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README.md

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 # Portal-reproducibility
-Codes for reproducing the experiments of the paper "Adversarial domain translation networks for fast and accurate large-scale atlas-level integration of single-cell datasets".
+Codes for reproducing the experiments of the paper "Adversarial domain translation networks enable fast and accurate large-scale atlas-level single-cell data integration".
+
++ [Integration of mouse spleen datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-Spleen.html) (we reproduce the result of performance metrics in this notebook as an example). [Benchmarking](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Benchmarking-Spleen.html). 
++ [Integration of mouse marrow datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-Marrow.html).
++ [Integration of mouse bladder datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-Bladder.html).
++ [Integration of mouse brain cerebellum datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-MouseBrain-CB.html).
++ [Integration of mouse brain hippocampus datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-MouseBrain-HC.html).
++ [Integration of mouse brain thalamus datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-MouseBrain-TH.html).
++ [Integration of human PBMC datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-sensitivity.html) (sensitivity analysis).
++ [Integration of entire mouse cell atlases from the Tablula Muris project](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-TabulaMuris-full.html).
++ [Integration of mouse brain scRNA-seq and snRNA-seq datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-MouseBrain-CellNuclei.html).
++ [Integration of human PBMC scRNA-seq and human brain snRNA-seq datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-BloodCell-BrainNuclei.html).
++ [Integration of scRNA-seq and scATAC-seq datasets](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-PBMC-ATACseq.html).
++ [Integration of developmental trajectories](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-trajectory.html).
++ [Integration of spermatogenesis differentiation process across multiple species](https://htmlpreview.github.io/?https://github.com/jiazhao97/Portal-reproducibility/blob/main/Reproduce-Spermatogenesis.html). Gene lists from Ensembl Biomart (we only use genes that are assigned with the type "ortholog_one2one" in the lists): [orthologues (human vs mouse)](https://github.com/jiazhao97/Portal-reproducibility/raw/main/orthologues_human_mouse.txt), [orthologues (human vs macaque)](https://github.com/jiazhao97/Portal-reproducibility/raw/main/orthologues_human_macaque.txt).