NEWS.md

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Changes in version 1.9.6 (2022-01-28)

• Addressed warning for non-ascii in cell_info2

Changes in version 1.9.5 (2022-01-26)

• Updated lincs_pert_info2 and cell_info2

Changes in version 1.9.3 (2021-12-17)

• Supported searching against the newest LINCS 2020 beta database in devel version
• Modified gess_* functions to support adding customized compound annotation table to the GESS result table.

Changes in version 1.9.2 (2021-12-06)

• Move eh to .onLoad function

Changes in version 1.7.3 (2021-08-24)

• Improved get_targets function by supporting different output format.

Changes in version 1.7.2 (2021-06-14)

• Supported automatic downloads of ExperimentHub cached files.

Changes in version 1.5.8 (2021-05-18)

• Added FDA phase and other information to lincs_pert_info from ChEMBL db.

Changes in version 1.5.7 (2021-05-03)

• Added donor_sex column in cell info

Changes in version 1.5.6 (2021-04-24)

• Added PCID column in GESS results

Changes in version 1.5.3 (2021-04-12)

• 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.

Changes in version 1.5.3 (2021-03-18)

• Supported dtnetplot on Reactome pathway

Changes in version 1.5.2 (2021-02-22)

• Supported 3 enrichment methods in TSEA on Reactome pathway

Changes in version 1.2.4 (2020-08-14)

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

Changes in version 1.2.2 (2020-07-11)

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

Changes in version 1.0.6 (2020-04-19)

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

Changes in version 1.0.5 (2020-04-10)

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

Changes in version 1.0.4 (2020-04-02)

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

Changes in version 1.0.3 (2020-02-07)

• 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

Changes in version 1.0.2 (2020-01-21)

• 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

Changes in version 1.0.1 (2019-11-10)

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

Changes in version 1.0.0 (2019-10-23)

• Initial version

Changes in version 0.99.20 (2019-10-22)

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

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.