Changes in version 1.16.0                        

New features

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

                       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