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