Discover niemasd/TreeSwift-Paper Open Source project

Efficient phylogenetic clustering of viral sequences

TreeCluster

Reference-guided multiple sequence alignment of viral genomes

ViralMSA

FAVITES (FrAmework for VIral Transmission and Evolution Simulation)

FAVITES

Source code for Learn Programming: Python

Learn-Programming-Python-Source

Fast viral consensus genome reconstruction

ViralConsensus

Convert MemCard PRO folders to/from human-readable names

MemCard-PRO-Renamer

ViReport analysis of COVID-19 using GISAID data

ViReport-COVID-19

PyFF7

Niema's toolkit for playing with files from the Final Fantasy VII PC (and Switch) port

A collection of command-line tools I wrote to make various repetitive tasks more convenient

tools

teaching

My teaching resources

Repository for source code of the Data Structures online textbook (Niema Moshiri and Liz Izhikevich, 2016)

Data-Structures-Textbook

Niema's databases for games from various consoles

GameDB

Identify a game using GameDB

GameID

MESS: Moshiri Exam Similarity Score

MESS

GameDB-PSX

Sony PlayStation (PSX)

An elastically-scaling automated AWS pipeline for viral consensus sequence generation

ViReflow

Automated workflow for performing standard viral phylogenetic analyses and generating a report

ViReport

Scripts/tools for automating wedding planning (don't judge me...)

Wedding-Planning

Handbook for the Bioinformatics & Systems Biology (BISB) and Biomedical Informatics (BMI) PhD programs at UC San Diego

Image2TEX

Image2TEX by Borde

Visual Basic

BISB-BMI-Handbook

Tool for generating useful visualizations from a SAM/BAM file

SamBamViz

Non-parametric distance-based transmission cluster identification

TreeN93

My scripts/notes from the San Diego COVID sequencing effort

SD-COVID-Sequencing

FAVITES-Lite: A lightweight framework for viral transmission and evolution simulation

FAVITES-Lite

Repo to store source and binaries of Borde's Kimera tool

Kimera

Visual Basic

TreeSAP

TreeSAP: Tree SAmpling under Phylogenetic models

A simplified (and much faster) simulation pipeline specifically for COVID-19 contact + transmission + phylogeny + sequence simulation

FAVITES-COVID-Lite

Analysis of SARS-CoV-2 FASTQs from PRJCA008874

PRJCA008874-Analysis

AGC-Virus-Benchmark

Niema's benchmarking experiment of Assembled Genomes Compressor (AGC) on viral data

curriculum-vitae

Niema Moshiri's Curriculum Vitae (CV)

ViralConsensus-Paper

CoaTran: Coalescent tree simulation along a transmission network

CoaTran

A simplified simulation pipeline specifically for ABM-HIV SD

Game-Saves

My backups of game saves

FAVITES-ABM-HIV-SD-Lite

Installing ChromeOS Flex on an ASUS T100TA

ChromeOS-Flex-T100TA

GameDB-PSP

Sony PlayStation Portable (PSP)

GameDB-N64

Nintendo 64

GameDB-PS2

Sony PlayStation 2 (PS2)

ViralMSA demo for VEME 2021

GameDB-GC

Nintendo GameCube (GC)

ViralMSA-Demo-VEME-2021

Linux-ASUS-T100TA

A repo for documenting how I installed Linux on my old ASUS T100TA

Black-Chocobo

Mirror of source code for Black Chocobo, by sithlord48 and vegetass4

Niema's files regarding UCSD FYE (e.g. SEV 1) instruction

FYE-Instruction

UI-PRMD-Analysis

My analyses on the UI-PRMD dataset

Code and simulation data for "A two-state model of tree evolution and its applications to Alu retrotransposition"

Dual-Birth-Model

My code to make an artwork out of a map

MapArt

ViReaDB: Viral Read Database

ViReaDB

ViralMSA-Paper

ViralMSA Paper

My TamperMonkey/GreaseMonkey userscript for Pandora

Niema-Pandora-Userscript

JavaScript

GameDB-XBOX360

Microsoft XBOX 360

rpi-arlo-usb-mount

Mount a Raspberry Pi to an Arlo Base Station as an emulated USB mass storage device

GameDB-GB

Nintendo Game Boy (GB)

BISB-Website

Analysis of SARS-CoV-2 FASTQs from PRJNA698267

PRJNA698267-Analysis

ff7-save-checksum

Writes the correct checksum to every save slot in a Final Fantasy VII (PC?) save file

Benchmark of cawlign and bealign

cawlign-bealign-benchmark

Final version of data/figures repository for ProACT paper

ProACT-Paper-Final

An open-source pure-Python package for handling Illumina sequencing BCL files

PyBCL

A Python tool for dating a rooted phylogenetic tree using various molecular clock assumptions

PyTreeDate

A Python package for performing network analyses on MOSS results

MossNet

O(n) simulator of trees under the Dual-Birth (and Yule) model

Dual-Birth-Simulator

Repository for source code of the Models of Evolution online textbook (Niema Moshiri, 2018)

Models-of-Evolution-Textbook

biotenzar

Bioinformatics Tools for the Tenzar Platform

samhead

Print the first n entries in a given SAM passed via stdin

Simple command line Python tool for exploring a public Steam account

SteamTools

Niema's Ph.D. Dissertation

GEMF

PhD-Dissertation

NiemaDS is a Python library that implements useful non-standard data structures

NiemaDS

NES-Switch-Converter

SEPIA-Paper-BMC-Bioinformatics-

Karen-s-Cookbook

Karen's Cookbook

ProACT: Prioritization using AnCesTral edge lengths

ProACT

Config files for my GitHub profile.

niemasd

NiemaGraphGen-Paper

Simulations for LogDate project

LogDateSimulations

ProACT-JAIDS-

CoaTran-Paper

Source code from Ficedula's Cosmo editor (version 0.91)

Cosmo

Pascal

OpenMR3

An open-source tool for working with Noraxon MR3 data

Exam-Similarity-Detection-Paper

ViReaDB-Paper

ViReaDB Paper

Collection of public domain HIV data for various projects

Virus-Data

Viral-Primer-Design

Niema's scripts/data for designing viral primers

Tree-Based-Clustering-Paper

Files for TreeCluster Paper

TreeCluster-Paper

ProACT-Paper

ProACT Paper

bgtools: A Python package for managing playing board games

bgtools

Niema's toolkit for playing with video game ROMs/images and saves

ROM-Save-Tools

Niema's C++ implementations of graph generators

NiemaGraphGen

ViReflow-Paper

NiemaGraphGen-Paper-GigaByte-

Placeholder for TreeCluster

ClusterPickerII

GameDB-PS3

Sony PlayStation 3 (PS3)

An online training module to provide instructors guidance in developing and offering fully-online and hybrid courses

How-to-Teach-Online

GameDB-Switch

GameDB-Wii

HuffSplit

Rosing-Knight-Moshiri-Demo-2022

Notes/files for the 2022 Rosing-Knight-Moshiri lab collaboration demo

100

ViReport-MERS

Analysis of MERS data