ncborcherding

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scTregs

 4  1

fishplot

 1  0
Create timecourse "fish plots" that show changes in the clonal architecture of tumors

GDC-tricks

 1  0
tricks to use the Genomics Data Commons portal from the National Cancer Institute

HLAClustRView

 1  0
R package specialized in HLA typing clustering and visualization based on specific similarity metrics

mtscATACpaper_reproducibility

 1  0
Repository to reproduce all analyses for Lareau*, Ludwig*, et al. 2020

STARTRAC

 1  0
STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)

tcrpheno_analysis

 1  0
Code for analysis of TCR and T cell state data in Lagattuta, et al. bioRxiv (2023)

vdjdb-db

 1  0
Git-based TCR database storage & management. Submissions welcome!

Maier_et_al_nature_2020

 0  1
This repository contains scripts used for analysis and figure generation in Maier, B., Leader, A.M., Chen, S.T. et al. A conserved dendritic-cell regulatory program limits antitumour immunity. Nature 580, 257–262 (2020). https://doi.org/10.1038/s41586-020-2134-y

psupertime

 0  1
psupertime is pseudotime ordering for single cell RNA-seq data with sequential labels
HTML

TRGAted

 9  6
Survival Analysis for Protein-Level TCGA Analysis
PostScript

ccRCC

 19  6
Single-Cell Analysis of Immune Cells from Renal Clear Cell Carcinoma
R

scRepertoire

 297  48
A toolkit for single-cell immune profiling

escape

 130  16
Easy single cell analysis platform for enrichment

utility

 81  7
Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR

Trex

 46  1
Using TCR and expression for sequence embedding

Ibex

 18  1
Using BCR and expression for sequence embedding

CellPilot

 4  0

exigence

 3  1

immApex

 3  0
Tools for immune receptor sequence-based neural networks

TCGAcalc

 0  1
Some requested analyses tools for TCGA work