Daniel Osorio dosorio
dosorio
/ install_sybilSBML.sh
Last active
August 1, 2023 19:34
Commands to install sybilSBML R package on MacOS/Linux
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| wget https://downloads.sourceforge.net/project/sbml/libsbml/5.17.0/stable/libSBML-5.17.0-core-plus-packages-src.tar.gz | |
| tar -xxvf libSBML-5.17.0-core-plus-packages-src.* | |
| cd libSBML-5.17.0-Source | |
| ./configure --prefix=/usr/local/ \ | |
| --enable-cpp-namespace \ | |
| --enable-fbc \ | |
| --enable-shared \ | |
| --with-gnu-ld \ | |
| --enable-layout \ | |
| --enable-comp \ |
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| for f in *.epub | |
| do | |
| anytomobi --dest-profile=Kindle "$files" | |
| done |
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| clear all; clc; | |
| %% How PCA works - Data | |
| rng(0); | |
| data(:,1) = randn(30,1); | |
| data(:,2) = 3.4 + 1.2 * data(:,1); | |
| data(:,2) = data(:,2) + 0.2*randn(size(data(:,1))); | |
| data = sortrows(data,1); | |
| figure | |
| axes('LineWidth',0.6,... |
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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| 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/" |
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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/") | |
| # 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) |
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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| # 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") |
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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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