---
# System prepended metadata

title: Haniffa Lab introduction reading

---

# Haniffa Lab introduction reading

## Schedule (week starting 28th Feb)

Fri 14:00 NICD all hands (Catalyst)
__________________________________
Mon 09:00 Haniffa Lab (Zoom)
Mon 10:00 NCL-RSE
Mon 11:00 Coffee/lunch with Muzz Haniffa
Tue 13:00 Embryo atlas call (Zoom)
Tue 14:00 Bake off @ medical school


# Single cell RNA 

## History and development:
https://www.youtube.com/watch?v=k9VFNLLQP8c
https://www.youtube.com/watch?v=qygm29zQTGY
https://www.youtube.com/watch?v=tlf6wYJrwKY&t=976s

## scRNA analysis
* [Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data (Review article)](https://www.nature.com/articles/s41596-020-00409-w)
https://www.singlecellcourse.org/introduction-to-single-cell-rna-seq.html

### Dimentionality reduction techniques:

#### Matrix factorization
* PCA
#### Manifold learning
##### Projection/Mapping
* Umap
* t-SNE

### AnnData (.h5ad)

https://anndata.readthedocs.io/en/latest/

https://www.youtube.com/watch?v=BzoC-BbmZBs&t=223s

### scanpy
Toolkit for analyzing single-cell gene expression data 
https://scanpy.readthedocs.io/en/stable/#

Scanpy plotting functions: 
https://scanpy.readthedocs.io/en/stable/api.html#module-scanpy.pl

Specifically: 
* dotplot
* heatmaps
* matrix plots
* violin plots

### Visualising anndata in web portals

History and alternatives:
* [cellxgene](https://github.com/chanzuckerberg/cellxgene)

## "Omics" multi omics
Transcriptomics - RNA
protein
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02577-8

## Adifa

https://github.com/haniffalab/sci-adifa

# Spatial Transcriptomics

"Method of the year" https://www.nature.com/articles/s41592-020-01033-y

Microscopy image data: OME
OME-TIFF https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/
OME-NGFF https://ngff.openmicroscopy.org/latest/

Spatial transcriptomics techniques: 
* [In-situ sequencing](https://www.nature.com/articles/nmeth.2777)
* [10x Visium](https://www.10xgenomics.com/products/spatial-gene-expression)

[VITESSCE]( https://github.com/vitessce/vitessce)

Sitting underneath the Vitessce system, it is important to understand these concepts:

* [Zarr](https://zarr.readthedocs.io/en/stable/): Format for storage of N-dimensional arrays
* [React](https://reactjs.org/): Frontend Javascript library ([Tutorial videos playlist](https://www.youtube.com/playlist?list=PLC3y8-rFHvwgg3vaYJgHGnModB54rxOk3))
* [Deck.gl](https://deck.gl/): WebGL-powered framework for visual data analysis of large datasets


# Data collection (framework for hosting a data collection website)
https://github.com/haniffalab/jekyll-cellatlas-io-collections (requires access)

# Anaconda + jupyter notebooks

## Sample h5ad files and analysis notebooks

# Tech stack
* [Flask](https://flask.palletsprojects.com/en/2.0.x/): Python micro web framework
* [Sphinx](https://www.sphinx-doc.org/en/master/): documentation framework
* [Github pages](https://pages.github.com/)
* [Github actions](https://docs.github.com/en/actions)
* [Jekyll](https://jekyllrb.com/): static site content generator
* [pytest](https://docs.pytest.org/en/7.0.x/index.html): Python testing
* [codecov](https://docs.codecov.com/docs): code coverage service
* [zenodo](https://github.com/zenodo/zenodo): software DOI generation

# Other useful resources

* [Viv](https://github.com/hms-dbmi/viv): A WebGL-powered toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets.
* https://docs.google.com/document/d/12jK7-y04dtGwlYJAvc9BP27Co3WdONwMZ7p_an9wWcQ/edit?usp=sharing (requires access)
* [Embryo data web portal project milestones google doc](https://docs.google.com/document/d/1Rhf7uo1tY9HR-HbRQYOhPKfI_I67NNmaFcrjMvO7_Z8/edit?usp=sharing)




## Inductions tasks
* Email access
* SmartCard
* Induction slides (RSE)
* Extend meeting invites:
    * RSE team meeting
    * RSE subteam meeting
    * Haniffa lab meeting
    * Sanger/OME web portal meetings (bi weekly)
* Annual leave system (Georgia.Carr@newcastle.ac.uk)
* Add to mailing lists (RSE team, HaniffaLab, Catalyst).
* Create Google account (associated with work email)


## Data Collections portal session

* Explain motivation for framework
* Website walkthrough
* Jekyll
* Clone repo, and install
* Run locally
* Explain framework architecture
* Add new yolk sac collection
    * collection md
    * front matter (especially slug)
    * csv
* Push

## Others tasks



## Jupyter notebook
* Shared server or workspace for RSEs?