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

by Andres F Vallejo [email protected]

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

notebook scRNA analysis

https://colab.research.google.com/github/afvallejo/Workshop_New_frontiers/blob/main/1_QC_to_Annotation_workshop_CP.ipynb

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/