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mycroft-core

Mycroft Core, the Mycroft Artificial Intelligence platform.

nativernaseqcomplextranscriptome

Code for the paper "A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes"

neural-networks-and-deep-learning

Code samples for my book "Neural Networks and Deep Learning"

papers_for_protein_design_using_dl

List of papers about Proteins Design using Deep Learning

pipeline-nanopore-ref-isoforms

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

porechop

adapter trimmer for Oxford Nanopore reads

proteinmpnn

Code for the ProteinMPNN paper

python_for_image_processing_apeer

https://www.youtube.com/playlist?list=PLHae9ggVvqPgyRQQOtENr6hK0m1UquGaG

python_for_microscopists

https://www.youtube.com/channel/UC34rW-HtPJulxr5wp2Xa04w?sub_confirmation=1

pytorch-grad-cam

Advanced AI Explainability for computer vision. Support for CNNs, Vision Transformers, Classification, Object detection, Segmentation, Image similarity and more.

pytorch-image-models

PyTorch image models, scripts, pretrained weights -- ResNet, ResNeXT, EfficientNet, NFNet, Vision Transformer (ViT), MobileNet-V3/V2, RegNet, DPN, CSPNet, Swin Transformer, MaxViT, CoAtNet, ConvNeXt, and more

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

pytorchzerotoall

Simple PyTorch Tutorials Zero to ALL!

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

scbert

scrnaseq

Pipelines for single-cell RNA-Seq analysis

sleuth_paper_analysis

Code to reproduce analyses from the sleuth paper

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

spliceai

A deep learning-based tool to identify splice variants

splicefinder

SpliceFinder applies convolutional neural network to classify sequences to donor, acceptor or non-splice-site. With a sliding window, it can predict the exact positions of every splice site on long genomic sequences with less false positives and high recall.

stable-diffusion

A latent text-to-image diffusion model

subread_to_dexseq

A way to use FeatureCounts output for DEXSeq

tensorflow_cookbook

Code for Tensorflow Machine Learning Cookbook

v2ray-core

A platform for building proxies to bypass network restrictions.

v2rayn

x-transformers

A simple but complete full-attention transformer with a set of promising experimental features from various papers