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Update README.md - commented & fixed format
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bhavyaac authored Sep 6, 2023
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└── reference2
```

## Output files
<!--- ## Output files --->


# :gear: Installation and Dependencies
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- Tangram
```
# :floppy_disk: Resources
<!--- # :floppy_disk: Resources --->
Add table with resource usage for different sice references and queries
<!--- Add table with resource usage for different size references and queries --->
# :woman_mechanic: Adding new tools
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## scClassify

Documentation written by: Bhavyaa Chandarana

Date written: 2023-07

scClassify workflow was generated using the tutorial below:
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## scPred

Documentation written by: Alva Annett

Date written: 2023-07

Normalization and parameters based on this tutorial:
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## singleCellNet

Documentation written by: Rodrigo Lopez Gutierrez

Date written: 2023-08-01

singleCellNet workflow was generated following the tutorial below:
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## Correlation

Documentation written by: Rodrigo Lopez Gutierrez

Date written: 2023-08-02

The Correlation tool runs a correlation-based cell type prediction on a sample of interest, given the mean gene expression per label for a reference.
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## scLearn

Documentation written by: Bhavyaa Chandarana, updated by Tomas Vega Waichman

Date written: 2023-08-04

scLearn workflow was generated using the following tutorial: https://github.com/bm2-lab/scLearn#single-label-single-cell-assignment
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## singleCellNet

Documentation written by: Rodrigo Lopez Gutierrez

Date written: 2023-08-01

singleCellNet workflow was generated following the tutorial below:
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## ACTINN

Documentation written by: Alva Annett

Date written: 2023-08-08

ACTINN code is based on `actinn_format.py` and `actinn_predict.py` originally found here: https://github.com/mafeiyang/ACTINN
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## Tangram

Documentation written by: Tomas Vega Waichman

Date written: 2023-08-08

The Tangram workflow was generated following the tutorial provided below:
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## scAnnotate

Documentation written by: Tomas Vega Waichman

Date written: 2023-08-11

The scAnnotate workflow was generated following the tutorial provided below:
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## scID

Documentation written by: Tomas Vega Waichman

Date written: 2023-08-12

The scID workflow was generated following the tutorials provided below:
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## scNym

Documentation written by: Tomas Vega Waichman

Date written: 2023-08-14

The scNym workflow was generated following the tutorial provided below:
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## CellTypist

Documentation written by: Tomas Vega Waichman

Date written: 2023-08-16

The CellTypist workflow was generated following the tutorials provided below:

Training:
* https://celltypist.readthedocs.io/en/latest/celltypist.train.html
* https://github.com/Teichlab/celltypist#supplemental-guidance-generate-a-custom-model

Predicting:
* https://celltypist.readthedocs.io/en/latest/notebook/celltypist_tutorial_ml.html

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