SingCellaR: The SingCellaR Class The SingCellaR object stores all of...
In supatt-lab/SingCellaR: SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data
SingCellaR R Documentation
The SingCellaR Class
The SingCellaR object stores all of information required for the analyses.
The followings are the description of slots.
Description
The SingCellaR Class
The SingCellaR object stores all of information required for the analyses.
The followings are the description of slots.
Slots
dir_path_10x_matrixis the path to the directory that contains 'barcodes.tsv','genes.tsv', and 'matrix.mtx' matrices generated by the 10x Genomics Cell Ranger software.
sample_uniq_idis the unique name of the sample.
genes.infocontains the dataframe of gene information.
meta.datacontains the dataframe of cells information.
regressout_matrixcontain the normalised expression matrix (in log1p scale) that was regressed out the confounders.
pca.resultcontains the PCA analysis result from the IRLBA package
nnmf.resultcontains the NNMF analysis result.
tsne.resultcontains the TSNE analysis result.
diffusionmap.resultcontains the diffusionmap analysis result.
umap.resultcontains the UMAP analysis result.
lsi.resultcontans the LSI analysis result.
knn_graph.graphcontains the igraph object.
knn_graph.layoutcontains the graph layout.
knn_graph.kmeans.clustercontains the k-means clustering results derived from the 3D KNN graph layout.
igraph.graphcontains the igraph object.
fa2_graph.layoutcontains the graph layout generated by the ForceAtlas2 software.
sc.clusterscontains the cluster information.
marker.genescontains the list of identified marker genes per each cluster.
GenesExpressionMatrixFilecontains the file name of gene expression
CellsMetaDataFilecontains the dataframe of TARGET-seq cell information.
dir_path_SingCellR_object_filescontains the directory name that contains SingCellaR objects from multiple individual sample.
SingCellR_object_filescontains the vector of individual object names.
Variable.genescontains the list of identified variable genes.
SingCellaR.individual.clusterscontains the list of identified clusters information per individual sample.
GSEA.aligned.clusterscontains the list of GSEA results per indentified clusters in individual sample.
Scanorama.integrative.matrixcontains Scannorama integrative matrix.
Harmony.embeddingscontains Harmony integrative embeddings.
SupervisedHarmony.embeddingscontains SupervisedHarmony integrative embeddings.
Liger.embeddingscontains Liger integrative embeddings.
Seurat.embeddingscontains Seurat integrative embeddings.
Combat.embeddingscontains Combat integrative embeddings.
supatt-lab/SingCellaR documentation built on Aug. 24, 2023, 5:49 p.m.
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| SingCellaR | R Documentation |
The SingCellaR Class The SingCellaR object stores all of information required for the analyses. The followings are the description of slots.
Description
The SingCellaR Class The SingCellaR object stores all of information required for the analyses. The followings are the description of slots.
Slots
dir_path_10x_matrixis the path to the directory that contains 'barcodes.tsv','genes.tsv', and 'matrix.mtx' matrices generated by the 10x Genomics Cell Ranger software.
sample_uniq_idis the unique name of the sample.
genes.infocontains the dataframe of gene information.
meta.datacontains the dataframe of cells information.
regressout_matrixcontain the normalised expression matrix (in log1p scale) that was regressed out the confounders.
pca.resultcontains the PCA analysis result from the IRLBA package
nnmf.resultcontains the NNMF analysis result.
tsne.resultcontains the TSNE analysis result.
diffusionmap.resultcontains the diffusionmap analysis result.
umap.resultcontains the UMAP analysis result.
lsi.resultcontans the LSI analysis result.
knn_graph.graphcontains the igraph object.
knn_graph.layoutcontains the graph layout.
knn_graph.kmeans.clustercontains the k-means clustering results derived from the 3D KNN graph layout.
igraph.graphcontains the igraph object.
fa2_graph.layoutcontains the graph layout generated by the ForceAtlas2 software.
sc.clusterscontains the cluster information.
marker.genescontains the list of identified marker genes per each cluster.
GenesExpressionMatrixFilecontains the file name of gene expression
CellsMetaDataFilecontains the dataframe of TARGET-seq cell information.
dir_path_SingCellR_object_filescontains the directory name that contains SingCellaR objects from multiple individual sample.
SingCellR_object_filescontains the vector of individual object names.
Variable.genescontains the list of identified variable genes.
SingCellaR.individual.clusterscontains the list of identified clusters information per individual sample.
GSEA.aligned.clusterscontains the list of GSEA results per indentified clusters in individual sample.
Scanorama.integrative.matrixcontains Scannorama integrative matrix.
Harmony.embeddingscontains Harmony integrative embeddings.
SupervisedHarmony.embeddingscontains SupervisedHarmony integrative embeddings.
Liger.embeddingscontains Liger integrative embeddings.
Seurat.embeddingscontains Seurat integrative embeddings.
Combat.embeddingscontains Combat integrative embeddings.
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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