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Cell Ranger specifications


Unique identifier OMICS_15846
Name Cell Ranger
Alternative name Cell Ranger Single-Cell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes




No version available


  • person_outline Cell Ranger Team

Additional information


Publication for Cell Ranger

Cell Ranger citations


Single Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis

Cell Rep
PMCID: 5908225
PMID: 29590628
DOI: 10.1016/j.celrep.2018.03.010
call_split See protocol

[…] We used Cell Ranger version 1.3.1 (10x Genomics) to process raw sequencing data and Cell Ranger R kit version 2.0.0 and Seurat suite version 2.0.0 (; ) for downstream analysis. For clustering, principal-compo […]


Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single Cell RNA Sequencing

PMCID: 5850328
PMID: 29535194
DOI: 10.1128/mBio.00013-18

[…] We used Cell Ranger () software with the default settings to process the FASTQ files. The reference was created with the mkref Cell Ranger command, based on the Cell Ranger human hg19 reference and TB40E (NCB […]


Combinatory use of distinct single cell RNA seq analytical platforms reveals the heterogeneous transcriptome response

Sci Rep
PMCID: 5823859
PMID: 29472726
DOI: 10.1038/s41598-018-21161-y
call_split See protocol

[…] ere prepared according to the manufacturer’s instructions. We used a HiSeq. 2500 Rapid run platform to generate 50-base paired-end reads. RNA-seq tags from the Chromium experiments were aligned using Cell Ranger software. Using our Perl script, sequences with low quality and PCR duplicates were removed. Trimmed reads were sorted based on their cell barcode, and only cell barcodes with >5 k tags we […]


Regulatory Architecture of the LβT2 Gonadotrope Cell Underlying the Response to Gonadotropin Releasing Hormone

PMCID: 5816955
PMID: 29487567
DOI: 10.3389/fendo.2018.00034

[…] Single-cell RNA-seq data were processed using the Cell Ranger pipeline v1.3, which provides a data matrix of expression for all genes and all cells. Differentially expressed genes were analyzed using the sSeq method (), as implemented in the R packag […]


Single cell RNA sequencing of stem cell derived retinal ganglion cells

Sci Data
PMCID: 5810423
PMID: 29437159
DOI: 10.1038/sdata.2018.13

[…] s well as a tab separated matrix of Transcripts Per Million for each cell passing quality control filtering. BAM files can be generated by using the supplied repository to process the FASTQ files via Cell Ranger. […]


PIVOT: platform for interactive analysis and visualization of transcriptomics data

BMC Bioinformatics
PMCID: 5756333
PMID: 29304726
DOI: 10.1186/s12859-017-1994-0

[…] Read counts obtained from RNA-Seq quantification tools such as HTSeq [] or featureCounts [] can be directly uploaded into PIVOT as text, csv or Excel files. Data generated using the 10× Genomics Cell Ranger pipeline can also be readily read in and processed by PIVOT. PIVOT automatically performs user selected data transformations including normalization, log transformation, or standardization […]


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