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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.

gfainject

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

lollipop_wolverine

long-read_chip-enrichment

mango

mapgl

Phylogenetic mapping of DNA element gain and loss using multiple outgroup species.

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

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.

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.

sample_data

score_motifs

Calculate log-odds scores for transcription factor binding motifs.

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