We have developed a single cell pipeline which is a totally automated platform that is able to take raw input data files and perform the preprocessing, data normalization, quality control to final visualization and annotation of clusters. The information and instructions to use our tool are readily available with comprehensive vignettes and tutorials being currently developed.
We currently provide two modalities for employing the tool: Single Sample and Two Sample. The pipeline is entirely automated and only requires single cells data. While the pipeline does do its own quality assurance prior to analysis, we recommend using filtered, quality data for better results. Please feel free to contact us for more information or assistance in using the pipeline. More details can be found on the Tool Description and Usage page.
We estimate the Clonal Expansion Index (CEI) to measure the relative change in clonotypes between samples of a single individual from different time points, for example, two months after treatment vs. pre-treatment. CEI captures all the expansions for both CD4+ and CD8+ T-cell receptors. Additional filters for labeled TCRs can be applied to capture changes in specific cell populations.
We have developed a single cell pipeline which is a totally automated platform that is able to take raw input data files and perform the preprocessing, data normalization, quality control to final visualization and annotation of clusters. The information and instructions to use our tool are readily available with comprehensive vignettes and tutorials being currently developed.
We currently provide two modalities for employing the tool: Single Sample and Two Sample. The pipeline is entirely automated and only requires single cells data. While the pipeline does do its own quality assurance prior to analysis, we recommend using filtered, quality data for better results. Please feel free to contact us for more information or assistance in using the pipeline. More details can be found on the Tool Description and Usage page.
We estimate the Clonal Expansion Index (CEI) to measure the relative change in clonotypes between samples of a single individual from different time points, for example, two months after treatment vs. pre-treatment. CEI captures all the expansions for both CD4+ and CD8+ T-cell receptors. Additional filters for labeled TCRs can be applied to capture changes in specific cell populations.
