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NEWS.md

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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

Bug fixes and minor improvements

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