jorgeavilacartes

complexCGR

complex Chaos Game Representation for DNA sequences

CouGaR-g

Frequence Chaos Game Representation of DNA with Deep Learning

pangeblocks

pangenome from maximal blocks in an MSA

basecalling

an attempt of basecaller for ONT RNA signals

convolutional-networks

A series of files to learn deep learning

django3

Testing and increasing knowledge

making-my-own-executable-python

Define your own .ExecutableExtension to run python code (and others) with just one click

PandasFast

Faster computation of apply and progress_apply functions of pandas using concurrent library.

panricci

Alignment of Pangenome Graphs with Ricci Flow

panspace

Embedding-based indexing for compact storage, rapid querying, and curation of bacterial pan-genomes

jorgeavilacartes/panricci

Alignment of Pangenome Graphs with Ricci Flow

jorgeavilacartes/unsupervised-dna

Unsupervised models for DNA - Chaos Game Representation

jorgeavilacartes/alpang-hackaton

Workflow to use GraphAligner and PanAligner

jorgeavilacartes/basecalling

an attempt of basecaller for ONT RNA signals

jorgeavilacartes/algenomics

Library to understand genomics, with naming related to biology.

jorgeavilacartes/alpang_hackathon

ALPACA/PANGAIA ANNUAL WORKSHOP - Hackathon

jorgeavilacartes/api-cnn-fcgr

jorgeavilacartes/awesome-graph-classification

A collection of important graph embedding, classification and representation learning papers with implementations.

jorgeavilacartes/bash-utilities

bash scripts with some functionalities

jorgeavilacartes/bioconda-recipes

Conda recipes for the bioconda channel.

jorgeavilacartes/blog

A customizable Jekyll Portfolio theme which supports blogging.

jorgeavilacartes/CouGaR-s

jorgeavilacartes/DeLUCS

This repository contains all the source files required to run DeLUCS, a deep learning clustering algorithm for DNA sequences.

jorgeavilacartes/dl-supervised-learning-geof

jorgeavilacartes/DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

jorgeavilacartes/embedding-msa

Embedding space for MSAs to query similar fastq files from k-mer distributions

jorgeavilacartes/fcgr-var

Variational Autoencoder with FCGR

jorgeavilacartes/fcgr2seq

reconstruct sequence from FCGR with deep learning

jorgeavilacartes/gnn-dbg

classification of long reads with dBG and GNN

jorgeavilacartes/K-means-waveletEMD

K-means using wavelet Earth Mover's Distance

jorgeavilacartes/make_prg

Code to create a PRG from a Multiple Sequence Alignment file

jorgeavilacartes/mof-search

BLAST-like search across all pre-2019 bacteria on ordinary laptop and desktop computers within a few hours

jorgeavilacartes/similarity-learning-dna

Similarity Learning for DNA sequences using FCGR images.

jorgeavilacartes/snpsandhaps

given an haplotype panel, compute sets of SNPs that are used by a set of Haplotypes using maximal blocks

jorgeavilacartes/spike-protein-experiment

deep learning with FCGR to classify spike proteins sequences

jorgeavilacartes/spike2vec-exp

classification and clustering experiments with spike protein as a vector representation

jorgeavilacartes/splice-junction-classification

Tezi Marzi

jorgeavilacartes/streamlit-fastapi-model-serving

Simple web app example serving a PyTorch model using streamlit and FastAPI

jorgeavilacartes/synthesizer

Generate synthetic observations from 3D numerical simulations

jorgeavilacartes/TheSims4ScriptModBuilder

An instruction of build script mod for The Sims4