NEWS.md
In waldronlab/SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets

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

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)

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.

Added Ludwig Geistlinger as author (@lgeistlinger) for contributing the GTseq dataset.

Updated the reference in the SCoPE2 vignette (@cvanderaa).

scMultiome version 1.0.1 provides the 10X format for RNAseq data.

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 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

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)

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).

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)

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

Row names in the scNMT dataset properly show mouse ENSEMBL identifiers

waldronlab/SingleCellMultiModal documentation built on Nov. 3, 2024, 7:32 p.m.

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