Pinned Repositories
.tmux
🇫🇷 Oh My Tmux! Pretty & versatile tmux configuration / customization made with ❤️
2020-NGSInfectedBodyFluids
scripts and data for Gu et al Nature Medicine 2020 manuscript
7-Zip-zstd
7-Zip with support for Brotli, Fast-LZMA2, Lizard, LZ4, LZ5 and Zstandard
bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
misc
Useful small programs
pVACtools
sambamba
Tools for working with SAM/BAM/CRAM data
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
VEP_plugins
Plugins for the Ensembl Variant Effect Predictor (VEP)
WGS_of_Han_Chinese_genomes
linhxxx's Repositories
linhxxx/bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
linhxxx/7-Zip-zstd
7-Zip with support for Brotli, Fast-LZMA2, Lizard, LZ4, LZ5 and Zstandard
linhxxx/ABF-SDK
Resources for working with Axon Binary Format (ABF) Files
linhxxx/AECT
A deep learning based pipeline for TSS coverage denoising and feature extraction from shallow cell free DNA sequencing
linhxxx/Audio-Spectrogram
Generating sound spectrograms using short-time Fourier transform that can be used for purposes such as sound classification by machine learning algorithms.
linhxxx/awesome-nanopore
A curated list of awesome nanopore analysis tools.
linhxxx/bonito
A PyTorch Basecaller for Oxford Nanopore Reads
linhxxx/Butterworth-filter
Elegant Butterworth and Chebyshev filter implemented in C, with float/double precision support. Works well on many platforms. You can also use this package in C++ and bridge to many other languages for good performance.
linhxxx/cfDNApipe
cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
linhxxx/Chiron
A basecaller for Oxford Nanopore Technologies' sequencers
linhxxx/cragr
R package for CRAG
linhxxx/dorado
Oxford Nanopore's Basecaller
linhxxx/Griffin
A flexible framework for nucleosome profiling of cell-free DNA
linhxxx/Griffin_analyses
Scripts for analyses in the Griffin manuscript
linhxxx/intervaltree
A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.
linhxxx/matplotplusplus
Matplot++: A C++ Graphics Library for Data Visualization 📊🗾
linhxxx/molecular-cfDNA-fragmentomics
An et al. Nature Communications 2023
linhxxx/mosdepth
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
linhxxx/Msuite2
Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance
linhxxx/NA12878
Data and analysis for NA12878 genome on nanopore
linhxxx/pyABF
pyABF is a Python package for reading electrophysiology data from Axon Binary Format (ABF) files
linhxxx/pypysam
PyPy-compatible htslib routines for SAM/BAM alignment files
linhxxx/reproduce_lucas_wflow
linhxxx/RLM
Read level DNA methylation analysis of bisulfite converted sequencing data
linhxxx/RProp-1
Resilient backpropagation algorithm (RProp) optimizer implemented for Keras/TF
linhxxx/scrappie
Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group
linhxxx/serial_wave_port
基于Qt的串口调试助手，可绘制实时波形
linhxxx/VMwareWorkstation
手动上传官网的VMwareWorkstation安装包
linhxxx/wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
linhxxx/zstd
Zstandard - Fast real-time compression algorithm