NEWS.md

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

News

v1.3.4

• Fix bug in tests when run on Windows due to uninherited namespace imports for testthat::context and testthat::expect_equal inside a bplapply call

v1.3.3

• Debugging BioC build ERROR caused by updates to CoreGx

v1.3.2

• Fix a bug in computeLimmaDiffExpr where subsetting a ToxicoSet doesn't subset the protocolData of a SummarizedExperiment, causing coercing to an ExpressionSet inside the function to fail
• For now just deleting protocolData from the metadata of the SummarizedExperiment, but will eventually need to be fixed upstream in ORCESTRA

v1.3.1

• Molecular profile data is now subset in test to keep package size down

v1.3.0

• Spring 2021 Bioconductor release!

v1.1.0

• Continue to abstract functionality into CoreGx
• Add additional plotting functions such as grouped boxplots
• Extend coverage of unit tests to >90%
• Implement a faster version of drugPertubationSignature
• Add additional plotting functions
• Include scripts for differential expression analysis and GSEA of toxico-genomic data (limma)

v1.0.0

• Package archived on CRAN
• Package submitted to Biocondcutor
• Modified package to depend on updated CoreGx
• All molecularProfiles are now SummarizedExperiment instead of ExpressionSet
• Abstracted some additional functions to CoreGx

v0.1.2

• Updated downloadTSet function to use published Zenodo DOIs to retrieve data
• Modified rankGeneDrugsPerturbation to fix a bad unit conversion which would return concentrations in the wrong unit

v0.1.1

• Bug Fix: Regenerated TGGATESsmall (sample dataset) to fix make a result in the vignette consistent with previous releases.

v0.1.0

• Rewrote plots using ggplot2 to improve aesthetics
• Also can now extend plotting functions using standard ggplot2 syntax
• Improved package documentation

v0.0.1

• Minimal package submitted

bhklab/ToxicoGx documentation built on March 18, 2023, 6:44 a.m.