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dgrun's Projects

code_figurereproduce_ilc2-insitumaturation icon code_figurereproduce_ilc2-insitumaturation

Computational Analysis of In situ maturation and tissue adaptation of type 2 innate lymphoid cell progenitors. Code to reproduce analysis and figures. Raw count files to reproduce figures and RaceID analyses objects can be assessed at GEO under the accession code GSE141330 at the day of publication.

fateid icon fateid

R package for the inference of cell fate bias from single-cell RNA-seq data.

netid_package icon netid_package

A scalable method to infer fate specific gene regulatory network from single cell gene expression data

nico_tutorial icon nico_tutorial

A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.

raceid icon raceid

Algorithm for the inference of cell types from single-cell RNA-seq data.

raceid3_stemid2 icon raceid3_stemid2

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. Please download the R package from the RaceID3_StemID2_package repository, which contains the current version as an R package. This repository will not be updated anymore.

raceid3_stemid2_package icon raceid3_stemid2_package

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and StemID2 method including novel functionalities and performance improvements compared to the previous RaceID3/StemID2 version in the RaceID3_StemID2 repository. The RaceID3_StemID2 repository will not be updated anymore in the future.

stemid icon stemid

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.

varid_analysis icon varid_analysis

VarID analysis of murine hematopoietic progenitors and intestinal epithelial cells. VarID is part of RaceID v0.1.4

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