xhn's repositories
GeExCNV
analysis germline CNV (exon-level and gene-level) from capture data
pileup2vaf
detect snv and small indel using pysam pileup method
SimFastq
Simulation fastq files from a given reference genome
ClustalO_2019nCoV
ClustalO_2019nCoV plugin for Ion Torrent S5 Sequencing Platform
Xiaohuaniu0032.github.io
hexo web
octopus
Bayesian haplotype-based mutation calling
homopolymer_scan
Find all HP positions from an target BED file
ncbi_gb_download
automatic download NCBI genebank information
phylo-io
Phylo.IO JS tree viewer
IR-interpreter
Web app for clinical interpretation of Ion Reporter variant results
BAFplot
calculate BAF and plot BAF fig to assist the estimation the tumor purity and ploidy visually
splitFusion
detect DNA fusion using split read
kmerFusion
detect DAN fusion using kmer method
bioinfo_algorithm_collections
re-write classical bioinfo algorithms, such as simth-waterman local alignment, HMM, BWT, PCA et.al
PurityPloidyEst
estimate tumor purity and ploidy from tumor-only WES/Panel data
FLT3_ITD_Pindel
detect FLT3-internal tandem duplication using Pindel
SimVar2Fastq
Simulate SNV/InDel at a specific genome position to make Fastq files
OptiType
Precision HLA typing from next-generation sequencing data
InDelScan
precisely detect short and long insertion/deletion DNA variants from paired-end sequencing data
TS
Torrent Suite
IGV-web
build your browser-based IGV
igv-webapp
IGV Web App
fsz_substr_finding_problem
find all positions of a query string in a long sequence using exact matching