NEWS

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MatrixQCvis 1.13.5 (2024-06-27)

• add log10 as transformation method in transformAssay
• add "none" as imputation method in imputeAssay
• update shiny application with log10
• update vignette with log10
• update unit tests with log10 and "none"

MatrixQCvis 1.13.4 (2024-06-24)

• update vignette, add information on ComBat

MatrixQCvis 1.13.3 (2024-06-21)

• add functionality to perform batch correction using sva::ComBat
• improve visualisation of MAplot in shinyQC

MatrixQCvis 1.13.2 (2024-06-11)

• use DT::renderDT instead of shiny::renderDataTable
• use DT::DTOutput instead of shiny::dataTableOutput

MatrixQCvis 1.13.1 (2024-04-25)

• add batch2 and ... arguments in batchCorrectionAssay

MatrixQCvis 1.11.7 (2024-04-25)

• add dplyr:: in front of pull function in vignette to avoid errors

MatrixQCvis 1.11.6 (2024-04-23)

• add parameter ... to function updateSE that will be passed to SummarizedExperiment::assay within updateSE

MatrixQCvis 1.11.5 (2024-04-12)

• set parameter multiplyByNormalizationValue in normalizeAssay To TRUE in shinyQC

MatrixQCvis 1.11.4 (2024-04-02)

• add option to display size in dimensionReductionPlot

MatrixQCvis 1.11.3 (2024-03-20)

• allow quantile normalisation (method = "quantile") for assays with columns that contain only NA values

MatrixQCvis 1.11.2 (2024-03-18)

• fix warning in normalizeAssay

MatrixQCvis 1.11.1 (2024-03-15)

• add parameter multiplyByNormalizationValue in normalizeAssay

MatrixQCvis 1.9.1 (2023-07-19)

• fix bug in scree plot (subset the dimensionReduction object)

MatrixQCvis 1.7.7 (2023-04-20)

• add package statmod to Suggests

MatrixQCvis 1.7.6 (2023-04-19)

• add package jpeg to Suggests

MatrixQCvis 1.7.5 (2023-04-18)

• adjust test ERROR messages

MatrixQCvis 1.7.4 (2023-01-26)

• add ExperimentHub and GEOquery to NAMESPACE

MatrixQCvis 1.7.3 (2023-01-23)

• use TCGA RNA-seq and cell line proteomics datasets from ExperimentHub in vignette to showcase the functionality of the package

MatrixQCvis 1.7.2 (2022-11-24)

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

MatrixQCvis 1.7.1 (2022-11-08)

• adjust errors in unit tests after updating the packages

MatrixQCvis 1.5.9 (2022-10-19)

• add ShinyApps to biocViews

MatrixQCvis 1.5.8 (2022-09-30)

• replace vegan::metaMDS by MASS::isoMDS for NMDS dimension reduction

MatrixQCvis 1.5.7 (2022-09-29)

• change renderUI functions to update...Input whenever possible
• remove the dual interface for measured/missing values help pages in the values tab
• improve the formula/expression checks in the DE tab using the model.matrix and makeContrasts functions

MatrixQCvis 1.5.6 (2022-09-23)

• speed up non-server functions

MatrixQCvis 1.5.5 (2022-08-23)

• add unit tests for imputation of missing values
• bug fix (ncol instead of nrow) for calculation of BPCA imputation

MatrixQCvis 1.5.4 (2022-08-18)

• improve the imputation of missing values

MatrixQCvis 1.5.3 (2022-08-01)

• only use a subset of maximum 5000 features in the calculation of Hoeffding's D values. In case there are less than 10000 features in the SummarizedExperiment object, all features of the SummarizedExperiment are taken
• createBoxplot precalculates the values of the boxplot instead on relying on geom_boxplot for calculation of the statistics

MatrixQCvis 1.5.2 (2022-07-20)

• remove the functions biocrates, maxQuant, and spectronaut from MatrixQCvis and move to the MatrixQCUtils package

MatrixQCvis 1.5.1 (2022-07-18)

• load package MatrixQCvis in report_qc.Rmd

MatrixQCvis 1.3.8 (2022-04-12)

• change unit tests after changing namespace in 1.3.7

MatrixQCvis 1.3.7 (2022-04-12)

• change namespace in module_measuredValues_missingValues.R

MatrixQCvis 1.3.6 (2022-04-08)

