ReadME

1. HuEm_stable_reference_projection_tool Folder

This folder contains an offline version of the prediction tool.

• Input Gene Expression Matrix: Users can modify the path of the input gene expression matrix file or provide their own expression data when using the pipeline.
• Running MiloR: The `para.list$runMiloR` parameter is used to determine whether to run neighborhood aggregation using miloR.
• Group Information: If users want to perform aggregation within a specific group, they can provide the group information. Otherwise, this field can be left empty.

2. reference_construction Folder

This folder contains scripts for constructing the human embryonic reference and recording the necessary files for stabilized projection.

• HEEM.Stable.reference.construct.fastMNN.R: This script is used for constructing the human embryonic reference and recording the needed files for stabilized projection.
• HEEM.Stable.reference.create.SVM.model.R: This script is used to find the best parameters for the SVM classifier for each lineage.
• HEEM.stable.reference.SCP.main.traj.R: This script is used for trajectory analysis and inferring pseudo-time.

3. cross_species_integration Folder

This folder contains scripts for cross-species integration among human, marmoset, and cynomolgus monkey data.

• merge.Human.Marmoset.Cyno.data.R: This script is used to perform cross-species integration among human, marmoset, and cynomolgus monkey data.

4. Installation

• compatible package version: users can refer to the session info of projecting_query_dataset.html to find the compatible version of packages.
• Available docker:  https://hub.docker.com/r/zhaocheng/shiny-tools-eeptools. (around 15 mins to pull it down)
• projecting_query_dataset.R can be used for the test (around 10 mins)

To use the docker (example)

`docker run -it -v /local/folder/HumanEarlyEmbryoRefProjection/:/home/docker/Install/ --name eeptools zhaocheng/shiny-tools-eeptools:v1 /bin/bash`

`cd /home/docker/Install ## which has the R package environment`

`R`

License This project is licensed under the terms of the GNU General Public License v3.0 or later. 

If you think it is helpful, please cite

our paper:  Zhao et al., 2024 (DOI: 10.1038/s41592-024-02493-2)

and 

Original MNN paper : Haghverdi et al., 2018 ( DOI: 10.1038/nbt.4091)

If you're using miloR to do aggregation, please cite miloR paper: Dann et al., 2022 (DOI: 10.1038/s41587-021-01033-z) as well.