Code

GitHub

Packages

• kitchen: automated manipulation and processing of scRNA-seq counts files from command line (documentation)
  

• cnmf: packaged and streamlined version of cNMF, adapted from [Kotliar, et al. (2019)] (documentation)
  

• MILWRM: Multiplexed Image Labeling With Regional Morphology [Kaur, et al. (2024) Communications Biology] (documentation)
  

• dropkick: Single-cell RNA-seq quality control and filtering package [Heiser, et al. (2021) Genome Research] (documentation)
  

Repositories (Publication Code)

• spatial_CRC_atlas & spatial_CRC_atlas_imaging: Code for reproducing analyses in [Heiser, et al. (2023) Cell]

• STAR_protocol: Single-cell RNA-seq quality control and analysis protocol [Chen, et al. (2021) STAR Protocols]

• DR-structure: Quantification of global and local structure preservation by dimensionality reduction techniques [Heiser & Lau (2020), Cell Reports] (documentation)