NEWS
signatureSearch 1.9.6 (2022-01-28)
- Addressed warning for non-ascii in cell_info2
signatureSearch 1.9.5 (2022-01-26)
- Updated lincs_pert_info2 and cell_info2
signatureSearch 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.
signatureSearch 1.9.2 (2021-12-06)
- Move
eh to .onLoad function
signatureSearch 1.7.3 (2021-08-24)
- Improved
get_targets function by supporting different output format.
signatureSearch 1.7.2 (2021-06-14)
- Supported automatic downloads of ExperimentHub cached files.
signatureSearch 1.5.8 (2021-05-18)
- Added FDA phase and other information to
lincs_pert_info from ChEMBL db.
signatureSearch 1.5.7 (2021-05-03)
- Added
donor_sex column in cell info
signatureSearch 1.5.6 (2021-04-24)
- Added
PCID column in GESS results
signatureSearch 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.
- Supported dtnetplot on Reactome pathway
signatureSearch 1.5.2 (2021-02-22)
- Supported 3 enrichment methods in TSEA on Reactome pathway
signatureSearch 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
signatureSearch 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
signatureSearch 1.0.6 (2020-04-19)
- Supported searching refdb parallelly by using multiple cores on a single machine
signatureSearch 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.
signatureSearch 1.0.4 (2020-04-02)
- Added instructions for GESS batch queries in vignette
- Added runWF function to run entire GESS/FEA workflow
signatureSearch 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
signatureSearch 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
signatureSearch 1.0.1 (2019-11-10)
- Support windows by not depending
gCMAP package
- Deal with HDF5 files with functions in
HDF5Array package
signatureSearch 1.0.0 (2019-10-23)
signatureSearch 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