abundanceContig |
Demonstrate the relative abundance of clonotypes by group or sample. |
addVariable |
Adding variables after the combination of contigs. |
alluvialClonotypes |
Exploring interaction of clonotypes by seurat or SCE dynamics |
clonalDiversity |
Examine the clonal diversity of samples |
clonalHomeostasis |
Examining the clonal homeostasis |
clonalNetwork |
Visualize clonal network along reduced dimensions |
clonalOverlap |
Examining the clonal overlap between groups or samples |
clonalOverlay |
Visualize distribution of clonal frequency overlaid on dimensional reduction plots |
clonalProportion |
Examining the clonal space occupied by specific clonotypes |
clonesizeDistribution |
Hierarchical clustering of clonotypes on clonotype size and Jensen-Shannon divergence |
clonotypeBias |
Examine clonotype bias |
clusterTCR |
Clustering T cell receptors |
combineBCR |
Combining the list of B Cell Receptor contigs |
combineExpression |
Adding clonotype information to a Seurat or SCE object |
combineTCR |
Combining the list of T Cell Receptor contigs |
combineTRUST4 |
Combining the list of T or B cell Receptors from TRUST4 pipeline |
compareClonotypes |
Demonstrate the difference in clonal proportion between clonotypes |
contig_list |
A data set of T cell contigs as a list outputed from the filter_contig_annotation files. |
createHTOContigList |
Generate a contig list from a multiplexed experiment |
expression2List |
Allows users to take the meta data in Seurat/SCE and place it into a list that will work with all the functions |
getCirclize |
Generate data frame to be used with circlize R package to visualize clonotypes as a chord diagram. |
highlightClonotypes |
Highlighting specific clonotypes in Seurat |
lengthContig |
Demonstrate the distribution of lengths filtered contigs. |
loadContigs |
Loading the contigs derived from single-cell sequencing |
occupiedscRepertoire |
Visualize the number of single cells with clonotype frequencies by cluster |
quantContig |
Quantify the unique clonotypes in the filtered contigs. |
scatterClonotype |
Scatter plot comparing the expansion of two samples |
screp_example |
A seurat object of 1000 single T cells derived from 3 clear cell renal carcinoma patients. |
Startrac |
The Startrac Class |
Startrac-class |
The Startrac Class |
StartracDiversity |
Diversity indices for single-cell RNA-seq |
stripBarcode |
Removing any additional prefixes to the barcodes of filtered contigs. |
subsetContig |
Subset the product of combineTCR() combineBCR() or expression2List() |
vizGenes |
Visualizing the distribution of gene usage |