开发的计算工具

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•GRANGER：基于格兰杰因果关系和循环神经网络用时序单细胞RNA测序数据预测基因调控网络模型。(2025)

Inferring Gene Regulatory Networks from Time-Series scRNA-seq Data via Granger Causal Recurrent Autoencoders (The related article: DOI: 10.1093/bib/bbaf089)

Source code: https://github.com/shaoqiangzhang/GRANGER

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•DeepBID：基于深度聚类的多批次单细胞RNA测序数据整合模型。(2024)

A deep learning model for batch integration of single-Cell RNA-seq data by deep clustering (The related article: PMID:38778573)

Source code: https://github.com/shaoqiangzhang/DeepBID

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•DeepIMAGER：基于有监督深度学习的单细胞RNA测序数据的基因调控网络预测算法。(2024)

A supervised deep-learning model for predicting cell-specific gene regulatory networks from scRNA-seq and ChIP-seq data. (The related article: PMID:39062480)

Source code: https://github.com/shaoqiangzhang/DeepIMAGER

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•DeepScena：基于深度学习的单细胞RNA测序数据的聚类算法。(2023)

Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations. (The related article: PMID:37769630)

Source code: https://github.com/shaoqiangzhang/DeepScena

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•DEGman：单细胞RNA测序数据的差异基因分析工具。(2022)

differentially-expressed genes of scRNA-seq data (The related article: PMID: 36009024)

Source code: https://github.com/shaoqiangzhang/DEGman

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•SCENA：单细胞RNA测序数据的细胞聚类算法。(2021)

Consensus clustering of single-cell RNA-seq data by enhancing network affinity (The related article: PMID:34160582)

Source code: https://github.com/shaoqiangzhang/SCENA

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•FisherMP：对ChIP-Seq结合峰数据进行模体发现的高效并行算法工具。(2019)

FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets (The related article:PMID:30957858)

Source code: https://github.com/shaoqiangzhang/fishermp

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•MotifClick：一个预测转录因子结合位点的模体发现算法。（2011）

MotifClick: A novel motif finding tool for predicting transcription factor binding sites. (The related article: PMID:21679436)

Source code: https://github.com/shaoqiangzhang/motifclick

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•SPIC：模体相似性近似计算公式。(2013)

SPIC: a novel metric for calculating transcription factor binding motif similarity (The related publication: PMID:24564945)

Source code: https://github.com/shaoqiangzhang/spic

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•CLIMP：一个大规模模体数据并行聚类算法。(2016)

CLIMP：a clustering algorithm for massive data with openMP parallel computing design (The related article:PMID:27487245)

Source code: https://github.com/shaoqiangzhang/climp

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