https://github.com/carmonalab/projectils_casestudies
A repository of case studies using ProjecTILs
Science Score: 13.0%
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○Scientific vocabulary similarity
Low similarity (4.7%) to scientific vocabulary
Repository
A repository of case studies using ProjecTILs
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- Stars: 12
- Watchers: 3
- Forks: 3
- Open Issues: 0
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Metadata Files
README.md
ProjecTILs Case Studies
We will be posting here interesting/instructive case studies of single-cell data analysis using ProjecTILs:
1. MC38 TILs with clonotype analysis
In this case study, we build an integrated scRNA-seq analysis workflow to interpret the transcriptional (scRNA-seq) and clonal structure (scTCR-seq) of tumor-infiltrating T cells in MC38 colon adenocarcinoma.
2. Project human data on mouse TIL atlas
Exploiting the ortholog mapping functionality of ProjecTILs, we project scRNA-seq from melanoma patients (Sade-Feldman, 2018) onto a mouse reference atlas, to interpret T cell phenotype differences between responders and non-responders to checkpoint blockade therapy.
3. T cell diversity across multiple tissues
Apply ProjecTILs to investigate transcriptional profiles of CD8 T cells in chronic infection from six different tissues.
4. Exhausted CD8 T cells are associated with ICB responsiveness in breast cancer
Re-analysis of the dataset by Bassez et al. Nat Med (2020) of breast cancer patients treated with anti-PD-1 therapy
5. Memory phenotypes of CD4+ T cells after acute infection
A case study of projection of virus-specific CD4+ T cells in late acute infection.
6. Detecting novel/unrepresented cell states
Projection of tumor-specific T cells on a viral reference, illustrating how one can interpret subtypes not represented in the reference.
7. Effect of anti-PD-L1 therapy on CD4+ T cells
Analysing the transcriptional phenotype of CD4+ T cells in chronic infection after treatment with an anti-PD-L1 antibody.
8. Exploring dendritic cell diversity in human spleen
Projection of human DCs from spleen from the study of Brown et al. Cell (2019)
Owner
- Name: Cancer Systems Immunology Lab
- Login: carmonalab
- Kind: organization
- Location: Lausanne, Switzerland
- Website: https://agora-cancer.ch/laboratory/carmona-lab
- Twitter: carmonation
- Repositories: 16
- Profile: https://github.com/carmonalab
At Ludwig Cancer Research Lausanne and Department of Oncology, University of Lausanne & Swiss Institute of Bioinformatics
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