feature: integrate directLFQ for label-free quantification, using the directLFQ python package MannLabs/directlfq (Ammar, C., Schessner, J. P., Willems, S., Michaelis, A. C. & Mann, M. “Accurate label-free quantification by directLFQ to compare unlimited numbers of proteomes”, 2023, doi:10.1101/2023.02.17.528962), adapted via the code of RdirectLFQ package (author: Zhenhuan Feng) with modifications.
SpectroPipeR 0.4.3
feature: add automatic missing value imputation by halve all values within the lowest 1% quantile distribution of ion quantities to create a new dataset used for imputing missing values.
SpectroPipeR 0.4.2
FIX: for duplicated raw file name in path
SpectroPipeR 0.4.1
add Spectronaut colors to XIC (MS1 and MS2) plot (optional: Spectronaut_colors = TRUE)
SpectroPipeR 0.4.0
add graphical user interface (GUI) function
add identified and not-identified ion intensity plot
updated HTML reports
detailed description of condition-wise filtering & removing of oxidized methionine ions
