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liayson (version 1.0.5)

Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes

Description

Given an RNA-seq derived cell-by-gene matrix and an DNA-seq derived copy number segmentation, LIAYSON predicts the number of clones present in a tumor, their size, the copy number profile of each clone and the clone membership of each single cell (Andor, N. & Lau, B., et al. (2018) ).

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install.packages('liayson')

Monthly Downloads

35

Version

1.0.5

License

GPL-2

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Repository

https://github.com/noemiandor/liayson

Maintainer

Noemi Andor

Last Published

September 29th, 2022

Functions in liayson (1.0.5)

Grouping cells into clones.

Gene-by-cell matrix of expression from NCI-N87 cell line.

aggregateSegmentExpression

Aggregating genes across copy number segments.

saveClusteredCells

Saving clones to user-defined output.

assignCellsToClusters

Assigns cells to previously defined clones.

Clone size resolution.

Segment-by-cell matrix of copy number states from NCI-N87 cell line.

Segment-by-cell matrix of expression from NCI-N87 cell line.

segmentExpression2CopyNumber

Bulk copy number profile of NCI-N87 cell line.