Musketeer-D

terminal

The new Windows Terminal and the original Windows console host, all in the same place!

awesome-deep-learning

A curated list of awesome Deep Learning tutorials, projects and communities.

biopython

Official git repository for Biopython (originally converted from CVS)

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

xiazai

小手电官方版本下载 小手电 翻墙 代理 科学上网 外网 加速器 梯子 路由 Xiaoshoudian proxy vpn censorship-circumvention censorship gfw accelerator

TBtools-II

GUI/CommandLine Tool Box for biologistists to utilize NGS data.

GWA_tutorial

A comprehensive tutorial about GWAS and PRS

deepTools

Tools to process and analyze deep sequencing data.

Raspberry-Pi-OS-64bit

Repository for containing issues on the 64 bit operating system (as distinct from the 32 bit one)

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

EDTA

Extensive de-novo TE Annotator

bedops

:microscope: BEDOPS: high-performance genomic feature operations

gatk

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

my_WGCNA

f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

rerio

Research release basecalling models and configurations

ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data

genomation

R package for genomic feature analysis and visualization

wub

Tools and software library developed by the ONT Applications group

signalAlign

HMM-HDP models for MinION signal alignments

SAM

SAM (Significance Analysis of Microarrays) shiny app

pycoMeth

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

defining_genomic_regions

Define regions in the genome

USeq

180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC file manipulation, etc. Both GUI and cmd line interfaces.

gcf52ref

GpC methylation from fast5:s to reference anchored calls

peer

A factor analysis package

encode_dna_dynamics

Custom scripts used in "Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus"

CytosineMethylationAnalysis

Scripts and ipython notebooks for reproducing results from "Cytosine Methylation Variation Calling with MinION Nanopore Sequencing"

Gff3ToBed