Update README.md

Author: genecell

Diff for: README.md

@@ -5,17 +5,12 @@ Single cell papers with code can not only facilitate the reproducibility of biom
 
 'Papers with code' here means that authors provide necessary codes to reproduce figures or results in their papers.
 
-(Last update: May 09, 2023)
+(Last update: July 13, 2023)
 
 ### Tutorial
 
 - [[code | Python]](https://github.com/theislab/single-cell-tutorial) Luecken, M.D., and Theis, F.J. (2019). **Current best practices in single‐cell RNA‐seq analysis: a tutorial.** Mol. Syst. Biol. 15, e8746.
 
-### Benchmark study
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-- [[code | R]](https://github.com/oxwang/fda_scRNA-seq) Chen, W. et al. [**A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples.**](https://www.nature.com/articles/s41587-020-00748-9) Nat. Biotechnol. (2020) doi:10.1038/s41587-020-00748-9.
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 ### Cell Atlas
 
 - [[code | R]](https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/Tumor-Immune-Cell-Atlas) Nieto, P., Marc Elosua-Bayes, M., Trincado, J.L., Marchese, D., Massoni-Badosa, R., Salvany, M., Henriques, A., Mereu, E., Moutinho, C., Ruiz, S., et al. (2020). **A Single-Cell Tumor Immune Atlas for Precision Oncology.** BioRxiv 2020.10.26.354829.
@@ -24,7 +19,6 @@ Single cell papers with code can not only facilitate the reproducibility of biom
 
 - [[code | R]](https://github.com/krasnowlab/HLCA) Travaglini, K. J. et al. **A molecular cell atlas of the human lung from single-cell RNA sequencing.** Nature 587, 619–625 (2020).
 
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 - [[code | Python and R]](https://github.com/haniffalab/HCA_skin) Reynolds, G. et al. [**Poised cell circuits in human skin are activated in disease.**](https://www.biorxiv.org/content/10.1101/2020.11.05.369363v1) bioRxiv 2020.11.05.369363 (2020) doi:10.1101/2020.11.05.369363.
 
 - [[code | Python]](https://github.com/czbiohub/tabula-sapiens) Consortium TTS, Quake SR. The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans. bioRxiv 2021; 2021.07.19.452956
@@ -59,40 +53,38 @@ Single cell papers with code can not only facilitate the reproducibility of biom
 
 - [[code | Python and R]](https://github.com/niklaslang/PCLS_perturbations) Lang, N. J., Gote-Schniering, J., Porras-Gonzalez, D., Yang, L., De Sadeleer, L. J., Jentzsch, R. C., Shitov, V. A., Zhou, S., Ansari, M., Agami, A., Mayr, C. H., Kashani, B. H., Chen, Y., Heumos, L., Pestoni, J. C., Geeraerts, E., Anquetil, V., Saniere, L., Wögrath, M., … Schiller, H. B. (2023). [**Ex vivo tissue perturbations coupled to single cell RNA-seq reveal multi-lineage cell circuit dynamics in human lung fibrogenesis.**](https://www.biorxiv.org/content/10.1101/2023.01.16.524219v1) BioRxiv, 2023.01.16.524219. https://doi.org/10.1101/2023.01.16.524219.
 
-### Experimental research
-
-- [[code | R]](https://github.com/tgen/banovichlab) Habermann A, Gutierrez A, Bui L, Yahn S, Winters N, Calvi C, et al. **Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis.** Sci Adv 2020;6:eaba1972. https://doi.org/10.1101/753806.
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-- [[code | R]](https://github.com/marzamKI/neurogenic_astros) Zamboni, M., Llorens-Bobadilla, E., Magnusson, J.P., and Frisén, J. (2020). **A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury.** Cell Stem Cell 1–13.
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+### scATAC-seq
 
-- [[code | Python]](https://github.com/linnarsson-lab/ipynb-lamanno2016) La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L.E., Stott, S.R.W., Toledo, E.M., Villaescusa, J.C., et al. (2016). **Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.** Cell 167, 566-580.e19.
+- [[code | R, Python]](https://github.com/yal054/snATACutils) Li, Y.E., Preissl, S., Hou, X. et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598, 129–136 (2021). https://doi.org/10.1038/s41586-021-03604-1
 
-- [[code | R]](https://github.com/klarman-cell-observatory/ivPerturbSeq) Jin, X. et al. **In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes.** Science 370, eaaz6063 (2020).
+### Spatial transcriptomics
 
+- [[code | R]](https://github.com/saezlab/visium_heart/tree/master/snRNA_seq) Kuppe, C. et al. **Spatial multi-omic map of human myocardial infarction.** bioRxiv 2020.12.08.411686 (2020) doi:10.1101/2020.12.08.411686.
 
