Release.txt

RISC v1.6.0 release (03.22.2022)

Changes from the last release (v1.5)
This version mainly solves the problems that is caused by dependent package updates

Changes from the last release (v1)
(1) Replace dependent "RcppEigen" with "RcppArmadillo", fully support sparse matrix in core functions.
(2) Replace dependent "pbmcapply" with "pbapply"
(3) Optimize "scMultiIntegrate" function and reduce memory-consuming; the new RISC release can support integration of datasets with >1.5 million cells and 10,000 genes.
(4) Convert "logcounts" in the integrated RISC object "object@assay$logcount" from a large matrix to a list including multiple logcounts matrices, each corrected matrix for the corresponding individual data sets. To output full integrated matrix, mat0 = do.call(cbind, object@assay$logcount)
(5) Change function name "readscdata" -> "readsc"
(6) Change function name "read10Xgenomics" -> "read10X_mtx"
(7) Parameter names in some functions are changed.

Added new functions
(1) In "scMarker" and "AllMarker" functions, add Wilcoxon Rank Sum and Signed Rank model.
(2) In "scMarker", "AllMarker" and "scDEG" functions, add pseudo-cell (bin cells to generate meta-cells) option to detect marker genes.
(3) Add "slot" parameter in "DimPlot" function, external dimension reduction results can be added in RISC object, e.g. add phate results (phate0) to RISC object obj0@DimReduction$cell.phate = phate0; DimPlot(obj0, slot = "cell.phate", colFactor = 'Group', size = 2, label = TRUE)
(4) Add "read10X_h5" function for 10X Genomics h5 file.

Removed old functions
(1) delete "readHTSeqdata" function.