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statnet

Software Tools for the Statistical Analysis of Network Data (meta-package)

stig

Synthetic T-cell Informatics Generator

stitchr

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

stringtie

Transcript assembly and quantification for RNA-Seq

suppa

SUPPA2: Fast quantification of differential splicing

survclust

An outcome weighted supervised clustering algorithm, designed to classify patients according to their molecular as well as time-event or end point of interest data.

survival

Survival package for R

survival-1

survival.jianguo.zhou

survivalnma

R interface for survival network meta-analysis models

survrm2

:exclamation: This is a read-only mirror of the CRAN R package repository. survRM2 — Comparing Restricted Mean Survival Time

survrm2adapt

:exclamation: This is a read-only mirror of the CRAN R package repository. survRM2adapt — Flexible and Coherent Test/Estimation Procedure Based on Restricted Mean Survival Times

t-cell-extrect-figure-code-2021

Code used to produce figures in the paper "T cell quantification from DNA sequencing predicts immunotherapy response " by Bentham et al 2021

t-cell-inflamed-multicorrelates

This repo hosts the data tables and figures for Bao et al manuscript entitled "Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types" Under Review.

targetosteoanalysis

targetosteodatapackage

tcellextrect

tcellinflamed

Tcellinflamed_Function is the package to detect T cell inflamed subset to help interpret cancer gene expression data.

tcga

Microbial analysis in TCGA data

tcga-data-analysis

Examples on processing and working with TCGA mutation and RNA-Seq data

tcga-zmu

tcga_brca

tcga_clinical_2_csv

合并tcga网站上下载的clinical xml文件到一个csv

tcga_dbgap

tcga_example

tcgamutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

tcgasurvival

Scripts to analyze TCGA data

tcr

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

tcr-analysis

tcr-classifier

Classifier to determine CD8+ T-cell receptor characteristics underlying peptide recognition.