cellpypes - Cell Type Pipes for Single-Cell RNA Sequencing Data
Annotate single-cell RNA sequencing data manually based on marker gene thresholds. Find cell type rules (gene+threshold) through exploration, use the popular piping operator '%>%' to reconstruct complex cell type hierarchies. 'cellpypes' models technical noise to find positive and negative cells for a given expression threshold and returns cell type labels or pseudobulks. Cite this package as Frauhammer (2022) <doi:10.5281/zenodo.6555728> and visit <https://github.com/FelixTheStudent/cellpypes> for tutorials and newest features.
Last updated 1 years ago
celltype-annotationclassification-algorithmscrnaseqsingle-cell-rna-seq
4.41 score 51 stars 8 scripts 246 downloadsscUtils - Utility Functions for Single-Cell RNA Sequencing Data
Analysis of single-cell RNA sequencing data can be simple and clear with the right utility functions. This package collects such functions, aiming to fulfill the following criteria: code clarity over performance (i.e. plain R code instead of C code), most important analysis steps over completeness (analysis 'by hand', not automated integration etc.), emphasis on quantitative visualization (intensity-coded color scale, etc.).
Last updated 5 years ago
3.86 score 1 dependents 48 scripts 155 downloads