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assessme

Assess me – a cluster assessment tool for preprocessing and clustering optimisation

cell_cycle_scoring

cellranger-arc_snakemake_gcloud

demultiplex RNA/ATAC bcl files and align multiomic RNA/ATAC reads with cellranger-arc using snakemake on google cloud

clustering_visualisation_categorical_data

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.

python_seq_scripts

Python scripts to process and analyze sequencing data files and reference files

r_plotting_functions

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.

scatac.peak.annotation

tool to annotate scATAC Peaks and more

shiny_app_ilc2-insitumaturation

All relevant files for Shiny app related to ILC2-InsituMaturation (except RaceID files, which can be downloaded from GEO Series GSE141330). Shiny app hosted at: http://murine-ilc-atlas.ie-freiburg.mpg.de/