From 83ddf93ef1a1edd7b5617564ce3e1ce3e4a61e87 Mon Sep 17 00:00:00 2001 From: Rohit Farmer Date: Mon, 17 Oct 2022 12:21:10 -0400 Subject: [PATCH] Update README.md --- README.md | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 7a0c38a..2a1e75a 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ # Google Colab interface to HDStIM (High Dimensional Stimulation Immune Mapping) ## Abstract -HDStIM is a method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots. Documentation website: https://niaid.github.io/HDStIM/ Source code: https://github.com/niaid/HDStIM/ CRAN page: https://cran.r-project.org/package=HDStIM +HDStIM is a method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots. ![](ColabHDStIM.png) *Figure 1. Schematic outline for the use of multiple response markers by HDStIM to identify cells with a responding phenotype from unstimulated and stimulated experimental samples for a given stimulation - cell population combination.* ## Colab notebook -This notebook is an attempt to make it easier to use HDStIM. However, since it runs on [Google Colab](https://research.google.com/colaboratory/faq.html), it has its limitations. For example, uploading a large dataset is very slow and may not be straightforward. Also, the marker ranking function that utilizes multiple cores may be orders of magnitude slower than on a local machine with more than two cores. See the more information section at the bottom of the notebook on how to run this notebook locally (recommended). +This notebook is an attempt to make it easier to use HDStIM. However, since it runs on Google Colab, it has its limitations. For example, uploading a large dataset is very slow and may not be straightforward. Also, the marker ranking function that utilizes multiple cores may be orders of magnitude slower than on a local machine with more than two cores. See the more information section at the bottom of the notebook on how to run this notebook locally (recommended). | Notebook | Link | @@ -17,6 +17,11 @@ This notebook is an attempt to make it easier to use HDStIM. However, since it r *Note: Under default settings, the notebook should be able to run an example dataset.* ## Helpful links -1. [Google Colab Frequently Asked Questions](https://research.google.com/colaboratory/faq.html) -2. [Welcome to Colab!](https://colab.research.google.com/) -3. [Practical Introduction to Google Colab for Data Science (YouTube video)](https://www.youtube.com/watch?v=oCngVVBSsmA) \ No newline at end of file +1. HDStIM related + 1. Documentation website: [https://niaid.github.io/HDStIM/](https://niaid.github.io/HDStIM/) + 2. Source code: [https://github.com/niaid/HDStIM/](https://github.com/niaid/HDStIM/) + 3. CRAN page: [https://cran.r-project.org/package=HDStIM](https://cran.r-project.org/package=HDStIM) +2. Google colab related + 1. [Google Colab frequently asked questions](https://research.google.com/colaboratory/faq.html) + 2. [Welcome to Colab!](https://colab.research.google.com/) + 3. [Practical introduction to Google Colab for data science (YouTube video)](https://www.youtube.com/watch?v=oCngVVBSsmA) \ No newline at end of file