scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
https://github.com/ZJUFanLab/scCATCH
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安装

  1. # install devtools and install scCATCH
  2. install.packages(pkgs = 'devtools')
  3. devtools::install_github('ZJUFanLab/scCATCH')

scCATCH包可以自动对cluster进行注释，PS: 对于样本的组织来源要明确，准确度越高越好。比较依赖于组织特异性。
可以直接处理seurat流程输出的结果。

  1. ##load  package
  2. library(scCATCH)
  3. library(Seurat)

以测试数据为例

使用

  1. ##load data
  2. load("mouse_kidney_203_Seurat.RData")
  4. ##构建marker基因列表
  5. clu_markers <- findmarkergenes(object = mouse_kidney_203_Seurat,
  6.                                species = 'Mouse',###物种 现在只有Human和Mouse这两种
  7.                                cluster = 'All',###可以指定cluster
  8.                                match_CellMatch = FALSE,##对于大量的cluster数据，建议设置为TRUE
  9.                                cancer = NULL,
  10.                                tissue = NULL,
  11.                                cell_min_pct = 0.25,
  12.                                logfc = 0.25,
  13.                                pvalue = 0.05)
  14. ##对潜在标记基因进行注释
  15. clu_ann <- scCATCH(object = clu_markers$clu_markers,
  16.                    species = 'Mouse',
  17.                    cancer = NULL,##对于癌症组织有特定设定
  18.                    tissue = 'Kidney'##确定单细胞的组织来源
  19.                   )
  21. new.cluster.ids <- clu_ann$cell_type#把预测细胞类型与cluser进行匹配
  22. names(new.cluster.ids) <- clu_ann$cluster
  23. mouse_kidney_203_Seurat <- RenameIdents(mouse_kidney_203_Seurat, new.cluster.ids)#进行重新命名
  24. DimPlot(mouse_kidney_203_Seurat, reduction = "umap", label = TRUE, pt.size = 0.5) + NoLegend()

注释前：
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注释后：
image.png
cluster cell_type
1 Collecting Duct Intercalated Cell
2 Collecting Duct Principal Cell
3 Proximal Tubule Cell

