NEWS
SingleCellMultiModal 1.16.0
New features
- Added citation information to the package; see
citation("SingleCellMultiModal") and the vignette.
SingleCellMultiModal 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.
SingleCellMultiModal 1.12.0
Bug fixes and minor improvements
- Added Ludwig Geistlinger as author (@lgeistlinger) for contributing the
GTseq dataset.
SingleCellMultiModal 1.8.0
Bug fixes and minor improvements
- Updated the reference in the
SCoPE2 vignette (@cvanderaa).
SingleCellMultiModal 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.
SingleCellMultiModal 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)
SingleCellMultiModal 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)
SingleCellMultiModal 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