• set internally parameters (probs, batchColumn) in normalizeAssay and batchCorrectionAssay to default values when the parameters are NULL

MatrixQCvis 1.3.5 (2022-04-04)

• fix error message in cvFeaturePlot after updating packages

MatrixQCvis 1.3.4 (2022-02-10)

• fix bug in hoeffDValues for pivot_wider after updating tidyr (version 1.2.0)

MatrixQCvis 1.3.3 (2022-01-25)

• harmonize clustering method in distShiny for columns/rows

MatrixQCvis 1.3.2 (2021-12-09)

• add import of txt and xlsx files for function maxQuant
• change rounding in mosaic that the plot shows more detailed numbers

MatrixQCvis 1.3.1 (2021-12-01)

• use make.names for character vectors and colnames(colData(se)) in the functions for dimension reduction plot, drift plot, ECDF plot, mosaic plot, features along variable histogram, UpSet plot
• add method "log" in function transformationAssay
• add function spectronaut to upload spectronaut files

MatrixQCvis 1.1.3 (2021-09-30)

• shift batch correction in between of normalization and transformation
• add column "x5at1t1g161asy" instead of "rowname" (default) for rownames_to_column
• remove the stop button and return the modified SummarizedExperiment object when stopping the shiny application, the SummarizedExperiment will be returned only when the function call is assigned to an object

MatrixQCvis 1.1.2 (2021-09-06)

• take sample IDs for shinyQC from colnames(se)
• take feature IDs for shinyQC from rownames(se)
• fix error in report.Rmd (change input for create_boxplot to se)

MatrixQCvis 1.1.1 (2021-08-27)

• fix bug in biocrates and maxQuant function

MatrixQCvis 0.99.12 (2021-05-18)

• replace xlsx by openxlsx

MatrixQCvis 0.99.11 (2021-05-10)

• rename function normalize to normalizeAssay
• rename function transform to transformAssay
• rename function batch to batchCorrectionAssay
• rename function impute to imputeAssay

MatrixQCvis 0.99.10 (2021-05-06)

• bump version to trigger building

MatrixQCvis 0.99.9 (2021-04-29)

• add hexbin in Suggests
• fix bug in MAplot that plot is displayed properly

MatrixQCvis 0.99.8 (2021-04-28)

• set required version for S4Vectors to >= 0.29.15

MatrixQCvis 0.99.7 (2021-04-28)

• add version number of dependencies in Description file

MatrixQCvis 0.99.6 (2021-04-27)

• add MatrixQCvis to Watched Tags on the Bioconductor support site

MatrixQCvis 0.99.5 (2021-04-27)

• reduce file size of vignette by using partial_bundle for driftPlot

MatrixQCvis 0.99.4 (2021-04-26)

• reduce package dependencies - remove magick - use stats::cmdscale instead of ape::pcoa - remove MsCoreUtils - remove preprocessCore - remove Matrix
• add explained variance for PCoA
• add se argument in create_boxplot that allows for ordering the samples
• use ggplotly for driftPlot
• allow flexible addition of samples in MA-plot based on a supplied character vector of sample names
• return SummarizedExperiment when exiting the shiny application
• add function maxQuant that allows for creation of SummarizedExperiment objects from maxQuant output (.xlsx files)

MatrixQCvis 0.99.3 (2021-03-18)

• reduce file size of vignette by using partial_bundle for plotly figures

MatrixQCvis 0.99.2 (2021-03-18)

• reduce resolution of images in vignette to reduce file size

MatrixQCvis 0.99.1 (2021-03-17)

• reduce file size of vignette

MatrixQCvis 0.99.0 (2021-03-12)

• shinyQC including visualizations/functionality for - histogram of sample types, - information on number of missing/measured values - information on (intersecting, disjoint) sets for missing/measured values - barplot and violin plot for (count/intensity) values - visualization to detect drifts/trends in (count/intensity) values - coefficients of variation for samples, - mean-sd plots, - MA plots, - empirical cumulative distribution function, - visualizations of distances between samples, - intensities of features and coefficients of variation of features, - dimension reduction plots (PCA, PCoA, NMDS, tSNE, UMAP) - differential expression
• write functions for data manipulation and plots
• write tests for these functions
• create UI and server modules for shinyQC
• write tests for UI and server modules
• load different UI elements depending on the type of data (if the data contains missing values or is complete)
• load different UI if the SummarizedExperiment is loaded on start of shinyQC or not