重要参数

对于cancer和tissue的设置可以查看详细的参数

  1. ?scCATCH
  3. 1.1 For Human tissue, tissue types are listed as follows:
  5. Adipose tissue-related: Abdominal adipose tissue; Adipose tissue; Brown adipose tissue; Fat pad; Subcutaneous adipose tissue; Visceral adipose tissue; White adipose tissue.
  7. Bladder-related: Bladder; Urine.
  9. Blood-related: Blood; Peripheral blood; Plasma; Serum; Umbilical cord blood; Venous blood.
  11. Bone-related: Anterior cruciate ligament; Bone; Bone marrow; Cartilage; Intervertebral disc; Meniscus; Nucleus pulposus; Osteoarthritic cartilage; Periosteum; Skeletal muscle; Spinal cord; Synovial fluid; Synovium.
  13. Brain-related: Brain; Dorsolateral prefrontal cortex; Embryonic brain; Embryonic prefrontal cortex; Fetal brain; Hippocampus; Inferior colliculus; Midbrain; Sympathetic ganglion.
  15. Breast-related: Breast; Mammary epithelium.
  17. Embryo-related: Embryo; Embryoid body; Embryonic brain; Embryonic prefrontal cortex; Embryonic stem cell; Germ; Primitive streak.
  19. Esophagus-related: Esophagus.
  21. Eye-related: Cornea; Corneal endothelium; Corneal epithelium; Eye; Lacrimal gland; Limbal epithelium; Optic nerve; Retina; Retinal pigment epithelium; Sclerocorneal tissue.
  23. Fetus-related: Amniotic fluid; Amniotic membrane; Fetal brain; Fetal gonad; Fetal kidney; Fetal liver; Fetal pancreas; Placenta; Umbilical cord; Umbilical cord blood; Umbilical vein.
  25. Gonad-related: Corpus luteum; Fetal gonad; Foreskin; Gonad; Ovarian cortex; Ovarian follicle; Ovary; Seminal plasma; Testis.
  27. Hair-related: Chorionic villus; Hair follicle; Scalp.
  29. Heart-related: Heart; Myocardium.
  31. Intestine-related: Colon; Colorectum; Gastrointestinal tract; Gut; Intestinal crypt; Intestine; Jejunum; Large intestine; Small intestinal crypt; Small intestine.
  33. Kidney-related: Adrenal gland; Fetal kidney; Kidney; Renal glomerulus.
  35. Liver-related: Fetal liver; Liver.
  37. Lung-related:Airway epithelium; Alveolus; Bronchoalveolar system; Lung.
  39. Lymph-related: Lymph; Lymph node; Lymphoid tissue.
  41. Muscle-related: Muscle; Skeletal muscle.
  43. Nose-related: Nasal concha; Nasal epithelium; Sinonasal mucosa.
  45. Oral cavity-related: Laryngeal squamous epithelium; Oral mucosa; Salivary gland; Sputum; Submandibular gland; Thyroid; Tonsil; Vocal fold.
  47. Ovary-related: Corpus luteum; Ovarian cortex; Ovarian follicle; Ovary; Oviduct.
  49. Pancreas-related: Fetal pancreas; Pancreas; Pancreatic acinar tissue; Pancreatic islet.
  51. Prostate-related: Prostate.
  53. Skin-related: Dermis; Skin.
  55. Spleen-related: Spleen; Splenic red pulp.
  57. Stomach-related: Gastric corpus; Gastric epithelium; Gastric gland; Gastrointestinal tract; Pyloric gland; Stomach.
  59. Testis-related: Testis.
  61. Tooth-related: Deciduous tooth; Dental pulp; Gingiva; Molar; Periodontal ligament; Premolar; Tooth.
  63. Uterus-related: Endometrium; Endometrium stroma; Myometrium; Uterus; Vagina.
  65. Vessel-related: Adventitia; Antecubital vein; Artery; Blood vessel; Umbilical vein.
  67. Others: Ascites; Epithelium; Ligament; Pluripotent stem cell; Thymus; Whartons jelly.
  69. ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  71. 1.2 For Human tissue about cancer, cancer types and the corresponding tissue types are listed as follows:
  73. Acute Myelogenous Leukemia: Blood.
  75. Acute Myeloid Leukemia: Bone marrow.
  77. Adenoid Cystic Carcinoma: Salivary gland.
  79. Alveolar Cell Carcinoma: Serum.
  81. Astrocytoma: Brain.
  83. B-Cell Lymphoma: Lymphoid tissue.
  85. Bladder Cancer: Bladder.
  87. Brain Cancer: Blood vessel; Brain.
  89. Breast Cancer: Blood: Breast; Mammary gland.
  91. Cholangiocarcinoma: Liver; Serum.
  93. Chronic Lymphocytic Leukemia: Blood.
  95. Chronic Myeloid Leukemia: Blood.
  97. CNS Primitive Neuroectodermal Tumor: Brain.
  99. Colon Cancer: Blood; Colon; Serum.
  101. Colorectal Cancer: Blood; Colon; Colorectum; Gastrointestinal tract; Intestine; Liver; Lung; Venous blood.
  103. Cutaneous Squamous Cell Carcinoma: Skin.
  105. Endometrial Cancer: Endometrium.
  107. Ependymoma: Brain.
  109. Esophageal Adenocarcinoma: Esophagus.
  111. Fibroid: Myometrium.
  113. Follicular Lymphoma: Lymph node.
  115. Gallbladder Cancer: Gall bladder; Gastrointestinal tract.
  117. Gastric Cancer: Blood; Peripheral blood; Serum; Stomach.
  119. Glioblastoma: Blood; Brain.
  121. Glioma: Blood vessel; Brain.
  123. Gonadoblastoma: Embryo.
  125. Head and Neck Cancer: Blood; Brain; Oral cavity.
  127. Hepatoblastoma: Liver.
  129. Hepatocellular Cancer: Blood; Bone marrow; Embryo; Liver.
  131. High-grade glioma: Brain.
  133. Infantile Hemangiomas: Placenta.
  135. Intestinal Cancer: Gastrointestinal tract.
  137. Intracranial Aneurysm: Brain.
  139. Kaposi's Sarcoma: Lymph node.
