twesleyb

Tyler B's starred repositories

Python

All Algorithms implemented in Python

Language:PythonMIT181247 5928 1451

dvc

🦉 ML Experiments and Data Management with Git

Language:PythonApache-2.013290 140 4640

live-server

A simple development http server with live reload capability.

Language:JavaScript4353 54 291

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Language:CGPL-3.01468 107 294

single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

Language:Jupyter Notebook1311 45 101

box

Write reusable, composable and modular R code

Language:RMIT818 20 285

hexSticker

:sparkles: Hexagon sticker in R

Language:R730 16 51

awesome-multi-omics

List of software packages for multi-omics analysis

MIT680 53 6

ggupset

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

Language:R320 7 36

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

Language:RGPL-3.0312 9 230

fontawesome

Easily insert FontAwesome icons into R Markdown docs and Shiny apps

Language:RNOASSERTION290 10 71

fulltext

:warning: ARCHIVED :warning: Search across and get full text for OA & closed journals

Language:RNOASSERTION270 18 213

JuliaCall

Embed Julia in R

Language:HTMLNOASSERTION261 9 186

SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)

Language:HTMLGPL-3.0258 20 156

ssGSEA2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

Language:RNOASSERTION227 13 29

rcrossref

R client for various CrossRef APIs

Language:RNOASSERTION165 23 202

NMF

NMF: A Flexible R package for Nonnegative Matrix Factorization

Language:R130 16 175

conquer_comparison

Code for evaluation of differential expression methods in single-cell RNA-seq data

Language:RMIT108 5 9

MDsim

[TMLR 2023] Training and simulating MD with ML force fields

Language:PythonMIT101 5 6

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

Language:R93 6 58

everystreet

An algorithm finding #everystreet route on Open Street Map (OSMnx)

Language:Jupyter NotebookMIT92 8 17

ggkeyboard

Make a keyboard using ggplot2.

Language:RNOASSERTION91 5 3

nextflow-vim

Nextflow plugin for VIM

Language:Vim script45 4 3

zinbwave

Clone of the Bioconductor repository for the zinbwave package, see https://bioconductor.org/packages/zinbwave

Language:R42 8 66

zinbwaveZinger

Integrating zingeR with ZINB-WaVE weights

Language:TeX22 9 4

zingeR

zero-inflated negative binomial gene expression in R

Language:R19 5 6

Avant-garde (AvG) is a new tool to refine Data-Independent Acquisition (and Parallel Reaction Monitoring) by removing interfered transitions, adjusting integration boundaries and scoring peaks to control the FDR.

Language:RBSD-3-Clause9 2 3

NeuralDynamics.jl

This package contains a convenient analysis and visualization pipeline for simple dynamical models of neurons and networks of neurons.

Language:JuliaMIT7 1 1