Daniel Osorio dosorio
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| args = commandArgs(trailingOnly=TRUE) | |
| proteins <- list.files(args[1], full.names = "TRUE") | |
| ligands <- list.files(args[2], full.names = "TRUE") | |
| nRun <- 10 | |
| seedValues <- c(6, 12, 18) | |
| # proteins <- list.files("proteins/", full.names = TRUE) | |
| # ligands <- list.files("ligands/", full.names = TRUE) |
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| # Install Packages | |
| install.packages('scTenifoldNet') | |
| BiocManager::install('monocle') | |
| install.packages('reticulate') | |
| library(reticulate) | |
| reticulate::install_miniconda() | |
| reticulate::conda_install(packages = 'scipy', envname = 'scipy') | |
| reticulate::use_condaenv('scipy') |
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| # Review | |
| # https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1850-9 | |
| # Install Harmony | |
| library(devtools) | |
| install_github("immunogenomics/harmony") | |
| # Install SVA | |
| BiocManager::install('sva') |
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| # Install Packages | |
| install.packages(c('devtools','ggplot2')) | |
| BiocManager::install(c('fgsea', 'MAST', 'ensembldb', 'GenomeInfoDb')) | |
| devtools::install_github('cailab-tamu/scTypeGSEA') | |
| # Loading libraries | |
| library(Seurat) | |
| library(MAST) | |
| library(ggplot2) | |
| library(scTypeGSEA) |
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| # Loading Seurat | |
| library(Seurat) | |
| # Moving to downloads | |
| setwd("../Downloads/") | |
| # Getting the input files from 10X Genomics | |
| inputFile <- "http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.tar.gz" | |
| download.file(inputFile, "PBMC.tar.gz") | |
| untar("PBMC.tar.gz") |
dosorio
/ installManiNetCluster.R
Created
August 26, 2019 22:02
Commands to install ManiNetCluster in Windows 64bit
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| devtools::install_github("namtk/ManiNetCluster" ,INSTALL_opts=c("--no-multiarch")) |
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| setwd("../Downloads/") | |
| # BiocManager::install(c('TFBSTools', 'ggbio', 'motifmatchr', | |
| # 'BSgenome','BSgenome.Hsapiens.UCSC.hg19', | |
| # 'EnsDb.Hsapiens.v75','hdf5r')) | |
| # devtools::install_github("timoast/signac") | |
| library(Signac) | |
| library(Seurat) | |
| library(GenomeInfoDb) | |
| library(EnsDb.Hsapiens.v75) | |
| library(ggplot2) |
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| source("https://raw.githubusercontent.com/dosorio/utilities/master/idConvert/hsa_SYMBOL2ENTREZ.R") | |
| source("https://raw.githubusercontent.com/dosorio/utilities/master/enrichments/hsa_KEGG_ENTREZ.R") | |
| setwd("../Downloads/") | |
| # 1K Cells | |
| download.file("http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_v3/pbmc_1k_v3_filtered_feature_bc_matrix.tar.gz", destfile = "PBMC1K.tar.gz") | |
| # 10K Cells | |
| download.file("http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_10k_v3/pbmc_10k_v3_filtered_feature_bc_matrix.tar.gz", destfile = "PBMC10K.tar.gz") | |
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| setwd("../Downloads/") | |
| # Getting the input files from 10X Genomics | |
| inputFile <- "http://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.tar.gz" | |
| download.file(inputFile, "PBMC.tar.gz") | |
| untar("PBMC.tar.gz") | |
| #Input Folder | |
| inputFolder <- "filtered_feature_bc_matrix/" |
dosorio
/ readSalmonAlevin.R
Created
February 20, 2019 21:27
Function to read the binary output of salmon alevin in R (single-cell RNA-seq)
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| readSalmonAlevin <- function(alevinFolder){ | |
| matrixFile <- paste0(alevinFolder, "/quants_mat.gz") | |
| matrixFile <- gzfile(description = matrixFile, open = 'rb') | |
| genes <- readLines(paste0(alevinFolder,"/quants_mat_cols.txt")) | |
| cells <- readLines(paste0(alevinFolder,"/quants_mat_rows.txt")) | |
| n <- length(genes)*length(cells) | |
| counts <- readBin(matrixFile,what = 'numeric', n = n) | |
| close.connection(matrixFile) | |
| countMatrix <- matrix(data = counts, | |
| nrow = length(cells), |
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