NEWS.md

Changes in version 1.26.0

Bug fixes and minor improvements

• Replaced local pull request workflow with reusable GitHub Actions wrapper
• Updated author, contributor, and funding metadata in DESCRIPTION and CITATION.cff
• Trimmed unnecessary software references from CITATION.cff

Changes in version 1.22.0

Bug fixes and minor improvements

• Updated vignette authorship information
• Added sticker to README.md
• Enhancements to GitHub Actions workflows

Changes in version 1.20.0

Bug fixes and minor improvements

• Minor fixes to documentation and imports in NAMESPACE.
• Use Markdown in documentation.

Changes in version 1.18.0

Bug fixes and minor improvements

• Added CITATION.cff file to the package and note in the DESCRIPTION file.

Changes in version 1.16.0

New features

• Added citation information to the package; see citation("SingleCellMultiModal") and the vignette.

Bug fixes and minor improvements

• Update imports from SingleCellExperiment, S4Vectors, and SummarizedExperiment
• Add package anchors to links in documentation
• Use markdown in documentation

Changes in version 1.14.0

New features

• The ontomap function provides a reference table of ontology IDs and cell names by data type available in the package.
• scRNAseq colData added to cord_blood and peripheral_blood datasets provided by the CITEseq function. (@drighelli)

Bug fixes and minor improvements

• When using HDF5 as format input in scMultiome, the filtering of file paths obtained from ExperimentHub has been fixed.
• Using BiocBaseUtils internally to handle assertions and checks.

Changes in version 1.12.0

Bug fixes and minor improvements

• Added Ludwig Geistlinger as author (@lgeistlinger) for contributing the GTseq dataset.

Changes in version 1.8.0

Bug fixes and minor improvements

• Updated the reference in the SCoPE2 vignette (@cvanderaa).

Changes in version 1.6.0

New features

• scMultiome version 1.0.1 provides the 10X format for RNAseq data.

Bug fixes and minor improvements

• Updates to seqFISH vignette and documentation.
• Updated to changes in SummarizedExperiment where assayDimnames are checked.
• scNMT defaults to version '1.0.0's QC filtered cells. For unfiltered cells see version section in ?scNMT.

Changes in version 1.4.0

New features

• SingleCellMultiModal function allows the combination of multiple multi-modal technologies.
• GTseq data from Macaulay et al. (2015) now available (@lgeistlinger)
• SCoPE2 data from Specht et al. now available thanks to @cvanderaa (#26)
• scMultiome provides PBMC from 10X Genomics thanks to @rargelaguet

Bug fixes and minor improvements

• Metadata information (function call and call to technology map) included in SingleCellMultiModal
• scNMT includes the original call in the MultiAssayExperiment metadata
• Improved and edited Contributing Guidelines for clarity
• seqFISH uses the spatialData argument with DataFrame input based on changes to SpatialExperiment (@drighelli)
• Removed the extra column in the sampleMap in CITEseq (@drighelli)

Changes in version 1.2.0

New features

• CITEseq function, vignette, and 'cord_blood' data available (@drighelli, #18)
• Include seqFISH function, vignette, and 'mouse_visual_cortex' data (v1 and v2 from @drighelli, #14)
• New 'mouse_gastrulation' dataset released (version "2.0.0").
• Use version argument to indicate the mouse_gastrulation data version
• The data includes all cells not only the ones that passed the QC of all three 'omics (thanks @rargelaguet, @ajabadi).

Bug fixes and minor improvements

• Caching mechanism uses tools::R_user_dir and not rappdirs.
• Improved display of available data using ExperimentHub metadata.
• Improved documentation explaining versioning differences.
• Contribution guidelines available at https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines
• Default version argument in scNMT function now set to "2.0.0" (version "1.0.0" still available)

Changes in version 1.0.0

New features

• scNMT serves the mouse gastrulation dataset from Argelaguet et al. 2019
• Data set is provided by Argelaguet and colleagues via CloudStor link: https://cloudstor.aarnet.edu.au/plus/s/Xzf5vCgAEUVgbfQ
• GitHub repository for the dataset by the authors available at: https://github.com/rargelaguet/scnmt_gastrulation

Bug fixes and minor improvements

• Row names in the scNMT dataset properly show mouse ENSEMBL identifiers