO2 | GO Term Enrichment with Hypergeometric Test |
enrichKEGG2 | KEGG Pathway Enrichment with Hypergeometric Test |
enrichMOA | MOA Category Enrichment with Hypergeometric Test |
enrichReactome | Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test. |
feaResult | Constructor for 'feaResult-class' |
feaResult-class | feaResult object |
GCT object | An S4 Class to Represent a GCT Object |
gctx2h5 | Convert GCTX to HDF5 File |
gessResult | Constructor for 'gessResult-class' |
gessResult-class | gessResult object |
gess_cmap | GESS Methods |
gess_cor | GESS Methods |
gess_fisher | GESS Methods |
gess_gcmap | GESS Methods |
gess_lincs | GESS Methods |
gess_res_vis | GESS Result Visualization |
getALLEG | getALLEG |
getDb | getDb |
getDEGSig | Draw GESs from Reference Database |
getSig | Draw GESs from Reference Database |
getSPsubSig | Draw GESs from Reference Database |
getTreats | Get Treatment Information |
get_targets | Target Gene/Protein IDs for Query Drugs |
gmt2h5 | Convert GMT to HDF5 File |
gseGO2 | Modified GSEA with GO Terms |
gseKEGG2 | Modified GSEA with KEGG |
gseReactome | Modified GSEA with Reactome |
head | Return the First Part of an Object |
head-method | Return the First Part of an Object |
lincs_expr_inst_info | Instance Information of LINCS Expression Database |
lincs_pert_info | LINCS 2017 Perturbation Information |
lincs_pert_info2 | LINCS 2020 Perturbation Information |
lincs_sig_info | LINCS Signature Information |
list2df | Named list to data frame |
list_rev | Reverse list |
mabsGO | MeanAbs Enrichment Analysis for GO |
mabsKEGG | MeanAbs Enrichment Analysis for KEGG |
mabsReactome | MeanAbs Enrichment Analysis for Reactome |
matrix2h5 | Write Matrix to HDF5 file |
meanExpr2h5 | Calculate Mean Expression Values of LINCS Level 3 Data |
moa_conn | Summarize GESS Results on MOA Level |
parse_gctx | Parse GCTX |
qSig | Helper Function to Construct a 'qSig' Object |
qSig-class | Class "qSig" |
rand_query_ES | Generate WTCS Null Distribution with Random Queries |
read_gmt | Read in gene set information from .gmt files |
result | Method to Extract Result Slots |
result-method | Method to Extract Result Slots |
runWF | Run the Entire GESS/FEA Workflow |
set_readable | Set Readable |
show | show method |
show-method | show method |
signatureSearch | Environment for Gene Expression Signature Searching Combined with Functional Enrichment Analysis |
sim_score_grp | Summary Scores by Groups of Cell Types |
tail | Return the Last Part of an Object |
tail-method | Return the Last Part of an Object |
targetList | Target Sample Data Set |
tarReduce | Show Reduced Targets |
tsea_dup_hyperG | FEA Methods |
tsea_mabs | FEA Methods |
tsea_mGSEA | FEA Methods |
vec_char_redu | Reduce Number of Character |