ALGW71

mastering-shiny

Mastering Shiny: a book

covid-sim

This is the COVID-19 CovidSim microsimulation model developed by the MRC Centre for Global Infectious Disease Analysis hosted at Imperial College, London.

circlize

Circular visualization in R

immunedeconv

A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods

mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

MuSiC

Multi-subject Single Cell Deconvolution

xCell

Cell types enrichment analysis

sas-prog-for-r-users

Teaching and lab materials for the "SAS Programming for R Users" course, including course notes, data, and code.

vdjdb-db

🗂️ [vdjdb.cdr3.net is up and running] Git-based TCR database storage & management. Submissions welcome!

gliph

Grouping of Lymphocyte Interactions by Paratope Hotspots

tcr-dist

Software tools for the analysis of epitope-specific T cell receptor (TCR) repertoires (scroll down for the README)

Benchmarks

ECP-CANDLE Benchmarks

R-swat

The SAS Scripting Wrapper for Analytics Transfer (SWAT) package is the R client to SAS Cloud Analytic Services (CAS). It allows users to execute CAS actions and process the results all from R.

IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

OLGA

Compute generation probabilities of CDR3 amino acid and nucleotide sequences

TidyTuesday

ALICE

Detecting TCR involved in immune responses from single RepSeq datasets

DeepSeqPanII

A sequence-based pan model for peptide-MHC II binding affinity prediction.

turboGliph

R implementation of GLIPH (Grouping of Lymphocyte Interactions by Paratope Hotspots), an algorithm developed by Glanville et al to identify specificity groups in the T cell receptor repertoire based on local (motif sharing) and global (hamming distance) similarities.

tcr-annotation-methodology

📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery

sas-viya-the-R-perspective

Companion to the book: SAS® Viya®: The R Perspective by Yue Qi, Kevin D. Smith, and Xiangxiang Meng

quickstart-sas-viya

AWS Quick Start Team

cardiff2019sessions

6R0E_artwork

Artwork made from PDB accession code 6R0E

ICU_Dashboard

ALICE_sample_data

Datasets to use with ALICE