Benchmark datasets for 'diffcyt' evaluations and comparisons

Data files for all benchmark datasets used in the benchmarking evaluations and comparisons in our paper introducing the 'diffcyt' framework. There are four benchmark datasets: AML-sim, BCR-XL-sim, Anti-PD-1, and BCR-XL. These are described in detail in the accompanying paper and supplementary material. Code scripts to prepare datasets, run analyses, and generate figures are available from GitHub at: https://github.com/lmweber/diffcyt-evaluations. The 'diffcyt' R package is available from Bioconductor at: http://bioconductor.org/packages/diffcyt.
Notes:
This repository contains a large number of .fcs, .csv, and .xlsx files (note that .csv and .xlsx files are available as 'attachments'). The complete set of files (and paths) for each benchmark dataset are listed in the files 'benchmark_data_paths_AML_sim.csv', 'benchmark_data_paths_BCR_XL_sim.csv', 'benchmark_data_paths_Anti_PD_1.csv', and 'benchmark_data_paths_BCR_XL.csv'. When files are downloaded from this repository, they will be saved into a single directory. To run the analysis scripts (available from GitHub at https://github.com/lmweber/diffcyt-evaluations), the original directory structure needs to be restored. This can be done by moving all data files into the correct directories, as shown in the file listings in the 'benchmark_data_files_...' .csv files above. Note that some data files could not be included in the repository, because FlowRepository does not allow duplicated files (containing the same data but with different filenames). This includes the .fcs files in 'AML_sim/data/less_distinct/less_50pc/healthy/' and 'AML_sim/data/less_distinct/less_75pc/healthy/' (duplicates from 'AML_sim/data/main/healthy/'); the .fcs files for 'base' condition in 'BCR_XL_sim/data/less_distinct/less_50pc/' and 'BCR_XL_sim/data/less_distinct/less_75pc/' (duplicates of files for 'base' condition from 'BCR_XL_sim/data/main/'); and .csv files from 'BCR_XL/Bodenmiller_BCR_XL_population_IDs/' (duplicates from 'BCR_XL_sim/population_IDs/'). To run the analysis scripts for these datasets, copy and save the duplicated data files using the filenames and paths shown in the 'benchmark_data_files_...' .csv files above.