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/VEP_plugins
Plugins for the Ensembl Variant Effect Predictor (VEP)
linhxxx/pVACtools
linhxxx/vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
linhxxx/adamajava
linhxxx/bamtools
C++ API & command-line toolkit for working with BAM data
linhxxx/bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
linhxxx/Bis-tools
A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clustering: alignWigToBed; )
linhxxx/bwa-mem2
The next version of bwa-mem (WIP; not recommended for production uses at the moment)
linhxxx/CancerLocator
A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.
linhxxx/cgranges
A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)
linhxxx/check-sex
Determine the biological sex of a human whole-genome BAM file
linhxxx/cnvkit
Copy number variant detection from targeted DNA sequencing
linhxxx/delfi_scripts
linhxxx/deTiN
DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
linhxxx/docker-bam_readcount_helper-cwl
linhxxx/ensembl-vep
The Variant Effect Predictor predicts the functional effects of genomic variants
linhxxx/facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
linhxxx/ichorCNA
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
linhxxx/IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
linhxxx/libevent
Event notification library
linhxxx/NeoPredPipe
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
linhxxx/ngs-filters
Filters for false-positive mutation calls in NGS
linhxxx/NuCMap
R package for chemical mapping of nucleosome positioning
linhxxx/openbilibili-go-common
哔哩哔哩 bilibili 网站后台工程 源码
linhxxx/PureCN
Copy number calling and variant classification using targeted short read sequencing
linhxxx/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
linhxxx/svict
Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA
linhxxx/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
linhxxx/tmux
tmux source code
linhxxx/tsnad
Detecting somatic mutations and predicting tumor-specific neo-antigens