  141. Larynx Cancer: Larynx.
  143. Leukemia: Bone marrow; Peripheral blood.
  145. Lipoma: Adipose tissue.
  147. Liver Cancer: Blood; Liver.
  149. Lung Adenocarcinoma: Lung.
  151. Lung Cancer: Blood; Lung.
  153. Lung Squamous Cell Carcinoma: Lung.
  155. Lymphoma: Blood; Brain; Kidney; Liver; Lymph; Lymph node.
  157. Malignant Insulinoma: Pancreas.
  159. Malignant Mesothelioma: Lung; Pleura.
  161. Malignant Peripheral Nerve Sheath Tumor: Brain.
  163. Medulloblastoma: Brain.
  165. Melanoma: Blood; Peripheral blood; Skin.
  167. Mucoepidermoid Carcinoma: Salivary gland.
  169. Multiple Myeloma: Bone marrow; Peripheral blood.
  171. Myeloma: Bone marrow.
  173. Natural Killer Cell Lymphoma: Lymph node.
  175. Nephroblastoma: Kidney.
  177. Non-Small Cell Lung Cancer: Blood; Lung; Peripheral blood.
  179. Oesophageal Cancer: Blood.
  181. Oligodendroglioma: Brain.
  183. Oral Cancer: Oral cavity.
  185. Oral Squamous Cell Carcinoma: Oral cavity; Peripheral blood.
  187. Osteosarcoma: Bone.
  189. Ovarian Cancer: Ascites; Ovarian cortex; Ovary; Peripheral blood.
  191. Pancreatic Cancer: Blood vessel; Pancreas.
  193. Pancreatic Ductal Adenocarcinomas: Pancreas.
  195. Papillary Thyroid Carcinoma: Thyroid.
  197. Prostate Cancer: Blood; Peripheral blood; Prostate.
  199. Renal Cell Carcinoma: Kidney; Serum.
  201. Renal Clear Cell Carcinoma: Lymph node.
  203. Retinoblastoma: Eye.
  205. Salivary Gland Tumor: Parotid gland; Salivary gland.
  207. Sarcoma: Muscle.
  209. Small Cell Lung Cancer: Lung.
  211. Testicular Germ Cell Tumor: Peripheral blood; Testis.
  213. Thyroid Cancer: Thyroid.
  215. Tongue Cancer: Tongue.
  217. Uterine Leiomyoma: Uterus.
  219. Vascular Tumour: Lymph node.
  221. ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  223. 2.1 For Mouse tissue, tissue types are listed as follows:
  225. Adipose tissue-related: Adipose tissue; White adipose tissue.
  227. Bladder-related: Bladder.
  229. Blood-related: Blood; Peripheral blood; Serum; Umbilical cord blood.
  231. Bone-related: Bone; Bone marrow; Meniscus; Skeletal muscle; Spinal cord.
  233. Brain-related: Brain; Cerebellum; Fetal brain; Hippocampus; Neural tube.
  235. Breast-related: Mammary epithelium; Mammary gland.
  237. Calvaria-related: Neonatal calvaria.
  239. Ear-related: Cochlea; Inner Ear.
  241. Embryo-related: Embryo; Embryoid body; Embryonic heart; Embryonic stem cell.
  243. Esophagus-related: Esophagus.
  245. Eye-related: Corneal epithelium; Eye; Ganglion cell layer of retina; Inner nuclear layer of retina; Lacrimal gland; Retina.
  247. Fetus-related: Fetal brain; Fetal intestine; Fetal liver; Fetal lung; Fetal stomach; Placenta; Umbilical cord; Umbilical cord blood.
  249. Gonad-related: Gonad; Ovary; Testis; Yolk sac.
  251. Hair-related: Hair follicle.
  253. Heart-related: Embryonic heart; Heart; Heart muscle; Neonatal heart.
  255. Intestine-related: Colon; Colon epithelium; Fetal intestine; Gastrointestinal tract; Ileum; Intestinal crypt; Intestine; Mesenteric lymph node; Small intestine.
  257. Kidney-related: Kidney; Mesonephros.
  259. Liver-related: Fetal liver; Liver.
  261. Lung-related: Bronchiole; Fetal lung; Lung; Trachea.
  263. Lymph-related: Lymph node; Lymphoid tissue; Mesenteric lymph node; Peyer patch.
  265. Muscle-related: Heart muscle; Muscle; Neonatal muscle; Skeletal muscle.
  267. Neonate-related: Neonatal calvaria; Neonatal heart; Neonatal muscle; Neonatal pancreas; Neonatal rib; Neonatal skin.
  269. Oral cavity-related: Submandibular gland; Taste bud.
  271. Ovary-related: Ovary; Yolk sac.
  273. Pancreas-related: Neonatal pancreas; Pancreas; Pancreatic islet.
  275. Prostate-related: Prostate.
  277. Skin-related: Dermis; Epidermis; Neonatal skin; Skin.
  279. Spleen-related: Spleen.
  281. Stomach-related: Fetal stomach; Gastrointestinal tract; Stomach.
  283. Testis-related: Testis.
  285. Uterus-related: Uterus.
  287. Vessel-related: Aorta; Artery; Blood vessel; Carotid artery.
  289. Others: Basilar membrane; Epithelium; Peritoneal cavity; Thymus.
  291. ———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
  293. 2.2 For Mouse tissue about cancer, cancer types and the corresponding tissue types are listed as follows:
  295. Breast Cancer: Lymph node; Breast; Lung.
  297. Chronic Myeloid Leukemia: Blood.
  299. Colon Cancer: Colon.
  301. Colorectal Cancer: Lymph node; Colon; Colorectum.
  303. Cutaneous Squamous Cell Carcinoma: Skin.
  305. Hepatocellular Cancer: Blood; Liver.
  307. Liver Cancer: Liver.
  309. Lung Cancer: Lung.
  311. Melanoma: Lung.
  313. Pancreatic Cancer: Blood.
  315. Papillary Thyroid Carcinoma: Thyroid.
  317. Prostate Cancer: Prostate.
  319. Renal Cell Carcinoma: Kidney.
  321. Supratentorial Primitive Neuroectodermal Tumor: Brain.

可参考的博客：
https://www.jianshu.com/p/cf7a7341b0b6