+- [[code | Python and R]](https://github.com/Teichlab/HCA_Heart_ver2) Kanemaru, K., Cranley, J., Muraro, D., Miranda, A. M. A., Ho, S. Y., Wilbrey-Clark, A., Patrick Pett, J., Polanski, K., Richardson, L., Litvinukova, M., Kumasaka, N., Qin, Y., Jablonska, Z., Semprich, C. I., Mach, L., Dabrowska, M., Richoz, N., Bolt, L., Mamanova, L., … Teichmann, S. A. (2023). [**Spatially resolved multiomics of human cardiac niches.**](https://www.nature.com/articles/s41586-023-06311-1) Nature. https://doi.org/10.1038/s41586-023-06311-1
 
 ### Nanopore
 
 - [[code | Perl, Shell and R]](https://github.com/ucagenomix/sicelore) Lebrigand, K., Magnone, V., Barbry, P. & Waldmann, R. [**High throughput error corrected Nanopore single cell transcriptome sequencing.**](https://www.nature.com/articles/s41467-020-17800-6) Nat. Commun. 11, 4025 (2020).
 
+### Experimental research
 
-### scATAC-seq
+- [[code | R]](https://github.com/tgen/banovichlab) Habermann A, Gutierrez A, Bui L, Yahn S, Winters N, Calvi C, et al. **Single-cell RNA sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis.** Sci Adv 2020;6:eaba1972. https://doi.org/10.1101/753806.
 
-- [[code | R, Python]](https://github.com/yal054/snATACutils) Li, Y.E., Preissl, S., Hou, X. et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature 598, 129–136 (2021). https://doi.org/10.1038/s41586-021-03604-1
+- [[code | R]](https://github.com/marzamKI/neurogenic_astros) Zamboni, M., Llorens-Bobadilla, E., Magnusson, J.P., and Frisén, J. (2020). **A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury.** Cell Stem Cell 1–13.
 
+- [[code | Python]](https://github.com/linnarsson-lab/ipynb-lamanno2016) La Manno, G., Gyllborg, D., Codeluppi, S., Nishimura, K., Salto, C., Zeisel, A., Borm, L.E., Stott, S.R.W., Toledo, E.M., Villaescusa, J.C., et al. (2016). **Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.** Cell 167, 566-580.e19.
 
-### Spatial transcriptomics
+- [[code | R]](https://github.com/klarman-cell-observatory/ivPerturbSeq) Jin, X. et al. **In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes.** Science 370, eaaz6063 (2020).
 
-- [[code | R]](https://github.com/saezlab/visium_heart/tree/master/snRNA_seq) Kuppe, C. et al. **Spatial multi-omic map of human myocardial infarction.** bioRxiv 2020.12.08.411686 (2020) doi:10.1101/2020.12.08.411686.
+### Benchmark study
 
+- [[code | R]](https://github.com/oxwang/fda_scRNA-seq) Chen, W. et al. [**A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples.**](https://www.nature.com/articles/s41587-020-00748-9) Nat. Biotechnol. (2020) doi:10.1038/s41587-020-00748-9.
 
 ### Trajectory analysis
 
 - [[code | Python]](https://github.com/rajewsky-lab/planarian_lineages) Plass, M., Solana, J., Alexander Wolf, F., Ayoub, S., Misios, A., Glažar, P., Obermayer, B., Theis, F.J., Kocks, C., and Rajewsky, N. (2018). **Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.** Science. 360.
 
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 ### Visualization
 
 - [[code]](https://github.com/faryabib/NatMethods_TooManyCells_analysis) Schwartz GW, Zhou Y, Petrovic J, Fasolino M, Xu L, Shaffer SM, et al. **TooManyCells identifies and visualizes relationships of single-cell clades.** Nat Methods 2020. https://doi.org/10.1038/s41592-020-0748-5.