Package 'cbmc'

Title: Raw and Processed Matrices of the CITE-seq CBMC Dataset
Description: Provides expression matrices from 8,617 cord blood mononuclear cells generated with CITE-seq. The CITE-seq technique and CBMC dataset are described in <doi:10.1038/nmeth.4380>
Authors: Paul Hoffman [aut, cre]
Maintainer: Paul Hoffman <[email protected]>
License: CC BY 4.0
Version: 0.1.0
Built: 2025-01-08 16:34:49 UTC
Source: https://github.com/mojaveazure/cbmc

Help Index

CBMC

Description

CITE-seq data from 8,617 cord blood mononuclear cells (CBMC); the dataset is split into two matrices: one for the RNA expression data and one for the cell-surface protein (ADT) expression data

Usage

cbmc.rna

cbmc.adt

Format

cbmc.rna: A dgCMatrix with the raw RNA expression data

cbmc.adt: A dgCMatrix with the raw ADT expression data

Source

NIH GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866

Nature Methods article: http://www.nature.com/nmeth/journal/v14/n9/full/nmeth.4380.html

References

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 2017 Sep;14(9):865-868.

CBMC Annotations

Description

Cell-type annotations for the CBMC dataset, as generated using the Seurat standard workflow

Usage

cbmc.annotations

Format

A data frame with annotations for the CBMC dataset; the data frame contains the following columns as factors:

  • “rna_annotations”: annotations derived from the RNA expression matrix

  • “protein_annotations”: annotations derived from the ADT expression matrix; note some values are NA

Cell barcodes are present in the row names of the data frame

CBMC Normalized

Description

Normalized versions of the CBMC dataset using standard Seurat normalization techniques. The collapsed RNA expression matrix is normalized using log-normalization. The ADT expression matrix is normalized using centered log ratio normalization

Usage

cbmc.rna.norm

cbmc.adt.norm

Format

cbmc.rna.norm: A dgCMatrix with the log-normalized RNA expression data

cbmc.adt.norm: A dgCMatrix with the CLR-normalized ADT expression data

Source

The Seurat multimodal vignette

NIH GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866

Nature Methods article: http://www.nature.com/nmeth/journal/v14/n9/full/nmeth.4380.html

See Also

Seurat::NormalizeData() for details on log- and CLR-normalization

CBMC Collapsed

Description

Species-collapsed version of the CBMC dataset. Species-collapsing consists of:

  • stripping the prefix “HUMAN_” from all feature names where it is present

  • determining the top 100 negative control features prefixed with “MOUSE_” and removing all other negative control features

For the CBMC dataset, only the RNA matrix needs to be collapsed

Usage

cbmc.rna.collapsed

Format

A dgCMatrix with the species-collapsed RNA expression matrix

Source

The Seurat multimodal vignette

NIH GEO accession: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866

Nature Methods article: http://www.nature.com/nmeth/journal/v14/n9/full/nmeth.4380.html

See Also

Seurat::CollapseSpeciesExpressionMatrix()