v031

cyCONDOR 0.3.1

changelog

• Added function condor_info to easily explore the content of a condor object.
• Solved Issue #31, color pallette is reversed in plot_marker_ridgeplot() function.
• Solved Issue #30, the pseudotime function can now use a prefix argument.
• Improved documentation regarding the use of different co-factors when using the archsin data transformation.
• Solved Issue #33, the plot_marker_dotplot function have now an alpha argument to control the transparency of the dots.
• Solved Issue #34, the plot_marker_ridgeplot now have a title argument.
• Solved Issue #19, if an empty fcs or csv file is provided the prep_fcd function will stop and point to the corrupted file.
• Added function order_param to allow manual ordering of an annotation or clustering variable.
• Added prefix argument to astir functions.
• Added function to export the condor object and sce for interoperability with other packages

v030

cyCONDOR 0.3.0

changelog

• 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.

v021

cyCONDOR 0.2.1

changelog

• 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

v020

cyCONDOR 0.2.0

changelog

• 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.

v016

cyCONDOR v0.1.6

changelog

• 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

v015

cyCONDOR v0.1.5

changelog

• 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

condor v0.1.4

Changelog

• 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

Docker image

To visit the dockerhub repository click here

Pull the docker image for condor v0.1.4

docker pull lorenzobonaguro/condor:v014

Install this version with devtool

While it is advised to use condor with the pre-built docker image it is possible also to install the package manually. In this case also all condor dependencies need to be installed

# Install condor locally

# *NOTE*
# To install condor on Windows or Mac you need to have a compiler installed to build the packages from source.
# On Windows install Rtools, the version should match the version of the majour R release used
# On Mac install xcode

BiocManager::install(update = T, ask = F, version = "3.17")

BiocManager::install(c("flowCore", "devtools", "Rtsne", "umap", "ggplot2", "ggpubr",
                       "vegan", "diffusionMap", "FlowSOM", "gplots", "grid", "gridExtra",
                       "reshape2", "RColorBrewer", "scatterplot3d", "rgl", "Biobase", "Rmisc",
                       "tidyverse", "pheatmap", "viridis", "rainbow", "destiny",
                       "SingleCellExperiment", "slingshot", "ggrastr",
                       "uwot", "FlowSOM", "caret", "factoextra", "harmony", "flowWorkspace",
                       "CytoML", "Biobase", "Hmisc", "CytoDx", "DelayedMatrixStats"), version = "3.17")

install.packages("https://cran.r-project.org/src/contrib/randomForest_4.7-1.1.tar.gz", repos=NULL, type="source")

devtools::install_github("JinmiaoChenLab/Rphenograph")

devtools::install_github("stuchly/Rphenoannoy")

devtools::install_url("https://github.com/lorenzobonaguro/condor/releases/download/v014/condor_0.1.4.tar.gz")

condor v0.1.3

Changelog

• 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

condor v0.1.2

Changelog

• 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

condor v0.1.1

Changelog

• 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