In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

This vignette demonstrates the import of alevin quantified counts into Seurat. Commands and parameters are based off of the alevin tutorial. If you use alevin in your work, please cite:

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery & Rob Patro

Genome Biology, 2019.

doi: 10.1186/s13059-019-1670-y

GitHub: https://github.com/COMBINE-lab/salmon

knitr::opts_chunk$set(
  tidy = TRUE,
  tidy.opts = list(width.cutoff = 95),
  message = FALSE,
  warning = FALSE
)

Prerequisites to install:

• SeuratWrappers
• tximport

library(SeuratWrappers)
library(tximport)

{.tabset .tabset-pills}

Import alevin quantified counts

pbmc <- ReadAlevin("~/alevin_out/alevin/quants_mat.gz")

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.