Hongyu Xie's repositories
seqtk
Toolkit for processing sequences in FASTA/Q formats
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
CfdnaPattern
Pattern Recognition for Cell-free DNA
genbioconductor
Materials for Genomics Data Science: Introduction to Bioconductor
SeqMaker.jl
Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
VarScan
Cloned from https://sourceforge.net/projects/varscan, with possible improvement
MutationScan
(Please use MutScan instead) MutationScan is a project implemented by pure Rust language for searching mutation point(s) directly in fastq files (support single-end or pair-end)
Nucleosome_ctDNA
Inferring expressed genes by whole-genome sequencing of plasma DNA
HTSLIB.jl
HTSLIB.jl is a julia wrapper of htslib for accessing common high-throughput sequencing data file formats such as BAM/SAM files
SFrame
SFrame, SArray, SGraph
FusionDirect.jl
Detect gene fusion directly from raw fastq files
tensorflow
Computation using data flow graphs for scalable machine learning
userguide
Userguide for Dato's GraphLab Create
bds-files
Supplementary files for my book, "Bioinformatics Data Skills"
bioawk
BWK awk modified for biological data