<div class="sc-jegwdG lhLRCf"><div class="sc-UEtKG dGqiYy sc-flttKd cguEtd"><div class="sc-fqwslf gsqkEc"><div class="sc-cBQMlg kAHhUk"><h2 class="sc-dcKlJK sc-cVttbi gqEuPW ksnHgj">About Dataset</h2></div></div></div><div class="sc-davvxH eCVTlP"><div class="sc-jCNfQM dTyvWO"><div style="min-height: 80px;"><div class="sc-etVRix jqYJaa sc-gVIFzB gQKGyV"><p>Remark: for cell cycle analysis see paper <a rel="noreferrer nofollow" aria-label="https://arxiv.org/abs/2208.05229 (opens in a new tab)" target="_blank" href="https://arxiv.org/abs/2208.05229">https://arxiv.org/abs/2208.05229</a><br>

"Computational challenges of cell cycle analysis using single cell transcriptomics" Alexander Chervov, Andrei Zinovyev</p>

<h3>Data and Context</h3>

<p>Data - results of single cell RNA sequencing, i.e. rows - correspond to cells, columns to genes (or vice versa).<br>

value of the matrix shows how strong is "expression" of the corresponding gene in the corresponding cell.<br>

<a rel="noreferrer nofollow" aria-label="https://en.wikipedia.org/wiki/Single-cell_transcriptomics (opens in a new tab)" target="_blank" href="https://en.wikipedia.org/wiki/Single-cell_transcriptomics">https://en.wikipedia.org/wiki/Single-cell_transcriptomics</a></p>

<p>See  tutorials: <a rel="noreferrer nofollow" aria-label="https://scanpy.readthedocs.io/en/stable/tutorials.html (opens in a new tab)" target="_blank" href="https://scanpy.readthedocs.io/en/stable/tutorials.html">https://scanpy.readthedocs.io/en/stable/tutorials.html</a><br>

("Scanpy" - main Python package to work with scRNA-seq data). <br>

Or <a rel="noreferrer nofollow" aria-label="https://satijalab.org/seurat/ (opens in a new tab)" target="_blank" href="https://satijalab.org/seurat/">https://satijalab.org/seurat/</a> "Seurat" - "R" package</p>

<p>Particular data:<br>

Paper: <br>

Izar B, Tirosh I, Stover EH, Wakiro I et al. A single-cell landscape of high-grade serous ovarian cancer. Nat Med 2020 Aug;26(8):1271-1279. PMID: 32572264<br>

<a rel="noreferrer nofollow" aria-label="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723336/ (opens in a new tab)" target="_blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723336/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723336/</a></p>

<p>Data:<br>

<a rel="noreferrer nofollow" aria-label="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146026 (opens in a new tab)" target="_blank" href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146026">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146026</a></p>

<h3>Related datasets:</h3>

<p>Other single cell RNA seq datasets can be found on kaggle:<br>

Look here: <a aria-label="https://www.kaggle.com/alexandervc/datasets (opens in a new tab)" target="_blank" href="https://www.kaggle.com/alexandervc/datasets">https://www.kaggle.com/alexandervc/datasets</a><br>

Or search kaggle for "scRNA-seq"</p>

<h3>Inspiration</h3>

<p>Single cell RNA sequencing is important technology in modern biology,<br>

see e.g.<br>

"Eleven grand challenges in single-cell data science"<br>

<a rel="noreferrer nofollow" aria-label="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1926-6 (opens in a new tab)" target="_blank" href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1926-6">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1926-6</a></p>

<p>Also see review :<br>

Nature. P. Kharchenko: "The triumphs and limitations of computational methods for scRNA-seq"<br>

<a rel="noreferrer nofollow" aria-label="https://www.nature.com/articles/s41592-021-01171-x (opens in a new tab)" target="_blank" href="https://www.nature.com/articles/s41592-021-01171-x">https://www.nature.com/articles/s41592-021-01171-x</a></p>

<p>Search scholar.google "challenges in single cell rna sequencing"<br>

<a rel="noreferrer nofollow" aria-label="https://scholar.google.fr/scholar?q=challenges+in+single+cell+rna+sequencing&amp;hl=en&amp;as_sdt=0&amp;as_vis=1&amp;oi=scholart (opens in a new tab)" target="_blank" href="https://scholar.google.fr/scholar?q=challenges+in+single+cell+rna+sequencing&amp;hl=en&amp;as_sdt=0&amp;as_vis=1&amp;oi=scholart">https://scholar.google.fr/scholar?q=challenges+in+single+cell+rna+sequencing&amp;hl=en&amp;as_sdt=0&amp;as_vis=1&amp;oi=scholart</a><br>

gives many interesting and highly cited articles</p>

<p>(Cited 968) Computational and analytical challenges in single-cell transcriptomics<br>

Oliver Stegle, Sarah A. Teichmann, John C. Marioni<br>

Nat. Rev. Genet., 16 (3) (2015), pp. 133-145<br>

<a rel="noreferrer nofollow" aria-label="https://www.nature.com/articles/nrg3833 (opens in a new tab)" target="_blank" href="https://www.nature.com/articles/nrg3833">https://www.nature.com/articles/nrg3833</a></p>

<p>Challenges in unsupervised clustering of single-cell RNA-seq data<br>

<a rel="noreferrer nofollow" aria-label="https://www.nature.com/articles/s41576-018-0088-9 (opens in a new tab)" target="_blank" href="https://www.nature.com/articles/s41576-018-0088-9">https://www.nature.com/articles/s41576-018-0088-9</a><br>

Review Article  07 January 2019<br>

Vladimir Yu Kiselev, Tallulah S. Andrews &amp; Martin Hemberg<br>

Nature Reviews Genetics volume 20, pages273–282 (2019)</p>

<p>Challenges and emerging directions in single-cell analysis<br>

<a rel="noreferrer nofollow" aria-label="https://link.springer.com/article/10.1186/s13059-017-1218-y (opens in a new tab)" target="_blank" href="https://link.springer.com/article/10.1186/s13059-017-1218-y">https://link.springer.com/article/10.1186/s13059-017-1218-y</a><br>

Published: 08 May 2017<br>

Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani &amp; Itay Tirosh<br>

Genome Biology volume 18, Article number: 84 (2017)</p>

<p>Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges<br>

<a rel="noreferrer nofollow" aria-label="https://www.sciencedirect.com/science/article/pii/S1097276519303569 (opens in a new tab)" target="_blank" href="https://www.sciencedirect.com/science/article/pii/S1097276519303569">https://www.sciencedirect.com/science/article/pii/S1097276519303569</a><br>

Molecular Cell<br>

Volume 75, Issue 1, 11 July 2019, Pages 7-12<br>

Journal home page for Molecular Cell</p></div></div></div>