- Add version info
- filtering add mito&ribo filter
- config file content to R object
- function add return code
- fisher test ignore 0 cell clusters
- retain seurat_clusters when use removed_clusters
- External annotation, replace highest score with mean(x)*log(length(x)+1)
- install packages script add R-glue and py-grip(genereate markdown)
- viz cluster, fix bug when viz removed or merged clusters
- viz cluster, no display of 0 cell clusters
- viz DE, add heatmap
- viz FeaturePlot add cluster labels
- viz run shell add option to easily choose which to run
- viz add external markers violin dotplot and featureplot
- viz add project name
- GO analysis switch in between human and mouse databases
- Fix source sequencing data cannot load from absolute PATH
- Fix bug parameter and execution lost after splitting seurat Object during Integration
- Fix viz when there are no marker genes in some clusters
- Fix bug special characters for sheet names failed to produce excel results
- Fix bug GO analysis lose some results cause by non-GO terms
- Fix bug mito and ribo genes cannot recognized when analyzing Human organs
- Change Scale mito&ribo separately
- Change fishertest for clusters, 1vsothers to 1vs1
- Change findMarkers to keep all foldchange results for volcano plots
- Change GO analysis to keep all p adjust value for heatmap
- Add pathways KEGG,Reatome,Hallmark like GO analysis
- Add delete mito genes permanently, Dangerous to call!!!
- Add single sample without integration analysis function
- Add genesorteR analysis
- Add DE&GO stage 1 versus the rest
- Add cluster-wise filter to keep only cells meet the mito or ribo threshold
- Add Volcano plots and GO heatmap
- Fix install_packages.R scMCA from BiocManager to install_github
- Change cycyle var to regress from CC.Difference to G2M.Score&S.Score
- Add 3 function with cellcycle regressout
- Add G1.Score to Metadata G1.Score=1-S.Score-G2M.Score
- Add violin plot for cell cycle
- Add tables for quanlity check and clusters
- Fix fishertest failed due to the calculating order
- Fix more cpu cores used than being set
- Change organizing of the index file
- Change Regressout using conf rather than different functions
- Change Most of viz are based on scrna_phase_comparing.Rds
- Change execution plan to several groups, make it sample
- scrna_phase_preprocess -- QC and regressOut mito etc.
- scrna_phase_clustering -- integration & clustering
- scrna_phase_comparing -- all other analysis
- scrna_phase_singleton -- single sample
- Add static/phase.ini to control each group of analysis functions
- each section is a group defines which and order to run in this group
- if set to 0 will omit
- Add harmony integration
- Add 2 viz clustering Rmds to exclusively plot harmony and seurat clusters
- Add G1.Score to clustering viz
- Add catching exception when comparing has been calculated
- Add once encountering error, stop for viz
- Add unimplemented function scrna_HCLannotate
- add allinone optioin to decide store calculation result into seurat object or files.
- explicitly display parameters in run_example.sh
- compatible with Seurat 4
- viz add three ways of display features in umap(seurat,nebulosa and schex)
- viz doublets score
- viz QCC for a exisiting Seurat object
- viz improve the acolor scheme
- viz add references for some plot sections
- viz add geneset analysis
- viz tables to show counts and statistics of clusters and samples
- add PanglaoDB to external markers
- add ambient detection
- add doublet detection
- add scProportion to compare conditions
- add Rmagic to impute reads *
- improve the performance of saving and loading using compression options
- fix some bugs