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README.md
# scRepertoire #### A toolkit for single-cell immune profiling <img align="right" src="https://github.com/ncborcherding/ncborcherding.github.io/blob/master/images/hex_sticker_v2.png" width="305" height="352"> ### Introduction Single-cell sequencing is an emerging technology in the field of immunology and oncology that allows researchers to couple RNA quantification and other modalities, like immune cell receptor profiling at the level of an individual cell. A number of workflows and software packages have been created to process and analyze single-cell transcriptomic data. These packages allow users to take the vast dimensionality of the data generated in single-cell-based experiments and distill the data into novel insights. Unlike the transcriptomic field, there is a lack of options for software that allow for single-cell immune receptor profiling. Enabling users to easily combine RNA and immune profiling, scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat R package. ### Wrapper Functions scRepertoire v1.0.2 has the functionality of the [powerTCR](https://github.com/hillarykoch/powerTCR) approach to comparing clone size distribution, [please cite](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006571) the manuscript if using the ```clonesizeDistribution()``` function. In addition, we recently added the [Startrac](https://github.com/Japrin/STARTRAC) clonotype metrics, if using the ```StartracDiversity()``` please read and cite [the accompanying article](https://www.nature.com/articles/s41586-018-0694-x). ### Installation ``` devtools::install_github("ncborcherding/scRepertoire") ``` #### Most up-to-date version We are working on constantly improving the scRepertoire package - these improvements can be found under the "dev" branch. These changes will be incorporated into the main branch as they are tested more throughly. ``` devtools::install_github("ncborcherding/scRepertoire@dev") ``` #### Bioconductor [scRepertoire](https://www.bioconductor.org/packages/release/bioc/html/scRepertoire.html) is now on Bioconductor. Use the link to find out more information. scRepertoire (for R v4 or greater) can be installed from Bioconductor with: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("scRepertoire") ``` ### Getting Data Unfortunately, Github limits the size of individual files. In order to access the seurat object paired with scRepetoire please download the .rda from [here](https://drive.google.com/open?id=1np-EzG7U9W_Fz_SchBrsAhtqE3_rB_H9). ### Learning To Use scRepertoire Vignette available [here](https://ncborcherding.github.io/vignettes/vignette.html), includes almost 13,000 T cells across 3 patients with renal clear cell carcinoma. ### Please Cite Feel free to use, edit, modify scRepertoire, but if you do, please cite the [manuscript](https://f1000research.com/articles/9-47/v1). ### Contact Questions, comments, suggestions, please feel free to contact Nick Borcherding via this repository, [email](mailto:ncborch@gmail.com), or using [twitter](https://twitter.com/theHumanBorch). ### More Information On VDJ Biology Our publication is limited in scope and size and we were unable to review VDJ biology and issues relevant to high-throuhput immune receptor profiling. If you are interested in the biology of the process, please refer to the excellent reviews from [Jahong Ji](https://www.nature.com/articles/nri2941) and [Frederick Alt](https://www.cell.com/fulltext/S0092-8674(04)00039-X). Additionally, the complexities of sequencing and quantifications of VDJs are discussed [here.](https://www.nature.com/articles/nprot.2018.021?)