Single Cell data analysis tutorial on PBMC dataset using scanpy - Part1

In this video, we will go through standard steps to analyze a single-cell RNA sequencing dataset (PBMC) from 10X Genomics using the #scanpy package.
Jupyter notebook is available at: github.com/ram...
We cover the following sections:
1) Download public available PBMC dataset from 10X genomics website
2) Loading the gene count matrix (cell ranger output) into AnnData object
3) What:
- is AnnData object? Different components of AnnData object
- Section 1: Summary of AnnData object
- Section 2: Inspection of newly created AnnData object
4) Section 3: Quality Control on AnnData object
5) Section 4: Filtering cells and genes
6) Section 5: Normalization of data
7) Section 6: Finding Highly variable genes
8) Section 7: Scaling the data
9) Section 8: Perform PCA analysis
10) Section 9: Finding Neighbors
11) Section 10: Running UMAP and Visualization
To get in touch:
Twitter: / prakki_rama
Github: github.com/ram...
LinkedIn: / prakki-sai-rama-sridat...
#bioinformatics #scanpy #python #singlecell #genomics #beginners #anndata

[@zebasultana930]

Nice tutorial! It is great that you give a summary of the way data and results from various steps are stored back in the object. Thanks!

[@ramadatta7046]

Thank you for your appreciation of the video! All the questions I had, I tried to find an answer and made a video!

[@megadarken]

That's a really good video! Thanks for it!

[@asearchforsolutions]

Thank you!

[@esmanur1562]

github link is not working

[@asearchforsolutions]

Hi. Thank you for the comment. I have updated the link now.

[@esmanur1562]

@@asearchforsolutions thank you so much