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atacseq-snakemake

Standard Parker Lab ATAC-seq processing pipeline in Snakemake form

blacklist

Application for making ENCODE Blacklists

boyle-lab.github.io

bulk_plasmid_seq_web

bulkplasmidseq

bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

cagi5-regdb

Training data for CAGI5 Regulation Saturation Challenge

cgimp

Clustered Genomic Interval Mapping Platform

easytutorial

Create and maintain tutorials of common tasks for Boyle lab.

encode-api-apps

Scripts for the Deciphering ENCODE examples

f-seq2

Improving the feature density based peak caller with dynamic statistics

f-seq2-paper-supplementary

F-Seq2 paper data accession numbers and scripts to run peak callers.

haplotaglr

A tool for phasing long-read sequencing results.

hmmstr

kohonen

Supervised and unsupervised self-organising maps

kohonen2

Fork of R kohonen package source 2.0.10 with hacks

mapgl

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

mergebw

Tool for merging many BigWig files for RegulomeDB

mouse-human-som

General repository for the mouse/human SOM manuscript.

nanopal-and-cas9-targeted-enrichment-pipelines

The pipelines for the project 'Cas9 targeted enrichment of mobile elements using nanopore sequencing', including NanoPal and Cleavage-site analysis

porechop

adapter trimmer for Oxford Nanopore reads

pyblast

Run NCBI BLAST with an easy-to-use Pythonic wrapper

pytfmpval

Python bindings for the TFM-Pvalue program.

read-based-te-enrichment

Repeat enrichment testing for short-read sequencing data using an assembly-free alignment approach.

regulomedb

Website for the Regulome Database

regulomedb-turf

Data repository for TURF paper

sempl

C++ implementation of the SEM algorithm

sempl_tools

Random tools for analysis of SEMs

semplme

Implementation of the SEM algorithm with incorporation of DNA methylation

short-read-seq_snakemake

SnakeMake pipeline for alignment, filtering, and peak-calling for short-read sequencing data.