NEWS.md
In signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Created cellNtestPlot function to visualize number of compounds tested in cell types along with primary site information
Added get_treat_info function to get the treatment information in reference database including pert, cell, pert_type columns.
Supported setReadable function and readable argument in TSEA functions to convert Entrez id to gene Symbols in the itemID column in the enrichment result table.

Supported dtnetplot on Reactome pathway

Supported 3 enrichment methods in TSEA on Reactome pathway

Supported defining gene set database from score matrix by setting higher, lower, as well as padj cutoffs for gCMAP and Fisher GESS methods

Supported converting gmt file to HDF5 file (01 matrix) as gene set reference database for gCMAP and Fisher GESS methods

Supported searching refdb parallelly by using multiple cores on a single machine

Fix bug: fixed null issue and throw warning messages when up or down gene sets share zero identifiers with refdb for gess_lincs method.

Added instructions for GESS batch queries in vignette
Added runWF function to run entire GESS/FEA workflow

Supported converting feaResult object to enrichResult object in the clusterProfiler package so that the plotting functionalities in the latter package such as dotplots and gene-concept networks could be applied to the FEA enrichment results
Supported searching against subset of refdb (subsetted specific columns (treatments) in the refdb (e.g. lincs)) for GESS methods
Updated comp_fea_res function to reduce number of characters in description
Added functions to draw different types of query GESs from refdb
Added deprof2subexpr function to get a subset of gene expression values from a differential expression profile

Fix bug: the enrichment results from DSEA methods and some of TSEA methods were added an aditional 'ont' column where the GO itmes were subsetted to the selected ontology

Support windows by not depending gCMAP package
Deal with HDF5 files with functions in HDF5Array package

Initial version

Submitted to Bioconductor
Major changes
used HDF5 file to read and write the matrix in batches
data stored in ExperimentHub

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signatureSearch documentation built on April 16, 2021, 6 p.m.

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