iosonofabio
Physics, bioinformatics, virology, evolution, data science, and bioengineering. I usually code in Python, C++, and Javascript.
UNSW SydneySydney, Australia
Pinned Repositories
htseq
HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
bi2-ss12-p6
Project 6 for Bioinformatics II SS12 Uni-Tübingen
hivwholeweb
Web application for deep sequencing on longitudinal HIV-1 samples from patients.
lshknn
k nearest neighbor (KNN) graphs via Pearson correlation distance and local sensitive hashing (LSH).
organic-box-factory
Docker/Singularity containers for high-throughput sequencing pipelines in the cloud and on the ground
pysang
A Sanger chromatograph viewer.
seqanpy
Fast pairwise sequence alignment using SeqAn, in Python.
singlet
Single cell RNA Seq data analysis with quantitative phenotypes
slmpy
Smart Local Moving community detection algorithm in Python and C++11/14
virtual_gamepad
You sometimes need to convince a video game that you own a gamepad...
iosonofabio's Repositories
iosonofabio/lshknn
k nearest neighbor (KNN) graphs via Pearson correlation distance and local sensitive hashing (LSH).
iosonofabio/seqanpy
Fast pairwise sequence alignment using SeqAn, in Python.
iosonofabio/singlet
Single cell RNA Seq data analysis with quantitative phenotypes
iosonofabio/slmpy
Smart Local Moving community detection algorithm in Python and C++11/14
iosonofabio/atlas_landmarks
Single cell gene expression data, averaged or subsampled by cell type
iosonofabio/bag_of_stars
STAR mapping on slurm clusters in bags
iosonofabio/BCR_Zanini_Diamond
BCR analysis for the Zanini Diamond collaboration
iosonofabio/ffpopsim
FFPopSim is a C++/Python library for efficient simulation of large recombining populations.
iosonofabio/anndata_kolmogorov_smirnov
Kolmogorov Smirnov test on all genes between two AnnData objects
iosonofabio/anndata_utils
A bunch of odds and evens I wish anndata had.
iosonofabio/backup_quake_sep_2019
Backup postdoc data
iosonofabio/covid19_scenarios
Models of COVID-19 outbreak trajectories and hospital demand
iosonofabio/example_repo_Lowy2
just for fun
iosonofabio/FitnessInference
Prediction fitness of leaves on a genealogical tree
iosonofabio/heptad_paper
Repo for the heptad paper, Thoms J et al (2020)
iosonofabio/leidenalg
Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
iosonofabio/lung_neonatal_immune
Repo for Neonatal lung immune cell paper
iosonofabio/lung_neonatal_mesenchymal
iosonofabio/maa
Mouse Cell Atlas markers
iosonofabio/mCMV
Single cell analysis of mCMV
iosonofabio/northstar_analysis
Jupyeter notebooks and scripts to perform atlas-based scRNA-seq analysis using Northstar
iosonofabio/scenery
Flexible VR Visualisation for Volumetric and Geometric Data on the Java VM, powered by Kotlin and Vulkan
iosonofabio/self-assembling-manifold
The Self-Assembling-Manifold (SAM) algorithm.
iosonofabio/single-cell-snakemake
iosonofabio/single-cell-snakemake2
example repo for single cell Snakemake pipelines
iosonofabio/singlecell-bcr
Adaptation of Derek Croote's pipeline to process assembled BCR sequences
iosonofabio/singlecell-ige
Alignment and antibody assembly pipelines for Croote et al. (Science, 2018)
iosonofabio/symbiont-website
Website for the Research Symbiont Awards
iosonofabio/ursaminor
iosonofabio/Zanini_et_al_DENV_patients_2018
Python scripts associated with the Zanini et al. (2018) paper on DENV infected patients