التفاصيل البيبلوغرافية
| العنوان: |
cellCounts |
| المؤلفون: |
Yang Liao (9001520), Dinesh Raghu (9493037), Bhupinder Pal (9493058), Lisa Mielke (9493028), Wei Shi (9483452) |
| سنة النشر: |
2022 |
| مصطلحات موضوعية: |
Bioinformatics, RNA sequencing, Single cell, Gene expression, Quantification, Software |
| الوصف: |
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. R (v4.0.0 or newer) https://www.r-project.orgTest/ Rsubread (v2.12.2 or newer) http://bioconductor.org/packages/3.16/bioc/html/Rsubread.htmlTest CellRanger (v6.0.1) https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcomeTest STARsolo (v2.7.10a) https://github.com/alexdobin/STARTest sra-tools (v2.10.0 or newer) https://github.com/ncbi/sra-toolsTest Seurat (v3.0.0 or newer) https://satijalab.org/seuratTest/ edgeR (v3.30.0 or newer) https://bioconductor.org/packages/edgeRTest/ limma (v3.44.0 or newer) https://bioconductor.org/packages/limmaTest/ mltools (v0.3.5 or newer) https://cran.r-project.org/web/packages/mltools/index.htmlTest 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): https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latestTest 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. |
| نوع الوثيقة: |
dataset |
| اللغة: |
unknown |
| العلاقة: |
https://figshare.com/articles/dataset/The_data_set_for_testing_cellCounts/21588276Test |
| DOI: |
10.26181/21588276.v3 |
| الإتاحة: |
https://doi.org/10.26181/21588276.v3Test |
| حقوق: |
CC BY 4.0 |
| رقم الانضمام: |
edsbas.7DC3CB0 |
| قاعدة البيانات: |
BASE |
