Fan-yuan
Follow
Starred repositories
Clinical interpretation of somatic mutations in cancer
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Tool to annotate outfiles from ExpansionHunter and TRGT with the pathologic implications of the repeat
Scripts and utilities related to analyzing short tandem repeats (STRs).
TREDPARSE: HLI Short Tandem Repeat (STR) caller
A suite of tools for detecting expansions of short tandem repeats
a hidden Markov model to infer simple repeats from genome sequences
A new tool to infer sex from massively parallel sequencing data.
Identifying, understanding, and correcting technical biases on the sex chromosomes in next-generation sequencing data
An R package for inferring the subclonal architecture of tumors
Clonality inference in multiple tumor samples using phylogeny
Create timecourse "fish plots" that show changes in the clonal architecture of tumors
Probabilistic model for inferring clonal population structure from deep NGS sequencing.
Fast method for inferring cancer clonal population structure from SNV data.
Python code to transform Sequenza segment output into PyClone input
📦 Automate Absolute Copy Number Calling using 'ABSOLUTE' package
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
A framework for semi-automated analysis of Amplicon Sequencing data
A fast and self-contained amplicon pipeline tool.
Computational pipeline to analyse Next Generation Targeted Amplicon Sequence data
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It u…
A python tool to detect internal tandem duplication with robust variant allele frequency estimation
for detecting internal tandem duplication from genome sequence data.
