v1.2.5

Main updates in current version 1.2.5
CopyKat outputs two additional intermediates before the final automatic prediction steps. This is particularly useful when normal cell names are provided.

copykat_raw_results_gene_by_cell.txt, in which cells are referred to normal cells, smoothed with DLM method, and segmented with MCMC.
copykat_raw_results_bin_by_cell.txt, in which cells are referred to normal cells, smoothed with DLM method, segmented with MCMC, and converted to genomic bins.
Both files are suitable for downstream analysis.

Minor feature of v1.2.5
Prior cell typing or clustering results can be added through the cell.group tab. It requires a vector of cell types or clusters, named with cell barcodes. As such, they will appear in the side bars of heatmap.

A conservative EMD is added to partially mitigate false positive prediction of aneuploid, though it sometimes appears as a trade-off at this stage. It's still under testing.

Full Changelog: v1.2.0...v1.2.5

V1.1.0

Changes in V1.1.0:

Put back 'not.defined' cells in final prediction table.

Introduced methods for calculating copy numbers from mouse scRNAseq data (to run mouse module, set genome="mm10" in the main function). This version outputs single cell copy number results in gene by cell dimension. Gene names are plotted in the bottom of heatmap. Zooming into the heatmap to read gene names.

Two coordinate errors related to new hg20 contigs were fixed.

Added heatmap of single cell copy number results with gene by cell matrix; genenames are plotted in the heatmap in the PDF files. Zooming into the bottom of the heatmap to find gene names in each segment. Due to the large file size, it could be slow. Default is: plot.genes="TRUE". Users can change it to plot.genes="FALSE" if gene names are not wanted.

Added the filtered cells back to the prediction results

Output the *.seg file, which can be loaded to IGV viewer to visualize the results directly. default: output.seg="FALSE". Users can change to:output.seg="TRUE".

Full Changelog: https://github.com/navinlabcode/copykat/commits/v1.1.0