cellCounts

<p>This page includes the data and code necessary to reproduce the results of the following paper:</p> <p>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.</p> <p>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.</p> <ul> <li>R (v4.0.0 or newer)  <a href="https://www.r-project.org/" target="_blank">https://www.r-project.org/</a></li> <li>Rsubread (v2.12.2 or newer) <a href="http://bioconductor.org/packages/3.16/bioc/html/Rsubread.html" target="_blank">http://bioconductor.org/packages/3.16/bioc/html/Rsubread.html</a></li> <li>CellRanger (v6.0.1) <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome" target="_blank">https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome</a></li> <li>STARsolo (v2.7.10a) <a href="https://github.com/alexdobin/STAR" target="_blank">https://github.com/alexdobin/STAR</a></li> <li>sra-tools (v2.10.0 or newer) <a href="https://github.com/ncbi/sra-tools" target="_blank">https://github.com/ncbi/sra-tools</a></li> <li>Seurat (v3.0.0 or newer) <a href="https://satijalab.org/seurat/" target="_blank">https://satijalab.org/seurat/</a></li> <li>edgeR (v3.30.0 or newer)  <a href="https://bioconductor.org/packages/edgeR/" target="_blank">https://bioconductor.org/packages/edgeR/</a></li> <li>limma (v3.44.0 or newer)  <a href="https://bioconductor.org/packages/limma/" target="_blank">https://bioconductor.org/packages/limma/</a></li> <li>mltools (v0.3.5 or newer) <a href="https://cran.r-project.org/web/packages/mltools/index.html" target="_blank">https://cran.r-project.org/web/packages/mltools/index.html</a></li> </ul> <p>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):</p> <p><a href="https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest" target="_blank">https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest</a></p> <p>After all these are done, you can simply run the shell script ‘<strong>test-all-new.bash</strong>’ 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 ‘<strong>test-all.log</strong>’ that contains all the screen outputs and speed/accuracy results of CellRanger, STARsolo and cellCounts.</p>