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Pipeline for SpatialTranscriptomics and 10X Visium data

R 21 7 Updated Aug 13, 2024

Unified access to several second-generation deconvolution methods

HTML 64 10 Updated Dec 3, 2024

Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks

Python 16 2 Updated Jun 2, 2022

Metacell - Single-cell mRNA Analysis

R 112 30 Updated Oct 11, 2023

MetaTiME: Meta-components in Tumor immune MicroEnvironment

Python 136 5 Updated Aug 11, 2023

Analysis of single cell RNA-seq data course

TeX 125 56 Updated Aug 8, 2022

EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.

R 192 41 Updated Mar 28, 2024

DRUGZ software

HTML 23 16 Updated Aug 9, 2021

Modeling of time series data for CRISPR KO experiments

Python 29 9 Updated Dec 9, 2024

抓取网络文章到github issues保存

Ruby 133 32 Updated Jan 14, 2025

Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

Python 95 25 Updated Jan 13, 2025
Python 46 9 Updated Dec 3, 2023

Deep Learning the T Cell Receptor Binding Specificity of Neoantigen

Python 78 21 Updated Jun 14, 2022

NewAnce is a java software tool for MSMS searching proteogenomics databases. See Chong et al. Nature Comm. 2020 (https://www.nature.com/articles/s41467-020-14968-9) and README for more information.

Java 5 3 Updated Oct 3, 2024

Priorization of neoantigens by machine learning

Python 8 2 Updated Dec 7, 2023
Jupyter Notebook 1,094 222 Updated Aug 1, 2024

A flexible framework for nucleosome profiling of cell-free DNA

Python 27 16 Updated Jul 27, 2023

cTPnet Package

Python 23 4 Updated Jul 12, 2022

Reproducibility of "Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response"

Jupyter Notebook 5 Updated Apr 2, 2023

This is the alpha version of the CellOracle package

Python 324 57 Updated Jan 8, 2025
Jupyter Notebook 13 1 Updated Sep 16, 2024

Updated SignatureAnalyzer-GPU with mutational spectra & RNA expression compatibility.

Python 74 21 Updated Jan 8, 2025

SSGCN

Python 5 4 Updated Jul 23, 2020

Super-resolved spatial transcriptomics by deep data fusion

Python 71 13 Updated Mar 30, 2023

Deciphering tumor ecosystems at super-resolution from spatial transcriptomics with TESLA

Jupyter Notebook 49 12 Updated Mar 18, 2024

cell type deconvolution for multi-condition bulk RNA-seq data

R 22 3 Updated Feb 28, 2022
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