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Changelog

cyCONDOR 0.3.0

  • Bug fix with data projection where specific parameters were removed in UMAP calculation
  • Updated official Docker image to the latest Bioconductor version (Bioconductor 3.20, R 4.4.2)
  • Completed documentation of the Astir workflow.
  • Added parameter to select number of PCs and markers for UMAP projection in learnUMAP function.
  • Added documentation and guide to install cyCONDOR in Silicon Mac. We now how a compiled version of the Rphenoannoy package.
  • Simplified installation process, now automatically installing also the GitHub dependencies.
  • Enable Geometric Sketching to subset a condor object with the function geometric_sketching
  • Developed a function (condor_session_info) to include the SessionInfo to the condor object to increase tackability of the analysis.
  • Included storage of the statistical test results in the condor object
  • Added the option to display statistics to the plot_frequency_boxplot function - so far for wilcox, t_test and diffcyt
  • Added function to correlate the cyCONDOR results and the manual gating with FlowJo or similar software (corr_plot_comparison)
  • Experimental: Added a function to write FCS files from a condor object (write_fcs). Currently the function if writing in the .fcs file the cyCONDOR transformed values, we will change to the original values in the next iteration after more extensive testing.

cyCONDOR 0.2.1

  • Included help function to assign metaclusters (Thanks to Lucas Secchim Ribeiro)
  • Removal of redundant color_palette parameter and other redundant lines in the source code
  • Added turkey hsd as post-hoc test to frequency_anova_test (see issue #10)
  • Modified emmeans test in frequency_anova_test (see issue #10)
  • Improvement of error messages

cyCONDOR 0.2.0

  • Bump of major version for official release and publication
  • Changed order of events in the prep_fcd function. This makes the process faster (especially in smaller machines) and reduces the usage of memory.
  • Added function subset_fcd_byparam. This function allows to randomly subset a condor object proportionally across a selected parameter. For example is not possible to randomly subset n cells from each samples.
  • Included more professionalization in the read_fcd function. This allows the user to customize few aspects of the condor object
  • Included cyCONDOR version in the condor object under the extras slot. This enables the user to trace the version used for the analysis.

cyCONDOR 0.1.6

  • Reorganization of existing visualization functions including harmonization of function names and function arguments, utilization of condor object as main input object and addition of more extensive documentation and error messages.
  • Added visualization functions plot_counts_barplot(), plot_marker_ridgeplot() and plot_marker_boxplot()
  • Added getTable() function to generate tables of cell population counts and frequencies, as well as mean or median marker expression for all cell population - sample - marker combinations.
  • boxplot_and_stats() function was replaces by plot_frequency_boxplot() function for visualization and several functions to conduct statistical tests on population frequencies.
  • Added wrapper functions around basic statistical tests to compare cell population frequencies between groups of samples (frequency_t_test(), frequency_wilcox_test(), frequency_anova_test(), frequency_kruskal_test(), frequency_friedman_test())
  • Added prepInputDiffcyt() function to transform the condor object into an SummarizedExperiment object compatible with the diffcyt package for differential testing.
  • Renaming of arguments in runPseudotime() function to harmonize within the package
  • Renaming of arguments in metaclustering() function to harmonize within the package
  • Updated documentation
  • Renaming of arguments in multiple function to harmonize within the package
  • Setting a default seed in multiple functions
  • Added functions to use the CytoNorm algorithm for batch normalization
  • Bug fixes in prep_flw() when merging annotation and removing parameters, saving of import parameters in extras slot of fcd
  • Added new parameters in runFlowSOM() to determine size of FlowSOM grid
  • implemented marker selection (runPCA(), runUMAP(), runDM(), runtSNE(), runPhenograph(), runFlowSOM()), saving of marker selection in extra slot of fcd
  • Added functions to extract all markers present in fcd (measured_markers()) or selected markers (used_markers())
  • Added function to visualize PC loadings
  • Simplified data loading and transformation function including useful error messages
  • Included arcsinh transformation with cofactor 5 for cyTOF data

cyCONDOR 0.1.5

  • Fix bug in the definition of tab separator when loading csv files
  • Added clr transformation for CITE-seq data together with minor improvements to the transformation function
  • Add clustering option in confusion matrix
  • Added visualization of 2D plots of PCA
  • Option to export plots as raster
  • Added function to plot conventional flow 2d plots
  • Added function to plot a density plot for marker expression
  • Implementation of Astir (with Python)
  • Restructured documentation and vignette
  • Added GitPages website with documentation and tutorials
  • Name change to cyCONDOR
  • Edited the pseudotime function to run in a loop for the starting clusters

cyCONDOR 0.1.4

Reference name: condor 0.1.4

  • Add ML classifier with CytoML
  • Included Hmisc as requirment for Violin plto marker function
  • Fix bug with UMAP plotting function when faceting (default for facet_by_fariable set to FALSE not NULL)
  • Fixed package loading message
  • Tested diffusion map and imporoved function
  • Tested pseutodime and improved function
  • Splittied functions in multiple files to make them easier to find
  • Improved package documentation
  • Improved package vignette

cyCONDOR 0.1.3

Reference name: condor 0.1.3

  • FlowSOM function can retain the model to plot the SOM tree afterwards
  • Added Function to read flowjo workspaces to a condor campatible format
  • Fixed filter function when the ‘extra’ slot is occupied

cyCONDOR 0.1.2

Reference name: condor 0.1.2

  • Several bug fixes
  • Added function to calculate tSNE dimensionality reduction
  • Possibility to limit the number of PC used for clustering and non-linear dimensionality reduction
  • Added function to calculate Pseudotime (slignshot)
  • Included an easy-to-export differential frequency table
  • Added a function for random subsetting of the dataset
  • Added visualization of PC loadings
  • Added Pseudobulk PCA Analysis
  • Added function to easily export cellular frequency
  • Added function to change the parameter names (of the fcs files)
  • Added function to visualize DRs as density plot
  • Added Violin plot visualization of marker expression
  • Included option to not cluster rows and columns in heatmaps
  • Included option to show cluster numbers in the dotplot
  • Add multicore support to tSNE
  • Added workflow for UMAP projection and label transfer

cyCONDOR 0.1.1

Reference name: condor 0.1.1

  • Add function to merge condor objects
  • Updated LoadFCS function to be fully compatible with .csv files
  • Updated UMAP function to run on multiple cores
  • Updated RPhenograph function to run on multiple cores
  • Added function to run FlowSOM clustering
  • Fix issues with UMAP parametes selections
  • Added option to specifiy the delimiter for the csv files

cyCONDOR 0.1.0

Reference name: condor 0.1.0

  • Initial release