From 3fa44dc02de5539d714f55cd4e8ead73edcfd0d6 Mon Sep 17 00:00:00 2001 From: Lorin Crawford Date: Wed, 28 Feb 2024 21:33:36 -0500 Subject: [PATCH] Update README.md --- README.md | 8 -------- 1 file changed, 8 deletions(-) diff --git a/README.md b/README.md index b1a2186..b5c0887 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,12 @@ # callback (Calibrated Clustering via Knockoffs) - [![R CMD check](https://github.com/lcrawlab/callback/actions/workflows/check-standard.yml/badge.svg)](https://github.com/lcrawlab/callback/actions/workflows/check-standard.yml) [![Docker Image CI](https://github.com/lcrawlab/callback/actions/workflows/docker-image.yml/badge.svg)](https://github.com/lcrawlab/callback/actions/workflows/docker-image.yml) - ## Introduction Standard single-cell RNA-sequencing (scRNA-seq) pipelines nearly always include unsupervised clustering as a key step in identifying biologically distinct cell types. A follow-up step in these pipelines is to test for differential expression between the identified clusters. When algorithms over-cluster, downstream analyses will produce inflated P-values resulting in increased false discoveries. Here, we present `callback` (Calibrated Clustering via Knockoffs): a new method for protecting against over-clustering by controlling for the impact of double-dipping. Importantly, our approach can be applied to any clustering algorithm (implemented here are the Louvain, Leiden, K-means, and hierarchical clustering algorithms). `callback` provides state-of-the-art clustering performance and can rapidly analyze large-scale scRNA-seq studies, even on a personal laptop. - ## Installation You can install the lastest development version by using the [devtools](https://CRAN.R-project.org/package=devtools) library. To install this package with devtools, use this command: @@ -18,7 +15,6 @@ You can install the lastest development version by using the [devtools](https:// devtools::install_github("lcrawlab/callback") ``` - ## Tutorial ```r @@ -27,7 +23,6 @@ library(SeuratData) library(callback) - set.seed(123) # load pbmc3k dataset @@ -64,6 +59,3 @@ A. DenAdel, M. Ramseier, A. Navia, A. Shalek, S. Raghavan, P. Winter, A. Amini, ## Questions and Feedback For questions or concerns with `callback`, please contact [Alan DenAdel](mailto:alan_denadel@brown.edu) or [Lorin Crawford](lcrawford@microsoft.com). Any feedback on the software, manuscript, and tutorials is appreciated. - - -