Chunk #36 — Online Methods — Analysis — Motif and kmer similarity tSNE

Source

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Embedded

yes

Text

For performing motif similarity tSNE, motifs or kmers with variability below a certain threshold (1.5) were first removed from the bias corrected deviations matrix, which was then used as input to the Rtsne package 28 with perplexity parameter set to 15.