JasonLinjc

awesome-CRISPR

List of software/websites/databases/other stuff for genome engineering

boda2

Computational Optimization of DNA Activity (CODA)

borzoi

RNA-seq prediction with deep convolutional neural networks.

Convolutional-KANs

This project extends the idea of the innovative architecture of Kolmogorov-Arnold Networks (KAN) to the Convolutional Layers, changing the classic linear transformation of the convolution to learnable non linear activations in each pixel.

CRISPR-GAN

Generative adversarial network for CRISPR OT detection

CRISPR-Net

A Recurrent Convolutional Network Quantifies CRISPR Off-target Activities with Indels and Mismatches

CRISPRattention

An artificial intelligence approach for gene editing off-target quantification: convolution neural network designs and considerations

deepMotifSyn

A deep learning approach to synthesize heterodimeric DNA motifs

CRISPR_WGS_Detection

EPInformer

code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

JasonLinjc/CRISPR-Net

A Recurrent Convolutional Network Quantifies CRISPR Off-target Activities with Indels and Mismatches

JasonLinjc/deepMotifSyn

A deep learning approach to synthesize heterodimeric DNA motifs

JasonLinjc/awesome-CRISPR

List of software/websites/databases/other stuff for genome engineering

JasonLinjc/boda2

Computational Optimization of DNA Activity (CODA)

JasonLinjc/borzoi

RNA-seq prediction with deep convolutional neural networks.

JasonLinjc/Convolutional-KANs

This project extends the idea of the innovative architecture of Kolmogorov-Arnold Networks (KAN) to the Convolutional Layers, changing the classic linear transformation of the convolution to learnable non linear activations in each pixel.

JasonLinjc/CRISPR-GAN

Generative adversarial network for CRISPR OT detection

JasonLinjc/CRISPRattention

An artificial intelligence approach for gene editing off-target quantification: convolution neural network designs and considerations

JasonLinjc/CRISPR_comparison

Snakemake workflow for comparing E-G links to experimental data

JasonLinjc/DeepSTARR

Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Drosophila melanogaster S2 cells

JasonLinjc/enformer_fine_tuning

For fine-tuning Enformer using paired WGS & gene expression data

JasonLinjc/EPCOT

JasonLinjc/epiformer

JasonLinjc/EPInformer

code to run EPInformer for gene expression prediction and gene-enhancer links prioritization

JasonLinjc/esm

JasonLinjc/GenBench

JasonLinjc/gReLU

gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

JasonLinjc/ProCapNet

Repository for modeling PRO-cap data with BPNet.

JasonLinjc/regLM

Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.

JasonLinjc/sei-framework

code to run sei and obtain sei and sequence class predictions