├── CONTRIBUTING.md ├── LICENSE ├── Pseudotime_tools.png ├── README.md ├── R_packages_for_scRNA-seq.pdf ├── data └── Pullin_McCarthy_2022.csv └── tools └── loom.R /CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # Contributing 2 | 3 | Your contributions are always welcome! 4 | 5 | * Open an issue with any suggestion/correction 6 | * Send a Pull Request 7 | * Contact me on Twitter @mikhaildozmorov or by e-mail mikhail.dozmorov@gmail.com 8 | 9 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Mikhail Dozmorov 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /Pseudotime_tools.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/scRNA-seq_notes/c72875fdb23fab0db2aed434ddb13d8beb3c40aa/Pseudotime_tools.png -------------------------------------------------------------------------------- /R_packages_for_scRNA-seq.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mdozmorov/scRNA-seq_notes/c72875fdb23fab0db2aed434ddb13d8beb3c40aa/R_packages_for_scRNA-seq.pdf -------------------------------------------------------------------------------- /data/Pullin_McCarthy_2022.csv: -------------------------------------------------------------------------------- 1 | Table S1: Expert marker genes: pbmc3k, 2 | Cell type,Marker genes 3 | Naive CD4+ T,"IL7R, CCR7" 4 | CD14+ Mono,"CD14, LYZ" 5 | Memory CD4+,"IL7R, S100A4" 6 | B,MS4A1 7 | CD8+ T,CD8A 8 | FCGR3A+ Mono,"FCGR3A, MS4A7" 9 | NK,"GNLY, NKG7" 10 | DC,"FCER1A, CST3" 11 | Platelet,PPBP 12 | Table S2: Expert marker genes: Lawlor, 13 | Cell type,Marker gene 14 | Beta,INS 15 | Stellate,COL1A1 16 | Ductal,KRT19 17 | Alpha,GCG 18 | Acinar,PRSS1 19 | Gamma/PP,PPY 20 | Delta,SST 21 | Table S3: Expert marker genes: Zeisel, 22 | Cell type,Marker gene 23 | interneurons,PNOC 24 | pyramidal SS,TBR1 25 | pyramidal CA1,SPINK8 26 | oligodendrocytes,HAPLN2 27 | microglia,AIF1 28 | endothelial-mural,ACTA2 29 | astrocytes-ependymal,ALDOC 30 | Table S4: Expert marker genes: Smart-seq3, 31 | Cell type,Marker gene 32 | NK cells,"NCAM1, KLRB1" 33 | Naive/Memory CD8 T,PECAM1 34 | Cytotoxic T,"GZMB, GZMA" 35 | Naive B,"CD27, IGHM, IGHD, IL4R" 36 | Dendritic cells,"KLF4, CD1C" 37 | CD14 monocytes,CD14 38 | plasmacytoid DC,"IL3RA, TLR7" 39 | Plasma cells,"PRDM1, IRF4" -------------------------------------------------------------------------------- /tools/loom.R: -------------------------------------------------------------------------------- 1 | # https://satijalab.org/loomR/loomR_tutorial.html 2 | # Install devtools from CRAN 3 | install.packages("devtools") 4 | # Use devtools to install hdf5r and loomR from GitHub 5 | devtools::install_github(repo = "hhoeflin/hdf5r") 6 | devtools::install_github(repo = "mojaveazure/loomR", ref = "develop") 7 | # Load loomR 8 | library(loomR) 9 | # Download an example file from http://loom.linnarssonlab.org/ 10 | download.file(url = "http://loom.linnarssonlab.org/clone/osmFISH/osmFISH_SScortex_mouse_all_cells.loom", destfile = "osmFISH_SScortex_mouse_all_cells.loom") 11 | # Connect to the loom file in read/write mode 12 | lfile <- connect(filename = "osmFISH_SScortex_mouse_all_cells.loom", mode = "r+") 13 | lfile 14 | lfile[["matrix"]][1:5, 1:5] 15 | 16 | 17 | 18 | --------------------------------------------------------------------------------