v1.1.0

CytoSPACE v1.1.0

• Python 3.9 support: Updated the conda environment for Python 3.9 compatibility and refreshed package dependencies.
• Sparse matrix input: Added capability for the R script get_cellfracs_seuratv3.R to handle sparse matrix input, for both spatial and single-cell RNAseq data, removing the need to save intermediate files to disk.
• Flexible file naming for sparse matrix input: Extended handling for various file names and extensions for Cell Ranger and Space Ranger sparse matrix outputs. Now supports .mtx or .mtx.gz for matrix files. Additionally, for auxiliary files, we've broadened compatibility to include the most common naming conventions and extensions: for the cell name file, cells or barcodes; and for the gene symbol files, features or genes, with support for both .csv and .tsv extensions, in compressed (.gz) and uncompressed formats.
• Space Ranger compatibility: Updated to accommodate the latest Space Ranger tissue positions file format.
• Unassigned spots handling: Spots with no cells assigned are now saved in a separate file, unassigned_locations.csv, for tracking of unassigned locations.
• Console output streamlining: Refined console messages for better clarity and less clutter.
• README updates: Revised documentation to reflect these changes.

For detailed information and usage instructions, please see the updated README.

v1.0.6

Updated environment to resolve glmGamPoi dependency

CytoSPACE v1.0.5

• Added support for sparse matrices as input (gene expression files)
• Minor changes in reading in Space Ranger tar.gz files as expression / coordinate data

CytoSPACE v1.0.4

• Added functionality to downsample scRNA-seq dataset to identical transcript count per cell by default
• Minor fix in plotting for better visualization
• Minor fix in cell type fraction estimation R script to prevent runtime errors when the input has only one cell type
• Added FAQ section to documentation

CytoSPACE v1.0.3 (April 27, 2023 Update)

Version with preliminary bug fixes for robustness across different operating systems, environments, and variations in input file format.
Please note that the last update for this version was made on April 27, 2023.