v.4.7.0

4.6.7 2024-05-11

Changed colors in heatmaps to a gradient ranging from blue-yellow-red. Added additional heatmaps that show log2-transformed and centered intensities (i.e., row-mean=0).

Highlighting of proteins in volcano and MA plots is now achieved via text. Figure legends were consequently removed.

Added optional GSEA analysis for mouse and human on the basis of the limma DE-testing results. GSEA result tables will be stored in "GSEA folder" alongside "dotplots"". Due to space constraints, the pdf report only shows enrichment maps.

Version v4.6.6

4.6.6 2023-03-10
Cassiopeia_LFQ is changed to read contaminant.fasta instead of previous con_table.txt.
Now it is easier if the user udered a different contamiant.fasta in the MaxQuant search. Just replace the one from Cassiopeia.

con_table.txt is removed. A contaminant.fasta is included. User could use their own contamiant database, just name it to contamiannt.fasta
4.6.5 2022-10-19
if batch is not NULL, a PCA plot after imputation and bactch correction is draw to show the success of batch correction.

Version v4.6.4

Update to support the latest Limma package 3.50.1.
Log used packages at the end of the PDF report.
This release was tested under R 4.1.3 with all packaged up to date.

v1.1

changed README

Cassiopeia LFQ

Initial release.