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# System prepended metadata

title: Tools and notebooks used in the workshop "New frontiers in systems biology applied to infection diseases research"

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# Tools and notebooks used in the Single Cell RNA-Seq Analysis Training Series


by Andres F Vallejo afvallejo@gmail.com


# notebook scRNA analysis 

1. Alingment [Sesion 1](https://hackmd.io/@afvallejo/BJuh6OyZkx)
2. Doublet and background removal [Sesion2](https://hackmd.io/@afvallejo/HkPkIGdbyx)
3. QC and Clustering [Sesion 3](https://hackmd.io/@afvallejo/rJeFhHbMyg)
4. Annotation exercise [Sesion 4](https://colab.research.google.com/github/afvallejo/AD_2023/blob/main/03_pbmc_colab_annotation.ipynb)
5. Integration [Sesion 5](https://hackmd.io/@afvallejo/H1A0756Pyg)
## Links to Google colab

### intro colab

https://colab.research.google.com/

### Alphafold

https://colab.research.google.com/github/afvallejo/Workshop_New_frontiers/blob/main/AlphaFold2.ipynb

### other tools
https://github.com/trekhleb/machine-learning-experiments

# Databases for scRNAseq data

1. 10x genomics https://www.10xgenomics.com/resources/datasets
2. Human cell atlas https://data.humancellatlas.org/
3. Covid 1M cells https://www.covid19cellatlas.org/
4. Broadinstitute https://singlecell.broadinstitute.org/single_cell
5. Biological Project Library (BioProject): https://bigd.big.ac.cn/bioproject/
6. Genome Sequence Archive (GSA): https://ngdc.cncb.ac.cn/gsa/
7. Gene Expression Omnibus (GEO): https://www.ncbi.nlm.nih.gov/geo/
8. European Nucelotide Archive (ENA): https://www.ebi.ac.uk/ena/browser/home
9. Sequence Read Archive (SRA): https://www.ncbi.nlm.nih.gov/sra

# Tools for cluster annotation
1. panglaodb https://panglaodb.se/search.html
2. EnrichR https://maayanlab.cloud/Enrichr/
3. GeneProfiler https://biit.cs.ut.ee/gprofiler/gost

# Courses
1.Sanger Analysis of single cell RNA-seq data https://www.singlecellcourse.org/