# synergyfinder 3.3.3 (2022-01-05) # Author: shuyu.zheng@helsinki.fi ## New features * Enable the setting of color bar range in plotting functions for heatmap, contour, and 3D surface plots. * Enable the setting of z-axis range in plotting functions for 3D surface plots. * Enable the setting of axis lines and ticks in plotting functions for contour and 3D surface plots. * Check the number of drugs-cell combo in each block. If there are more than one combo in some blocks. The ReshapeData stops and raises an error message. ## Debug * The input data with replicates and missing values caused errors while calculating synergy scores. Now this bug is fixed. # synergyfinder 2.99.0/2.4.8 (2021-03-10) ## Author: shuyu.zheng@helsinki.fi ## Major Update * Upgrade all existing functions to be compitible with multiple (more than 2) drugs combination data * Add functions for drug sensitivity score (CSS, RI) calucluation. * Add ploting functions for barometer, S-S plot, bar plot for multiple drug combinations. # synergyfinder 2.5.2/2.4.2 (2021-01-07) ## Author: shuyu.zheng@helsinki.fi ## Changes * "CorrectBaseLine": Use the minimu value (instead of mean) of the fitted single drug response as the baseline. # synergyfinder 2.3.5/2.2.5 (2020-12-01) ## Author: shuyu.zheng@helsinki.fi ## Changes * Enable the "ZIP" function to handle the N x 2 or 2 x N drug combination matrices. * Add "seed" parameter into function "ReshapeData" for generating the noise, if "noise = TRUE". # synergyfinder 2.1.2/2.0.2 (2019-11-08) ## Author: shuyu.zheng@helsinki.fi ## Changes * Fix the bug caused by changes in 2.1.1 # synergyfinder 2.1.1/2.0.1 (2019-10-30) ## Author: shuyu.zheng@helsinki.fi ## New features * Add "file.type" option in the "PlotSynergy" and "PlotDoseResponse" functions to specify the format of files when saving plots. * Add "file.name" parameter to plot functions. User can specify the name of the saved files. ## Changes * Delete the "warning" exceptions in "FitDoseResponse" function. # synergyfinder 1.99.1/2.0.1 (2019-06-14) ## Author: shuyu.zheng@helsinki.fi ## New features * Add data pre-process functions: AddNoise, ImputeNA to handle more data. * Make column names of input data compatible with "camel" and "snake" style. * Add one more method ("part") for correcting base line. * User can set adjusted in PlotDoseResponse function to plot original matrix. ## Changes * Updated algorithms in Loewe and ZIP functions. * Move correction argument from syngergy functions to ReshapeData function. * Delete Emin and Emax argument in CalculateSynergy function. * fixed the col.range and row.range in PlotSynergy function. # synergyfinder 1.5.1 ## New features * change license to Mozilla Public License 2.0 * update the citation information * fix for non-square dose response matrix # synergyfinder 1.3.0 ## New features * new kriging function in PlotSynergy function # synergyfinder 0.99.2 ## New features * Fixed the no convergence issue when fitting single drugs. * Fixed the Emin and Emax to 0 and 100 in PlotDoseResponse function. * User can set Emin and Emax for fitting single drugs. * Choose drug combination pair in PlotDoseResponse function. * Choose drug combination pair in PlotSynergy function. * Set legend starting and ending point in PlotSynergy function. # synergyfinder 0.99.1 ## New features * Fixed the issues in PlotSynergy function when the matrix is not 6*6. * Fixed the wrong labels of 3D synergy plot. * Fixed the index issues in Loewe function. # synergyfinder 0.99.0 ## New features * Four synergy score methods are implemented.