xia1yang Goto Github PK

2017-tcga-mc3_phial

Cohort analysis of TCGA mc3 with PHIAL

3dmapper

Map genetic variants and protein positions to protein interfaces in 3D

bayesdebulk

c3po_polygenic

Basic linear polygenic risk score to predict protein levels in CPTAC

causalpath

A project for exploring differentially active signaling paths related to proteomics datasets

cptac_pancan_ptm_2023

customprodbj

dellachiara_et_al_2021

desctools

Tools for Descriptive Statistics and Exploratory Data Analysis

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

immunesubtypeclassifier

An R package for classification of immune subtypes, in cancer, using gene expression data.

lincs-workshop-2020

CMap Notebooks for LINCS 2020 Workshop

luminal-snf

Multi-omic study of luminal breast cancer

msisensor

microsatellite instability detection using tumor only or paired tumor-normal data

neoflow

NeoFlow: a proteogenomics pipeline for neoantigen discovery

ngs-pipeline

By study this, it won't be costly or time-consuming to customize a NGS data analysis pipeline

ov-project-one

Contains the code and scripts used to process and analyze the data for my analysis of super-enhancer function in ovarian cancer cells (OVCAR3) and in patient RNA-seq and Copy Number data from The Cancer Genome Atlas (TCGA). This project was published by Nat. Communications in July 2022. https://doi.org/10.1038/s41467-022-31919-8

pancanatlasgermline

panoply

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)

rmats-turbo

s5cmd

Parallel S3 and local filesystem execution tool.

signatureanalyzer

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

ssgsea2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

star

RNA-seq aligner

subread_to_dexseq

Scripts to import your FeatureCounts output into DEXSeq

tsnet

TSNet - A New Method for Constructing Tumor Specific Gene Co-Expression Networks Based on Samples with Tumor Purity Heterogeneity