ProjecTILs_CaseStudies

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ProjecTILs_CaseStudies

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A repository of case studies using ProjecTILs

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# ProjecTILs Case Studies

We will be posting here interesting/instructive case studies of single-cell data analysis using [ProjecTILs](https://github.com/carmonalab/ProjecTILs):

## 1. [MC38 TILs with clonotype analysis](https://carmonalab.github.io/ProjecTILs_CaseStudies/Xiong19_TCR.html)

In [this case study](https://carmonalab.github.io/ProjecTILs_CaseStudies/Xiong19_TCR.html), 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](https://carmonalab.github.io/ProjecTILs_CaseStudies/SadeFeldman_ortho.html)

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](https://carmonalab.github.io/ProjecTILs_CaseStudies/Sandu_LCMV.html)

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](https://carmonalab.github.io/ProjecTILs_CaseStudies/Bassez_BC.html)

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](https://carmonalab.github.io/ProjecTILs_CaseStudies/Kunzli.html)

A case study of projection of virus-specific CD4+ T cells in late acute infection.

## 6. [Detecting novel/unrepresented cell states](https://carmonalab.github.io/ProjecTILs_CaseStudies/novelstate.html)

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](https://carmonalab.github.io/ProjecTILs_CaseStudies/Snell.html)

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](https://carmonalab.github.io/ProjecTILs_CaseStudies/Brown2019_humanDC.html)

Projection of human DCs from spleen from the study of Brown et al. *Cell* (2019)

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