| RefPT | A set of genomic coordinates around which to pileup signal (.bam or some other genomic features captured by a .bed/.gff file) |
| PFM | position frequency matrix is related to the position weight matrix (see PWM) |
| PWM | position weight matrix that represents the sequence preference of some motif feature (see also PFM), also known as a PSSM or PSWM |
| ssTFs | sequence-specific transcription factors, or transcription factors that bind certain specific sequences |
| TF | transcription factor, or a protein that binds promoters and influences (directly or indirectly) transcriptional activity |
| TFBS | transcription factor binding site |
| target | usually refers to the protein target for some sort of enrichment assay (e.g. antibody target for a ChIP-seq dataset) |
| weblogos | a visual representation of a motif PWM or PFM |