shishenyxx
Researcher in Bioinformatics and Human Genetics interested in somatic and germline mosaicism.
University of Utah
Pinned Repositories
Adult_brain_somatic_mosaicism
This repository collects pipelines, codes, and some intermediate results for adult brain somatic mosaicism study.
DeepMosaic
DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
eclip
Elements-of-Style-Workflow-Creation-Maintenance
Human_Inhibitory_Neurons
This repository contains codes and pipelines, as well as data used in the analysis of human inhibitory and excitatory neuronal clonal dynamics and lineage relationships, with cell-type-specific mosaic variant barcoding analysis (cMVBA).
MCD_mosaic
Malformations of cortical development (MCD) are neurological conditions displaying focal disruption of cortical architecture and disrupted cellular organization that occurs during embryogenesis. This repository contains the pipelines for data processing, codes for data analysis and plotting for the large-scale MCD data analysis.
MosaicBase
MosaicBase is a comprehensive knowledgebase for postzygotic mosaic variants from noncancer disease-related and healthy human individuals
PASM
Scripts for PASM, TAS/TASeq, and MPAS. We provided perl+R versions, python versions, and an extended snakemake version with all additional annotations. The scripts are useful for the calculation of variant allelic fractions for the validation and quantification of mosaic mutations.
Sperm_control_cohort_mosaicism
This repository collects pipelines, codes, and some intermediate results for the study of mosaic SNV/Indels for sperm, blood, and other samples of a control cohort.
Sperm_transmission_mosaicism
This repository collects pipelines, codes, and some intermediate results for the study of mosaic SNV/Indels for sperm, blood, saliva samples of a transmission genomic study.
shishenyxx's Repositories
shishenyxx/DeepMosaic
DeepMosaic is a deep-learning-based mosaic single nucleotide classification tool without the need of matched control information.
shishenyxx/Adult_brain_somatic_mosaicism
This repository collects pipelines, codes, and some intermediate results for adult brain somatic mosaicism study.
shishenyxx/MCD_mosaic
Malformations of cortical development (MCD) are neurological conditions displaying focal disruption of cortical architecture and disrupted cellular organization that occurs during embryogenesis. This repository contains the pipelines for data processing, codes for data analysis and plotting for the large-scale MCD data analysis.
shishenyxx/Sperm_control_cohort_mosaicism
This repository collects pipelines, codes, and some intermediate results for the study of mosaic SNV/Indels for sperm, blood, and other samples of a control cohort.
shishenyxx/Human_Inhibitory_Neurons
This repository contains codes and pipelines, as well as data used in the analysis of human inhibitory and excitatory neuronal clonal dynamics and lineage relationships, with cell-type-specific mosaic variant barcoding analysis (cMVBA).
shishenyxx/MosaicBase
MosaicBase is a comprehensive knowledgebase for postzygotic mosaic variants from noncancer disease-related and healthy human individuals
shishenyxx/PASM
Scripts for PASM, TAS/TASeq, and MPAS. We provided perl+R versions, python versions, and an extended snakemake version with all additional annotations. The scripts are useful for the calculation of variant allelic fractions for the validation and quantification of mosaic mutations.
shishenyxx/Sperm_transmission_mosaicism
This repository collects pipelines, codes, and some intermediate results for the study of mosaic SNV/Indels for sperm, blood, saliva samples of a transmission genomic study.
shishenyxx/eclip
shishenyxx/Elements-of-Style-Workflow-Creation-Maintenance
shishenyxx/MosaicHunter
A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples.
shishenyxx/gatk-docs
Documentation archive for GATK tools and workflows
shishenyxx/MosaicForecast
A mosaic detecting software based on phasing and random forest
shishenyxx/primer3
Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
shishenyxx/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods