jenni-westoby Goto Github PK

augmentor.jl

A fast image augmentation library in Julia for machine learning.

benchmark_bulk_analysis

This is the pipeline to perform the bulk RNA-seq simulation based benchmark.

benchmark_figures

benchmark_paper_isoforms

Instructions to perform isoform quantification on real bulk RNA-seq data.

benchmarking_pipeline

This is the pipeline used to perform the RSEM simulation based BLUEPRINT and Kolodziejczyk et al. benchmarks.

blueprint

Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5

calculator

Getting started with ANTLR.

coverage_cell_number_study

drop-seq_pipeline

This is the pipeline to perform a Drop-seq simulation based benchmark - see https://www.biorxiv.org/content/early/2018/01/17/248716

es_cell_pipeline

Benchmarking pipeline published in https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1571-5

hello_world

practice repository

heroku

ipredict_thesis

Record of code used to produce figures in chapter 3 of PhD thesis

isoform_cell_matrix_generation

Pipelines used to generate isoform-cell counts matrices, as described in [link]

julia_gpu_examples

Github host for Julia GPU tutorial hosted at https://jenni-westoby.github.io/Julia_GPU_examples/dev/

obstacles

Obstacles to Studying Alternative Splicing Using scRNA-seq

polyester_simulations

This is the pipeline to perform the Polyester and Splatter simulation based benchmark

rng_juliagpu

A basic GPU implementation of the Mersenne Twister algorithm in Julia

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

rsem_tutorial

A short tutorial on how to use RSEM

stayunfocusd

My CS50 final project - a Chrome Extension called StayUnfocusd. This is the minimum viable product for an extension in which users enter websites they want to avoid. If they subsequently visit those websites, they are rickrolled.

structural_inequality

github pages for structural inequality blog

tabula_muris_gencode