Adam Diehl's repositories
mapLoopLoci
Maps loop loci from ChIA-pet/Hi-C/etc. experiments across samples, which may be different species and/or cell types. Uses the bnMapper algorithm for cross-species mappings.
MapGL_analysis
Scripts and data sources to reproduce results presented in "MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony." Diehl AG, and Boyle AP. BMC Bioinformatics. 2020
score_motifs
Calculate log-odds scores for transcription factor binding motifs.
bioconda-recipes
Conda recipes for the bioconda channel.
ENCODE-API-Apps
Scripts for the Deciphering ENCODE examples
ENCODEdBTools
Tools for getting data from the ENCODE portal API
exact_grep
Simple word match utility to find lines of text in a file containing an exact word match.
graph_peak_caller
ChIP-seq peak caller for reads mapped to a graph-based reference genome
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
minigraph-cactus-nf
a nextflow pipeline for creating a pangenome with minigraph-cactus
novo2sam
Tool for converting novoalign output to sam
repeatMaskerUtils
Utilities for working with RepeatMasker Libraries and Annotations.
te_chia-pet_analysis
Analysis steps for TE-CTCF enrichments and overlaps with ChIA-PET datasets in human and mouse.
TRACE
TRACE: HMM for DNase footprinting and motif matching