Spatially Resolved Transcriptomics (SRT)
QuadST (Identifying cell-cell interaction changed genes on single-cell SRT data)
RECCIPE (cell-cell interaction on multi-cell SRT data) -- Will be implemented in next version of Giotto
sCCIgen SRT data simulator for cell-cell interactions beyond using SRT data
Integrative -Omic Data Analysis
MiXcan (cell-type-aware transcriptome-wide association analysis)
iProMix (cell-type specific association analysis for bulk profiling data)
iProFun (integrating multi-omics data to identify function consequences of DNA alterations)
ProTrack (Interactive web tool to visualize multi-omic data)
CPTACdream (Package of NCI-CPTAC DREAM Proteogenomics Challenge to predict protein levels from copy number and transcrpit levels and phosphorylation levels from protein levels.)
Quantile Regression