cellity: Quality Control for Single-Cell RNA-seq Data

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A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.

Author
Tomislav Illicic, Davis McCarthy
Date of publication
None
Maintainer
Tomislav Ilicic <ti243@cam.ac.uk>
License
GPL (>= 2)
Version
1.2.0

View on Bioconductor

Man pages

assess_cell_quality_PCA
ASSESS CELL QUALITY USING PCA AND OUTLIER DETECTION
assess_cell_quality_SVM
Assess quality of a cell - SVM version
cellity-package
Quality Control for Single-Cell RNA-seq Data
extract_features
Extracts biological and technical features for given dataset
extra_human_genes
Additional human genes that are used in feature extraction
extra_mouse_genes
Additional mouse genes that are used in feature extraction
feature_generation
Helper Function to create all features
feature_info
Information which genes and GO categories should be included...
mES1_features
Real test dataset containing all and common features from the...
mES1_labels
Real test dataset containing annotation of cells
multiplot
Internal multiplot function to combine plots onto a grid
normalise_by_factor
Internal function to normalize by library size
param_mES_all
Parameters used for SVM classification
param_mES_common
Parameters used for SVM classification
plot_pca
Plots PCA of all features. Colors high and low quality cells...
sample_counts
Sample gene expression data containing 40 cells
sample_stats
Sample read statistics data containing 40 cells
simple_cap
Converts all first letters to capital letters
sum_prop
Sums up normalised values of genes to groups.
training_mES_features
Original training dataset containing all and common features...
training_mES_labels
Original training dataset containing annotation of cells
uni.plot
Internal function to detect outliers from the mvoultier...

Files in this package

cellity/DESCRIPTION
cellity/NAMESPACE
cellity/R
cellity/R/cellity-package.R
cellity/R/data.R
cellity/R/filter_low_qual_cells.R
cellity/README.md
cellity/build
cellity/build/vignette.rds
cellity/data
cellity/data/extra_human_genes.RData
cellity/data/extra_mouse_genes.RData
cellity/data/feature_info.RData
cellity/data/mES1_features.RData
cellity/data/mES1_labels.RData
cellity/data/param_mES_all.RData
cellity/data/param_mES_common.RData
cellity/data/sample_counts.RData
cellity/data/sample_stats.RData
cellity/data/training_mES_features.RData
cellity/data/training_mES_labels.RData
cellity/inst
cellity/inst/NEWS.Rd
cellity/inst/cellity_overview.png
cellity/inst/doc
cellity/inst/doc/cellity_vignette.R
cellity/inst/doc/cellity_vignette.Rmd
cellity/inst/doc/cellity_vignette.html
cellity/man
cellity/man/assess_cell_quality_PCA.Rd
cellity/man/assess_cell_quality_SVM.Rd
cellity/man/cellity-package.Rd
cellity/man/extra_human_genes.Rd
cellity/man/extra_mouse_genes.Rd
cellity/man/extract_features.Rd
cellity/man/feature_generation.Rd
cellity/man/feature_info.Rd
cellity/man/mES1_features.Rd
cellity/man/mES1_labels.Rd
cellity/man/multiplot.Rd
cellity/man/normalise_by_factor.Rd
cellity/man/param_mES_all.Rd
cellity/man/param_mES_common.Rd
cellity/man/plot_pca.Rd
cellity/man/sample_counts.Rd
cellity/man/sample_stats.Rd
cellity/man/simple_cap.Rd
cellity/man/sum_prop.Rd
cellity/man/training_mES_features.Rd
cellity/man/training_mES_labels.Rd
cellity/man/uni.plot.Rd
cellity/tests
cellity/tests/testthat
cellity/tests/testthat.R
cellity/tests/testthat/test-assess_cell_quality_SVM.R
cellity/tests/testthat/test-extract_features.R
cellity/vignettes
cellity/vignettes/cellity_vignette.Rmd