From c57fe76facc674b59d93e360d4d5cdf8db4d2860 Mon Sep 17 00:00:00 2001
From: Dinithi Sumanaweera <83298091+dinithins@users.noreply.github.com>
Date: Mon, 13 May 2024 13:06:50 +0100
Subject: [PATCH] Update README.md

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-### Analysis notebooks and data used in the manuscript: ***"Gene-level alignment of single cell trajectories"*** <br>
+### Analysis notebooks and data used in the manuscript: <br> ***"Gene-level alignment of single cell trajectories"*** <br>
 [https://www.biorxiv.org/content/10.1101/2023.03.08.531713v3](https://doi.org/10.1101/2023.03.08.531713 ) (bioRxiv Preprint)
 
-Available datasets:
+**Available datasets:**
 
 1. Simulated trajectories using Gaussian Processes
-2. Simulated perturbations using the mouse pancreas development dataset from CellRank (https://github.com/theislab/cellrank)
-3. Negative control simulated dataset generated using the published script of Laidlaw et al (2023) at https://github.com/No2Ross/TrAGEDy  
-4. Anndata objects of the PAM/LPS treated Murine bone marrow-dreived dendritic cell dataset of Shalek et al. (2014) compiled from the datafiles at https://github.com/shenorrLabTRDF/cellAlign
-5. Preprocessed and analysed Healthy/IPF datasets <br>(original raw data of Adams et al. (2020) downloaded from GEO: GSE136831)
-6. Preprocessed and analysed Pan fetal reference datasets <br> (original raw data of Suo et al. (2022) downloaded from https://developmental.cellatlas.io/fetal-immune)
-7. Preprocessed and analysed Artificial thymic organoid datasets <br> (raw sequencing data available from ArrayExpress: E-MTAB-12720)
+2. Simulated trajectory perturbations using the mouse pancreas development dataset from CellRank (https://github.com/theislab/cellrank).
+3. Negative control simulated dataset generated using the published script of Laidlaw et al (2023) at https://github.com/No2Ross/TrAGEDy.
+4. Anndata objects of the PAM/LPS-treated murine bone marrow-dreived dendritic cell dataset of Shalek et al. (2014) compiled from the datafiles at https://github.com/shenorrLabTRDF/cellAlign.
+5. Preprocessed and analysed Healthy/IPF datasets: <br>(original raw data of Adams et al. (2020) downloaded from GEO: GSE136831).
+6. Preprocessed and analysed Pan fetal reference datasets: <br> (original raw data of Suo et al. (2022) downloaded from https://developmental.cellatlas.io/fetal-immune).
+7. Preprocessed and analysed Artificial thymic organoid datasets: <br> (raw sequencing data available from ArrayExpress: E-MTAB-12720).
 
 Large data objects are available at: https://zenodo.org/records/11182400