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posted on 2022-12-19, 00:37 authored by Yang LiaoYang Liao, Dinesh RaghuDinesh Raghu, Bhupinder PalBhupinder Pal, Lisa MielkeLisa Mielke, Wei ShiWei Shi

This page includes the data and code necessary to reproduce the results of the following paper:

Yang Liao, Dinesh Raghu, Bhupinder Pal, Lisa Mielke and Wei Shi. cellCounts: fast and accurate quantification of 10x Chromium single-cell RNA sequencing data. Under review.

A Linux computer running an operating system of CentOS 7 (or later) or Ubuntu 20.04 (or later) is recommended for running this analysis. The computer should have >2 TB of disk space and >64 GB of RAM. The following software packages need to be installed before running the analysis. Software executables generated after installation should be included in the $PATH environment variable.

Reference packages generated by 10x Genomics are also required for this analysis and they can be downloaded from the following link (2020-A version for individual human and mouse reference packages should be selected):

After all these are done, you can simply run the shell script ‘test-all-new.bash’ to perform all the analyses carried out in the paper. This script will automatically download the mixture scRNA-seq data from the SRA database, and it will output a text file called ‘test-all.log’ that contains all the screen outputs and speed/accuracy results of CellRanger, STARsolo and cellCounts.



  • School of Cancer Medicine