PeacoQC (version 1.9.3) ------------------------ Changed examples in RemoveMargins and changed NEWS page ================================================================================ PeacoQC (version 1.9.2) ------------------------ Added base before which issue ================================================================================ PeacoQC (version 1.9.1) ------------------------ Change in mistake in documentation ================================================================================ PeacoQC (version 1.7.2) ------------------------ Fix plot bug ================================================================================ PeacoQC (version 1.7.1) ------------------------ Solve which error in isolation tree function ================================================================================ PeacoQC (version 1.5.0) ------------------------ Update version with new bioconductor commit ================================================================================ PeacoQC (version 1.1.3) ------------------------ Fix bug in TooSmallClusters function ================================================================================ PeacoQC (version 1.1.4) ------------------------ Change parameter in TooSmallClusters function ================================================================================ PeacoQC (version 1.1.5) ------------------------ Add peak detection parameters ================================================================================ PeacoQC (version 1.3.4) ------------------------ Time parameter is now added to PeacoQC and plot function. Other colnames that time can be used now. ================================================================================ PeacoQC (version 1.3.3) ------------------------ Fix bugs ================================================================================ PeacoQC (version 1.3.2) ------------------------ Looking for filename in $FIL as well as $FILENAME ================================================================================ PeacoQC (version 1.3.1) ------------------------ Remove bugs ================================================================================ PeacoQC (version 1.3.0) ------------------------ New description label due to publication on Bioconductor ================================================================================ PeacoQC (version 1.1.2) ------------------------ Change package number ================================================================================ PeacoQC (version 1.4.0) ------------------------ dir.create has recursive set to TRUE ================================================================================ PeacoQC (version 1.1.1) ------------------------ Official release on Bioconductor ================================================================================ PeacoQC (version 0.99.42) ------------------------ Changed width parameter to nmad in RemoveDoublets Added check for Original_ID column in RemoveMargins ================================================================================ PeacoQC (version 0.99.41) ------------------------ Fix errors ================================================================================ PeacoQC (version 0.99.40) ------------------------ Clean up data ================================================================================ PeacoQC (version 0.99.39) ------------------------ Remove kmeans clustering ================================================================================ PeacoQC (version 0.99.38) ------------------------ Update FindEventsPerBin and heatmap ================================================================================ PeacoQC (version 0.99.36) ------------------------ Update FindEventsPerBin ================================================================================ PeacoQC (version 0.99.35) ------------------------ Update FindEventsPerBin ================================================================================ PeacoQC (version 0.99.34) ------------------------ Modify FindEventsPerBin to allow for better mass cytometry analysis Alter PeacoQC Peakfinding algorithm to speed up and improve ================================================================================ PeacoQC (version 0.99.33) ------------------------ Alter FindEventsPerBin function ================================================================================ PeacoQC (version 0.99.32) ------------------------ Fix determine_good_cells = FALSE bug ================================================================================ PeacoQC (version 0.99.31) ------------------------ Alter plot parameter in PeacoQC to a number when to plot Add Events per bin parameter in PeacoQC heatmap ================================================================================ PeacoQC (version 0.99.30) ------------------------ Alter plot function to only show MAD and IT results when necessary Add consecutive bin results to heatmap ================================================================================ PeacoQC (version 0.99.29) ------------------------ Added RemoveDoublets function ================================================================================ PeacoQC (version 0.99.27-28) ------------------------ Correct for different events_per_bin situations. Increase IT_limit default. Change kernel function for smooth.spline in MAD detection (less strict) ================================================================================ PeacoQC (version 0.99.26) ------------------------ Typo corrections + Original_ID bug fixed ================================================================================ PeacoQC (version 0.99.23-25) ------------------------ Test 100 bin max value ================================================================================ PeacoQC (version 0.99.22) ------------------------ Replaced description function with keyword function of flowCore ================================================================================ PeacoQC (version 0.99.21) ------------------------ Removed ff error ================================================================================ PeacoQC (version 0.99.20) ------------------------ Imported "Original_ID" column to cleaned flowframes. ================================================================================ PeacoQC (version 0.99.19) ------------------------ Remove general PeacoQC function and rename PeacoQCSignalStability to PeacoQC ================================================================================ PeacoQC (version 0.99.18) ------------------------ Split up PlotPeacoQC in multiple functions Alter code to suffice to Bioconductor rules Add warning to vignette that directories will be made in the working directory Remove figure from package ================================================================================ PeacoQC (version 0.99.17) ------------------------ Split up PeacoQCSignastability in multiple functions and alter descriptions ================================================================================ PeacoQC (version 0.99.16) ------------------------ Adapt warnings increasing and decreasing channel ================================================================================ PeacoQC (version 0.99.15) ------------------------ Make sure that the plot can also be made if there is no time channel present in the flowframe ================================================================================ PeacoQC (version 0.99.13) ------------------------ Improve the messages and errors ================================================================================ PeacoQC (version 0.99.11) ------------------------ Allow the usage of marker names instead of only allowing the indices. Change colors of PeacoQCHeatmap ================================================================================ PeacoQC (version 0.99.10) ------------------------ Make changes to allow for better mass cytometry data cleaning. Added the remove_zeros parameter and the time_units parameter. ================================================================================ PeacoQC (version 0.99.9) ------------------------ Changed peak detection to allow for negative peaks and modify PeacoQC function to make compensation and transformation not obligatory. ================================================================================ PeacoQC (version 0.99.3) ------------------------ Made one big PeacoQC function where margins are removed, where the data is compensated and transformed and where PeacoQC signal stability is used for quality control. ================================================================================ PeacoQC (version 0.99.2) ------------------------ Include time channel check. ================================================================================ PeacoQC (version 0.99.1) ------------------------ First version of the package.