ahmedaq

Making-elegant-Matlab-figures

A repository comprising multiple functions for making elegant publication-quality figures in MATLAB

Orthogonal-Clustering

A Bayesian method which utilises the rich structure embedded in the sensing matrix for fast sparse signal recovery

MPF-BML-GUI

Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters

RocaSec

RocaSec: A standalone GUI-based package for robust co-evolutionary analysis of proteins

RoCA

Software for identifying co-evolutionary sectors in proteins using RoCA

ACE

Fast and flexible code for solving the inverse Ising/Potts inference problem

BrewerMap

[MATLAB] The complete palette of ColorBrewer colormaps. Simple selection by scheme name and map length.

HCV-E2

Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them

MPF-BML

Fast and efficient code to solve the inverse Ising/Potts (aka maximum entropy) problem

PV-vp1

Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV

2019-nCoV-T-Cell-Vaccine-Candidates

R source code and associated data files for reproducing the results of a preliminary study on indentifying potential B cell and T cell targets for a vaccine against 2019-nCoV based on known immunological determinants of SARS-CoV.

COVIDep

COVIDep: Real-time reporting of vaccine target recommendations for the COVID-19 coronavirus (SARS-CoV-2)

HCV_E2_1a_1b_evolution

Evolutionary constraints vary across HCV subtypes

HCV_NS3_Drug_Resistance

Epistasis promotes resistance against HCV NS3 drugs

HCVE1E2

HIV-Gag-Immunogens

This repository includes source code scripts for all the analysis and figures reported in Ahmed et al.’s “Sub-dominant principal components inform new vaccine targets for HIV Gag”. The source code for the analysis is contained in the “Analysis” folder, while the scripts for generating the figures are in the “Figures” folder.

Robust-DENV-Vaccine-Candidates

RStudio project for reproducing the results and figures in the paper: "Robust candidates for a universal T cell vaccine against Dengue virus" [submitted]

SARS2TcellEpitopes

Summary of emerging data about experimentally-identified SARS-CoV-2 T cell epitopes compiled from 1,259 convalescent COVID-19 patients across 8 independent studies