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  • LGC Characterization and identification of long non-coding RNAs based on feature relationship

    Categories Protein-coding gene predictionTool Type: ToolkitTechnologies: Java, Python2Download Count: 4957
  • GAAP Genome-organization-framework Assisted Assembly Pipeline

    Categories Genome assembly dataTool Type: Pipeline & ProtocolTechnologies: Python2Download Count: 2756
  • BS-RNA An efficient mapping and annotation tool for RNA Bisulfite Sequencing data

    Categories RNA methylation predictionTool Type: Pipeline & ProtocolTechnologies: Perl, Python2Download Count: 4162
  • CandiHap A haplotype analysis toolkit for natural variation study

    Categories Variant effect predictionTool Type: ToolkitTechnologies: Perl, Python2, RDownload Count: 33259
  • MtBNN A Bayesian neural network for quantifying functional impact of non-coding variants

    Tool Type: ApplicationTechnologies: Python2
  • 多模态影像处理软件 从前列腺多模态、多参数MR影像中提取高通量特征,对特征与感兴趣区域相关联的稳定性展开分析,筛选有效特征,并成功建立预后分析数据模型。

    Categories Tumor purity and heterogeneity estimationTool Type: ApplicationTechnologies: Python2Download Count: 5
  • 基于药物相似性网络数据的药物组合预测方法 提出一种基于图表示学习进行药物组合治疗的预测方法

    Categories Drug targetsTool Type: ApplicationTechnologies: Python2
  • 基于多维网络的癌症细胞系治疗药物预测方法 提出一种基于癌症细胞系相关的多层面数据预测药物反应的方法

    Categories Drug sensitivityTool Type: ApplicationTechnologies: Python2
  • 一种基于专用语料库字向量的无监督中文分词方法 一种基于专用语料库字向量的无监督中文分词方法

    Tool Type: ApplicationTechnologies: Python2
  • SAME: Estimation of Potential Richness of Dark Matters in “Pan Metagenome” Estimation of Potential Richness of Dark Matters in “Pan Metagenome” Using Species Appearance Model

    Categories Other unclassified toolsTool Type: ToolkitTechnologies: Python2Download Count: 1812
  • DeepShape Estimating isoform-level ribosome abundance and distribution with Ribo-seq data

    Categories Ribo-seq analysisTool Type: ToolkitTechnologies: Python2, Python3Download Count: 4603
  • CIRIquant Comprehensive toolkit for circRNA quantification and differential expression analysis

    Categories Circular RNA detectionTool Type: ToolkitTechnologies: Python2Download Count: 3104
  • DeepCAGE Incorporating Transcription Factors in Genome-wide Prediction of Chromatin Accessibility

    Tool Type: ToolkitTechnologies: Python2Download Count: 5367
  • DeepMSA Frequency division feature extraction method based on convolutional neural network

    Tool Type: ApplicationTechnologies: Python2
  • Dr. Sim Dr.Sim is a general learning-based framework that automatically infers similarity measurement, and can be used to characterize transcriptional profiles for drug discovery with generalized good performance.

    Categories Drug repositioningTool Type: ApplicationTechnologies: Python2, Python3Download Count: 898
  • CARMEN Computational assessment of the expression-modulating potential for noncoding variants

    Categories Variant effect predictionTool Type: ApplicationTechnologies: Java, Python2, RDownload Count: 937
  • 高通量原位结构解析软件包 高通量原位结构解析算法主要用于细胞原位等具有叠合蛋白密度样品的目标蛋白结构解析,该算法基于相关性分析,通过施加最优的权重函数,可以在单张冷冻电镜数据上实现目标蛋白质的定位以及高分辨结构解析。由于无需断层重构,原位结构解析的数据采集通量提升了数十倍。

    Categories Structure refinementTool Type: ApplicationTechnologies: C, Python2Download Count: 1579
  • 高通量、高分辨率的原位结构解析 目前蛋白质原位结构的解析主要依赖Cryo-ET,然而,这种方法需要收集每个区域的倾转序列,使原位样品的数据收集效率严重降低,因此原位课题通常难以开展。 为了实现高通量、高分辨率的原位结构解析,课题组开发了新型原位结构解析方法-isSPA,在这个方法里,我们将非目标蛋白的密度视为非高斯噪声,在单张高剂量的电镜图像中直接探测目标蛋白,我们推导了最优蛋白质探测函数,极大地提高了在图像中识别目标蛋白的效率。此外,我们还开发了一个排序函数,能有效地消除模型偏差对分辨率的影响。由于不需要收集倾转序列,isSPA较断层方法的数据收集通量提高了至少30倍。 课题组与北京理工大学张法、万晓华课题组合作,对isSPA方法进行了GPU加速-GisSPA,GPU加速将计算效率提高了300-500倍。目前,课题组应用GisSPA已经解析了红藻细胞切片中的藻胆体和光系统II的结构(分辨率分别达到了3.4和3.9埃)和酵母细胞切片中的核糖体结构(分辨率为2.9埃)。

    Categories Protein structuresTool Type: ApplicationTechnologies: C++, Python2Download Count: 1