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chip_db

A lightweight database to deal with many ChIP-seq or similar whole-genome tracks. Allows for constant-time access of any position along the genome.

chromactivity

ChromActivity is a computational framework for the annotation of regulatory activity genomewide, through integration of data from epigenomic maps and multiple functional characterization assays.

chromgene

Gene-Based Modelling of Epigenomic Data

chromtime

Modeling Spatio-temporal Dynamics of Chromatin Marks

cmimpute

Cross-species and tissue imputation of species-level DNA methylation samples across mammalian species.

cnep

Constrained Non-Exonic Predictor (CNEP) provides a score of evidence that each base of the genome in a constrained non-exonic base from information within large-scale collections of epigenomic and transcription factor binding data.

conshmm

conshmm_cov

csrep

differential and summary chromatin states

ensas

Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence and sex information

epivarindividuals

ernstlab.github.io

full_stack_chromhmm_annotations

Data of genome annotation from full-stack ChromHMM model trained with 1032 datasets from 127 reference epigenomes

inpsyght_states

ChromHMM and ConsHMM state-based analysis for InPSYght samples

lecif

Learning a genome-wide score of conservation at the functional genomics level between human and mouse

lepae

mouse_fullstack_annotations

mouse_fullStack_annotations

sharprseq

x-cnn

Computational method for fine-mapping chromatin interactions, e.g., Hi-C