tanyaphung Goto Github PK

1000g_summary_stats

This repository contains scripts related to the empirical analyses of 1000 Genome dataset associated with Beichman et al. (2017) (https://www.ncbi.nlm.nih.gov/pubmed/28893846)

cheat_sheets

This repo contains cheat sheets for a variety of programs I use frequently

commonly_used_codes

This repo hosts scripts that I use regularly

customfiltervcf

dadi_tutorial

effectsofremapping

This repo reports the analysis comparing TPM and ASEReadCounter counts for between results from GTEX version 8 and results from remapping to sex-specific reference

gatk4_notes

Notes on GATK4

genetic_architecture

This repository contains scripts associated with the manuscript titled "Inferring the genetic architecture and extent of negative selection of human complex traits" (in prep)

ggplot2_howto

How to plot with ggplot2 in R

mutrec

This repo contains scripts to infer whether the process of recombination is mutagnenic.

neoantigens_prioritization

Prioritize neoantigens based on MHC binding affinity, MHC stability, and tumor abundance

neoepitope_prediction

ngs_pipeline

This repo contains scripts I use for processing reads and calling variants for next generation sequencing data set, specifically whole genome sequencing dataset.

nipt_analyses

par_nonpar_diversity_canines

This repository contains scripts related to analyzing genetic diversity in the pseudoautosomal regions and non-pseudoautosmal regions of the X chromosome in canines (Phung et al.) (in preparation)

parsegtex

This repo contains scripts for parsing gtex data

popgen_scripts

Useful programs and scripts in bioinformatics and population genetics

popgen_tools

This repository contains scripts that are often used in population genetics analyses (generating the site frequency spectrum or calculating genetic diversity)

process_rnaseq

This repo documents what I am learning about how to process RNAseq data

ptuneos

pTuneos: prioritizing Tumor neoantigen from next-generation sequencing data

rnaseq_analysis_scripts

This repo contains scripts relating to analysis of RNAseq data

run_hla_polysolver

sexbiased

tanyaphung.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

vcffiltering

vcfhelper

This repository contains scripts relating to analyzing vcf files

w2v