afg1
Bioinformatician @RNAcentral, part of EMBL-EBI in Cambridge, UK. Formerly part of @rrr-uom-projects
Pinned Repositories
cad2gdml
Simple program using CADMesh and Geant4 to export a GDML file from a CAD file (e.g. STL)
DataClassifier
Quick and dirty script to enable manual classification of images. Requires PyQt5
keyboard
RadNetAIDemo
Notebook for the radnet AI live coding session
seq-feat
Sequence features in Rust!
SOBPtools
A couple of python scripts I wrote to produce spread out bragg peak profiles in 2D (i.e. depth-dose curves)
trismus-atlas
A trismus related OAR atlas, developed by Dr Christina Hague, code by me. Rehosted here because UoM version is offline
rnacentral-import-pipeline
RNAcentral data import pipeline
rnacentral-webcode
RNAcentral website source code
FLARE21
https://flare.grand-challenge.org/FLARE21/
afg1's Repositories
afg1/RadNetAIDemo
Notebook for the radnet AI live coding session
afg1/trismus-atlas
A trismus related OAR atlas, developed by Dr Christina Hague, code by me. Rehosted here because UoM version is offline
afg1/DataClassifier
Quick and dirty script to enable manual classification of images. Requires PyQt5
afg1/pride-chatbot
afg1/keyboard
afg1/seq-feat
Sequence features in Rust!
afg1/afg1.github.io
afg1/ARISE
afg1/ARISE_feature_extraction
Small repo for the feature extraction code used in standard clustering
afg1/CPC2
Dockerising CPC2 for simplified use
afg1/DigitalHealthWorkshop
afg1/epmc-xml
afg1/go_def_scoring
afg1/jats-parser
python scripts parsing the Europe PMC interchange format JATS using the lxml library
afg1/litsumm-2
Improved version of LitSumm with better information extraction
afg1/llama.cpp
Port of Facebook's LLaMA model in C/C++
afg1/pi_calc
afg1/pombe-curation-model
afg1/progressive_build
Fast gene finder for expression atlas
afg1/prometheus2-litsumm-eval
afg1/pybedtools
Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
afg1/pymining
image based data mining in python/numpy
afg1/pysam
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
afg1/rna-lang-model
Try to make a language model for RNA!
afg1/rna-type-model
afg1/rnacentral-new-db-import
Code to create the needed tables and other changes in the RNAcentral database for new imports
afg1/RTMLExamples
RTML example notebooks
afg1/SoundCost
An image registration code in which the cost function in sonic!
afg1/timesheet
CLI thing to add entries to timesheet
afg1/uniprot-demos