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TreeSwift
TreeSwift: Fast tree module for Python 3TreeCluster
Efficient phylogenetic clustering of viral sequencesViralMSA
Reference-guided multiple sequence alignment of viral genomesFAVITES
FAVITES (FrAmework for VIral Transmission and Evolution Simulation)Learn-Programming-Python-Source
Source code for Learn Programming: PythonViralConsensus
Fast viral consensus genome reconstructionMemCard-PRO-Renamer
Convert MemCard PRO folders to/from human-readable namesViReport-COVID-19
ViReport analysis of COVID-19 using GISAID dataPyFF7
Niema's toolkit for playing with files from the Final Fantasy VII PC (and Switch) porttools
A collection of command-line tools I wrote to make various repetitive tasks more convenientteaching
My teaching resourcesData-Structures-Textbook
Repository for source code of the Data Structures online textbook (Niema Moshiri and Liz Izhikevich, 2016)GameDB
Niema's databases for games from various consolesGameID
Identify a game using GameDBMESS
MESS: Moshiri Exam Similarity ScoreGameDB-PSX
Sony PlayStation (PSX)ViReflow
An elastically-scaling automated AWS pipeline for viral consensus sequence generationViReport
Automated workflow for performing standard viral phylogenetic analyses and generating a reportWedding-Planning
Scripts/tools for automating wedding planning (don't judge me...)Image2TEX
Image2TEX by BordeBISB-BMI-Handbook
Handbook for the Bioinformatics & Systems Biology (BISB) and Biomedical Informatics (BMI) PhD programs at UC San DiegoSamBamViz
Tool for generating useful visualizations from a SAM/BAM fileTreeN93
Non-parametric distance-based transmission cluster identificationSD-COVID-Sequencing
My scripts/notes from the San Diego COVID sequencing effortFAVITES-Lite
FAVITES-Lite: A lightweight framework for viral transmission and evolution simulationKimera
Repo to store source and binaries of Borde's Kimera toolTreeSAP
TreeSAP: Tree SAmpling under Phylogenetic modelsFAVITES-COVID-Lite
A simplified (and much faster) simulation pipeline specifically for COVID-19 contact + transmission + phylogeny + sequence simulationPRJCA008874-Analysis
Analysis of SARS-CoV-2 FASTQs from PRJCA008874AGC-Virus-Benchmark
Niema's benchmarking experiment of Assembled Genomes Compressor (AGC) on viral datacurriculum-vitae
Niema Moshiri's Curriculum Vitae (CV)ViralConsensus-Paper
CoaTran
CoaTran: Coalescent tree simulation along a transmission networkGame-Saves
My backups of game savesFAVITES-ABM-HIV-SD-Lite
A simplified simulation pipeline specifically for ABM-HIV SDChromeOS-Flex-T100TA
Installing ChromeOS Flex on an ASUS T100TAGameDB-PSP
Sony PlayStation Portable (PSP)GameDB-N64
Nintendo 64GameDB-PS2
Sony PlayStation 2 (PS2)GameDB-GC
Nintendo GameCube (GC)TreeSwift-Paper
Repository to store data/figures for TreeSwift paperViralMSA-Demo-VEME-2021
ViralMSA demo for VEME 2021Linux-ASUS-T100TA
A repo for documenting how I installed Linux on my old ASUS T100TABlack-Chocobo
Mirror of source code for Black Chocobo, by sithlord48 and vegetass4FYE-Instruction
Niema's files regarding UCSD FYE (e.g. SEV 1) instructionUI-PRMD-Analysis
My analyses on the UI-PRMD datasetDual-Birth-Model
Code and simulation data for "A two-state model of tree evolution and its applications to Alu retrotransposition"MapArt
My code to make an artwork out of a mapViReaDB
ViReaDB: Viral Read DatabaseViralMSA-Paper
ViralMSA PaperNiema-Pandora-Userscript
My TamperMonkey/GreaseMonkey userscript for PandoraGameDB-XBOX360
Microsoft XBOX 360rpi-arlo-usb-mount
Mount a Raspberry Pi to an Arlo Base Station as an emulated USB mass storage deviceGameDB-GB
Nintendo Game Boy (GB)BISB-Website
Stuff related to my work in updating the UCSD BISB program websitePRJNA698267-Analysis
Analysis of SARS-CoV-2 FASTQs from PRJNA698267ff7-save-checksum
Writes the correct checksum to every save slot in a Final Fantasy VII (PC?) save fileProACT-Paper-Final
Final version of data/figures repository for ProACT paperPyBCL
An open-source pure-Python package for handling Illumina sequencing BCL filesPyTreeDate
A Python tool for dating a rooted phylogenetic tree using various molecular clock assumptionsMossNet
A Python package for performing network analyses on MOSS resultsDual-Birth-Simulator
O(n) simulator of trees under the Dual-Birth (and Yule) modelModels-of-Evolution-Textbook
Repository for source code of the Models of Evolution online textbook (Niema Moshiri, 2018)biotenzar
Bioinformatics Tools for the Tenzar Platformsamhead
Print the first n entries in a given SAM passed via stdinSteamTools
Simple command line Python tool for exploring a public Steam accountGEMF
PhD-Dissertation
Niema's Ph.D. DissertationNiemaDS
NiemaDS is a Python library that implements useful non-standard data structuresNES-Switch-Converter
SEPIA-Paper-BMC-Bioinformatics-
Karen-s-Cookbook
Karen's CookbookProACT
ProACT: Prioritization using AnCesTral edge lengthsniemasd
Config files for my GitHub profile.NiemaGraphGen-Paper
LogDateSimulations
Simulations for LogDate projectProACT-JAIDS-
CoaTran-Paper
Cosmo
Source code from Ficedula's Cosmo editor (version 0.91)OpenMR3
An open-source tool for working with Noraxon MR3 dataExam-Similarity-Detection-Paper
ViReaDB-Paper
ViReaDB PaperVirus-Data
Collection of public domain HIV data for various projectsViral-Primer-Design
Niema's scripts/data for designing viral primersTree-Based-Clustering-Paper
TreeCluster-Paper
Files for TreeCluster PaperProACT-Paper
ProACT Paperbgtools
bgtools: A Python package for managing playing board gamesROM-Save-Tools
Niema's toolkit for playing with video game ROMs/images and savesNiemaGraphGen
Niema's C++ implementations of graph generatorsViReflow-Paper
NiemaGraphGen-Paper-GigaByte-
ClusterPickerII
Placeholder for TreeClusterGameDB-PS3
Sony PlayStation 3 (PS3)How-to-Teach-Online
An online training module to provide instructors guidance in developing and offering fully-online and hybrid coursesGameDB-Switch
Nintendo SwitchGameDB-Wii
Nintendo WiiHuffSplit
HuffSplitRosing-Knight-Moshiri-Demo-2022
Notes/files for the 2022 Rosing-Knight-Moshiri lab collaboration demoViReport-MERS
Analysis of MERS dataLove Open Source and this site? Check out how you can help us