iansetliff Goto Github PK

airr-standards

MiAIRR: AIRR Community Minimal Standards WG

ampssembler

This project contains scripts,source codes, documents, etc. associated with the AMPssembler Project.

cite-seq-count

Small script that allows to count TAGS from a CITE-seq experiment

clonify-python

csv_to_fasta

Going from csv (or .txt, etc) to fasta format

gcdynamics

Model of germinal center B-cell affinity maturation.

gliph

Grouping of Lymphocyte Interactions by Paratope Hotspots

greiff2014

BCR repertoire analysis from Greiff 2014 data

iansetliff.github.io

site

ig_simulator

IgSimulator is a versatile tool for simulation of immunoglobulin repertoire

igphyml

A phylogenetic analysis program designed for B cell receptor sequence data. It implements the HLP17 codon substitution model which is capable of accounting for unusual features of affinity maturation such as context dependent hotspot mutations, nonreversible sequence evolution, and descent from a known germline sequence. Based off of codonPhyML.

imnet

AbNet: an Antibody Repertoire Network Construction Toolkit

influenza_vaccination_project

Software associated with the manuscript: "Statistical Inference of a Convergent Antibody Repertoire Response to Influenza Vaccine."

mhcquant

Identify and quantify peptides from mass spectrometry raw data

migmap

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

ooc_pkpd

Organ on Chip PK/PD Modeling

parametric-t-sne

A Python 2 porting of the parametric t-SNE algorithm

partis

B-cell receptor sequence annotation, simulation, and clonal family inference

partis_accre

All dependencies/setup for Vanderbilt's ACCRE cluster

presto_changeo_accre

All dependencies, etc for Vanderbilt's ACCRE cluster

python

Example Python Scripts

repertoire_analysis_r_scripts

Useful R scripts for BCR/TCR Repertoire Analysis

research_public

Quantitative research and educational materials

scleroderma

slurm

SLURM Example Scripts

trigs

A collection of bioinformatics tools for sequence analysis, with an emphasis on Next-Generation Sequencing and Rep-Seq.

vdj

python package for working with immune receptor sequence data

vdjfasta

A toolkit for repertoire analysis of antibodies and T cell receptors

vdjtools

Post-analysis of immune repertoire sequencing data

vidjil

Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire