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Cell Ranger — 10x Genomics official analysis pipeline for Chromium single-cell and spatial data. Performs FASTQ generation, alignment (STAR-based), barcode processing, UMI counting, V(D)J assembly, Fe
Use with AI
Install the MCP server or CLI to instantly fetch Cell Ranger documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/cellranger
Use when working with Conos (Clustering On Network Of Samples), the R package for joint analysis of multiple single-cell RNA-seq and spatial transcriptomics datasets. Covers building joint k-nearest-n
2 shared topics • 1 shared operation
DRIMSeq is a Bioconductor R package for Differential Transcript Usage (DTU) analysis using a Dirichlet-multinomial distribution to model transcript-level count proportions. Tests whether relative tran
2 shared topics • 1 shared operation
rMATS (Replicate Multivariate Analysis of Transcript Splicing) — statistical tool for detecting differential alternative splicing from RNA-seq data. Identifies five splicing event types: skipped exon
2 shared topics • 1 shared operation
STdeconvolve — reference-free cell-type deconvolution for spatial transcriptomics using Latent Dirichlet Allocation (LDA). Decomposes multi-cellular spatial pixels into cell-type proportions and trans
2 shared topics • 1 shared operation
Trinity — de novo transcriptome assembler for RNA-seq data. Reconstructs full-length transcript isoforms without a reference genome using three sequential modules: Inchworm (greedy k-mer assembly), Ch
2 shared topics • 1 shared operation