scglue.genomics

基因组学相关的操作

函数

cis_regulatory_ranking	Generate cis-regulatory ranking between genes and transcription factors
dist_power_decay	Distance-based power decay weight, computed as \(w = {\left( \frac {d + 1000} {1000} \right)} ^ {-0.75}\)
ens_trim_version	Trim version suffix from Ensembl ID
get_chr_len_from_fai	Get chromosome length information from fasta index file
interval_dist	Compute distance and relative position between two bed intervals
read_bed	Read BED file
read_ctx_grn	Read pruned TF-target GRN as generated by pyscenic ctx
read_gtf	Read GTF file
regulatory_inference	Regulatory inference based on feature embeddings
rna_anchored_guidance_graph	Build guidance graph anchored on RNA genes
rna_anchored_prior_graph	Deprecated, please use rna_anchored_guidance_graph() instead
window_graph	Construct a window graph between two sets of genomic features, where features pairs within a window size are connected.
write_links	Export regulatory graph into a links file
write_scenic_feather	Write cis-regulatory ranking to a SCENIC-compatible feather file

类

Bed	BED format data frame
Gtf	GTF format data frame