/Bioinformatics-Tools

记录学习的生物信息学相关工具

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Bioinformatics-Tools

记录学习的生物信息学相关工具

R语言

tidyverse

  1. tidyverse
  2. ggplot2

R 绘图

  1. ggalluvial
  2. DiagrammeR
  3. linkET
  4. circlize

单细胞空间转录组

  1. Seurat：R toolkit for single cell genomics
  2. DoubletFinder：R package for detecting doublets in single-cell RNA sequencing data
  3. anndata：a Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray
  4. MetaNeighbor：a method to rapidly assess cell type identity using both functional and random gene sets
  5. scrattch.hicat：Hierarchical, Iterative Clustering for Analysis of Transcriptomics
  6. WGCNA：an R package for weighted correlation network analysis
  7. hdWGCNA：high dimensional WGCNA
  8. Monocle：An analysis toolkit for single-cell RNA-seq
  9. CellChat：Inference and analysis of cell-cell communication
  10. NeuronChat：Inferring neuron-neuron communications from single-cell transcriptomics
  11. scCustomize：A collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R

机器学习深度学习

  1. XGBoost：Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library
  2. glmnet：Lasso and Elastic-Net Regularized Generalized Linear Models

图像处理

  1. nnUNet：a self-configuring method for deep learning-based biomedical image segmentation