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abe_cbe_spcas9

Model with great generalization applied in the trap-ABE, trap-CBE, and trap-spCas9

azimuth

Machine Learning-Based Predictive Modelling of CRISPR/Cas9 guide efficiency

bertlocrna

Using Large language model to predict localization

cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

cellphonedb

CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

crispr-trap-seq

This is a ML learning model to predict the gRNA efficiency of trap-based editing system. eg.ABE, CBE, Cas9

cytoself

Self-supervised models for encoding protein localization patterns from microscopy images

deep-learning

deeplocrna

This is the counterpart of DeepLoc, but in RNA level

deeprnagenerator

This is used to generate optimized RNA for vaccine design

delfi_scripts

dnabert

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

find_cell_marker

This is a software for identifying the cell type for single cell analysing

gnl_scorer

this is a software for sgRNA activity prediction with great generalization

gnl_script

The script of the paper

gnl_supplementary_script

graph-part

A biological sequence data partitioning method

hellow-

hellow-world

this is my first time in github

ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

introtoml-scvae

This is an instruction for scVAE about how it works and how to run the demo scripts

llmbenchmarking

Benchmarking the language model in genomic and transcriptome level

rankcomp

This is a learning framework to extract the DEG (Differential expression genes) by high fided gene pairs

rankcomp2

A learning framework to get DEG(Differential expression genes)

rctd

rna-localization

This repository can be used to data sharing, code sharing, and feedbacks

scdeepcluster

scDeepCluster for Single Cell RNA-seq data

st_simulation

trap-crispr

This is a ML learning model to predict the gRNA efficiency of trap-based editing system. eg.ABE, CBE, Cas9

trap-seq-data-processing

The scripts of score comparison shown in the Trap-seq paper