pmcarlton

Peter Carlton's starred repositories

Complete-Python-3-Bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

Language:Jupyter Notebook27320 2721 353

atuin

✨ Magical shell history

Language:RustMIT20318 63 817

wired-elements

Collection of custom elements that appear hand drawn. Great for wireframes or a fun look.

Language:TypeScriptMIT10496 129 122

pyWhat

🐸 Identify anything. pyWhat easily lets you identify emails, IP addresses, and more. Feed it a .pcap file or some text and it'll tell you what it is! 🧙‍♀️

Language:PythonMIT6537 70 82

napari

napari: a fast, interactive, multi-dimensional image viewer for python

Language:PythonBSD-3-Clause2180 46 3008

ColabFold

Making Protein folding accessible to all!

Language:Jupyter NotebookMIT1893 46 547

hoard-of-bitfonts

turns out I like bitmap fonts

Language:PascalNOASSERTION1337 24 18

ProtTrans

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

Language:Jupyter NotebookAFL-3.01097 32 149

ProteinMPNN

Code for the ProteinMPNN paper

Language:Jupyter NotebookMIT952 20 89

LinguaCafe

LinguaCafe is a self-hosted software that helps language learners read foreign languages.

Language:VueGPL-3.0853 8 289

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Language:CGPL-3.0779 19 318

localcolabfold

ColabFold on your local PC

Language:PythonMIT562 12 245

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Language:C++MIT529 27 650

figeno

Tool for plotting sequencing data along genomic coordinates.

Language:PythonGPL-3.0245 6 19

FASTGA

Pairwise whole genome aligner

Language:CNOASSERTION134 10 3

Cell_ACDC

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

Language:PythonBSD-3-Clause127 4 519

ProtFlash

ProtFlash: A lightweight protein language model

Language:PythonMIT99 2 3

mrcfile

A Python implementation of the MRC2014 file format

Language:PythonBSD-3-Clause78 3 51

3DeeCellTracker

A python algorithm for tracking cells in 3D time lapse images.

Language:PythonMIT51 4 11

LongStitch

Correct and scaffold assemblies using long reads

Language:MakefileGPL-3.045 11 49

AlphaRED

AlphaFold-initiated replica exchange protein docking

Language:PythonMIT41 4 5

pLM-BLAST

Detection of remote homology by comparison of protein language model representations

Language:PythonMIT41 4 29

Open-Omics-Acceleration-Framework

Intel lab's open sourced data science framework for accelerating digital biology

Language:Jupyter NotebookMIT36 7 3

napari-zelda

ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari

Language:HTMLBSD-3-Clause18 3 7

alignment_laser

How to build a simple alignment laser for typical optical alignment tasks.

Language:PythonGPL-3.01100

python_bioinfo_2022

Language:Jupyter NotebookCC-BY-SA-4.011 40

CATHe

Deep Learning tool trained on protein sequence embeddings from protein language models to accurately detect remote homologues for CATH superfamilies

Language:PythonMIT11 1 2

reads2genome

QC and assemble reads from different sequencing technologies into a genome obtained from a single organism

Language:NextflowMIT5 4 10

Cellpose_germlineNuclei

Language:Jupyter NotebookBSD-3-Clause3 10

Custom code (Matlab functions/scripts) associated with publication: White, M.A. et al. (2023). Crossover Interference Mediates Multiscale Patterning Along Meiotic Chromosomes. bioRxiv. https://doi.org/10.1101/2024.01.28.577645

Language:MATLABMIT1 10