Musketeer-D

wslg

Enabling the Windows Subsystem for Linux to include support for Wayland and X server related scenarios

zotero

Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

WhyNotWin11

Detection Script to help identify why your PC is not Windows 11 Release Ready. Now Supporting Update Checks!

CHM13

The complete sequence of a human genome

bioawk

BWK awk modified for biological data

pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

Winnowmap

Long read / genome alignment software

kentUtils

UCSC command line bioinformatic utilities

encoded

Metadata database for ENCODE project

selscan

Haplotype based scans for selection

GENIE3

Machine learning-based approach for the inference of gene regulatory networks from expression data.

MEGENA

Multiscale embedded gene co-expression network analysis

nanopore-methylation-utilities

pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

dynGENIE3

Semi-parametric approach for the inference of gene regulatory networks from time series of expression data

WheatHomoeologExpression

pyencoded-tools

nanopore-methylation-utilities

DNAModAnnot

R toolbox for DNA Modifications filtering and annotation

T2T-Epigenetics

Repository for analysis scripts for the T2T Epigenetics manuscript

Jump3

Hybrid machine learning/model-based approach for the inference of gene regulatory networks from time series of expression data.

T2T_Encode_Analysis

Scripts for recapitulating the Encode reanalysis using the T2T chm13 reference assembly

T2T_Encode_Analysis

Scripts for recapitulating the Encode reanalysis using the T2T chm13 reference assembly

GENIE3_scripts

Scripts used in the manuscript "Validation and characterisation of the wheat GENIE3 network using an independent RNA-Seq dataset." from Harrington et al. 2019

chm13_meth

Methylation analysis of chrx in chm13 assembly

GENIE3_scripts

Scripts used in the manuscript "Validation and characterisation of the wheat GENIE3 network using an independent RNA-Seq dataset." from Harrington et al. 2019

GENIE3_sysgen

Extension of the GENIE3 method for the inference of gene regulatory networks from systems genetics data.