Changelog • SingleCellMultiModal

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