regnerm2015 / scendo_scovar_2020

This repository holds the scripts used to analyze the data presented in "A multi-omic single-cell landscape of human gynecologic malignancies", Regner et al., 2021

Title: A multi-omic single-cell landscape of human gynecologic malignancies

Matthew J. Regner (1), Kamila Wisniewska (1), Susana Garcia-Recio, Aatish Thennavan, Raul Mendez-Giraldez, Venkat S. Malladi, Gabrielle Hawkins, Joel S. Parker, Charles M. Perou, Victoria L. Bae-Jump, and Hector L. Franco*

(1) These authors contributed equally

* Corresponding Author

Please cite our paper published in Molecular Cell.

Adapted from Figure 1

Please vist the wiki for an in depth walk-through of our data and analyses.

To download the data, please visit the Gene Expression Omnibus (GEO) accession GSE173682.

The original code associated with our publication is available on Zenodo, but please refer to this repository for the most updated versions.

Interested in more exciting research in cancer genomics? Visit https://www.thefrancolab.org/ to learn more!

scendo_scovar_2020's Issues

rds file request

Hi there,

Thank you for sharing your project code and data. I'm particularly interested in learning more about your analysis methods. Would you be able to let me know where I can download the files: endo_EEC_scRNA_processed.rds (the scRNA-seq object for the EEC cohort) and final_archr_proj_archrGS.rds (the scATAC-seq object for the EEC cohort) used in your code?

Thanks again!

Data request

Dear author, hello, I am a person who just contact analysis, in the process of learning your code, I did not find the 'HTAPP_Ovarian_referential.rds' comment file, may I ask you to provide the file?

patient 9's data

Hello, Dr. J. Regner,
I found that the RDS file in https://www.dropbox.com/sh/dii9hc5ptudyhar/AABCMu9wrjDk8BUAW7Iyca-9a/Regner_Wisniewska_etal_Annotated_Seurat_Objects?dl=0&subfolder_nav_tracking=1 seems to be missing patient 9's data. Could you please upload it?
Best wishes
Chunyu

asking for file

Dear Dr. J. Regner,
Thanks a lot，it is a great work. I have some difficult when running the script. so I want to know if you can upload the ".rds" in your code. Thanks a lot.

Read GSE173682_RAW

Hello, I'm interested in your dataset and have downloaded GSE173682_RAW from GEO. I was wondering how to read the three files into Seurat. The commands and error messages read as follows. Thank you.

I first renamed the files from GSM5276933_matrix-3533EL.mtx.gz to matrix.mtx.gz etc.

Some questions about Figure1

Dear Dr. J. Regner,
Hi! This article has great inspiration for our research. We are very interested in this article! Therefore, currently I am trying to reproduce the content of the article. But I encountered some difficulties in reproducing the chart in Figure 1, mainly due to the annotation of cell types, and it seems that I cannot obtain the RDS file of the reference dataset. At the same time, I am trying to use this tutorial [https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html] to complete the same work as you, but it seems that I cannot achieve the same results. Similarly, in order to obtain Figure 1B&C, which code should I use in sequence? I am eager to receive your reply, thank you very much!

Chunyu