EPIC.package: EPIC: a package to Estimate the Proportion of Immune and...
In GfellerLab/EPIC: Estimate the Proportion of Immune and Cancer cells
EPIC.package R Documentation
EPIC: a package to Estimate the Proportion of Immune and Cancer cells from
tumor gene expression data.
Description
EPIC package provides the function and cell reference profiles to
estimate the proportion of immune, stromal, endothelial and cancer or other
cells from bulk gene expression data.
Details
See the package vignette (command in the R console: vignette("EPIC") )
and function definitions below.
EPIC functions
EPIC is the main function to call to estimate the
various cells proportions from a bulk sample.
Included datasets
BRef: reference profiles from circulating immune cells.
TRef: reference profiles from tumor infiltrating non-malignant
cells obtained from single cell data of melanoma patients.
melanoma_data: example dataset containing data from lymph nodes
from patients with metastatic melanoma.
mRNA_cell_default: values of mRNA per cell for the main cell
types.
References
Racle, J., Jonge, K. de, Baumgaertner, P., Speiser, D.E., and
Gfeller, D. (2017). Simultaneous enumeration of cancer and immune cell
types from bulk tumor gene expression data. eLife Sciences, 6, e26476
(https://elifesciences.org/articles/26476)
Authors
Julien Racle <julien.racle@unil.ch> and David Gfeller
<david.gfeller@unil.ch>.
GfellerLab/EPIC documentation built on July 22, 2023, 2:06 a.m.
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| EPIC.package | R Documentation |
EPIC: a package to Estimate the Proportion of Immune and Cancer cells from tumor gene expression data.
Description
EPIC package provides the function and cell reference profiles to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data.
Details
See the package vignette (command in the R console: vignette("EPIC") ) and function definitions below.
EPIC functions
EPIC is the main function to call to estimate the
various cells proportions from a bulk sample.
Included datasets
BRef: reference profiles from circulating immune cells.
TRef: reference profiles from tumor infiltrating non-malignant
cells obtained from single cell data of melanoma patients.
melanoma_data: example dataset containing data from lymph nodes
from patients with metastatic melanoma.
mRNA_cell_default: values of mRNA per cell for the main cell
types.
References
Racle, J., Jonge, K. de, Baumgaertner, P., Speiser, D.E., and Gfeller, D. (2017). Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. eLife Sciences, 6, e26476 (https://elifesciences.org/articles/26476)
Authors
Julien Racle <julien.racle@unil.ch> and David Gfeller <david.gfeller@unil.ch>.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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