OutputType

class alphagenome.models.v2.dna_output.OutputType(value)

Enumeration of all the available types of outputs.

ATAC

ATAC-seq tracks capturing chromatin accessibility.

CAGE

CAGE (Cap Analysis of Gene Expression) tracks capturing gene expression.

DNASE

DNase I hypersensitive site tracks capturing chromatin accessibility.

RNA_SEQ

RNA sequencing tracks capturing gene expression.

CHIP_HISTONE

ChIP-seq tracks capturing histone modifications.

CHIP_TF

ChIP-seq tracks capturing transcription factor binding.

SPLICE_SITES

Condition-specific splice site classification probabilities (donor, acceptor, and non-splice-site padding).

SPLICE_SITE_USAGE

Splice site usage tracks capturing the fraction of the time that each splice site is used.

SPLICE_JUNCTIONS

Splice junction tracks capturing split read RNA-seq counts for each junction.

CONTACT_MAPS

Relative 3D chromatin contact frequencies (observed-over-expected).

SC_GENE_EXPRESSION

Protocol-specific single-cell RNA-seq expression tracks (in CPM) across training sequencing technologies, supported with both reference conditions (condition=) and expression conditioning (cell_conditioning=).

SC_ATAC

ATAC-seq tracks capturing single-cell chromatin accessibility.

SC_GENE_EXPRESSION_DENOISED

Denoised single-cell gene expression tracks (one channel per strand, in CPM) predicted from human expression conditioning inputs (cell_conditioning=).

CELL_EMBEDDINGS

Learned low-dimensional cell state representations derived from single-cell gene expression profiles.

METHYLATION

DNA methylation tracks capturing CpG methylation probabilities.