QICFIT stands for Quantitative Identity Classifier For Interrogating Transcriptomes. It's an R package which allows a user to assess which tissue a sample resembles based on its transcriptome.
QICFIT works by performing a Spearman rank correlation between an RNA-seq transcriptome and a set of reference trasncriptomes from the Genotype-Tissue Expression (GTEx) project. This means that QICFIT is scale-independent. Since a Spearman correlation is based on rank, it can compare RNA-seq data between linear and log scales without issue. The expression values themselve are irrelevant.
Currently, QICFIT is an in-house tool used by the Sareen lab to assess the success of stem cell differentiation protocols in maturing pluripotenet stem cells into differentiated cells. As such, I have no composed a user guide or tested QICFIT under a range of conditions and data types. If you would like to use QICFIT or assist in its development, feel free to email me.
