sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7a43a429eee88737891291485b9a02241aa26a89dc4b47d573ab5f96a658d2d5 | R | 1,707 | 45 | library(readxl)
library(data.table)
library(dplyr)
library(ggplot2)
library(DOSE)
library(scales)
##get dot wisker plot for GNOVA
Final_file<- fread("GNOVA_results.csv")
Final_file$Adjusted_P<- ifelse(Final_file$Adjusted_P < 0.05,Final_file$Adjusted_P,NA)
Final_file$Adjusted_P<- scientific(Final_file$Adjusted_P)
##a... |
b33aabbcb60ca455aca2d1a9a06e2f17c9aca3ecfedf3b1342fc86ced03ab307 | R | 1,707 | 46 | library(Seurat)
library(dplyr)
library(Matrix)
library(readr)
library(ggplot2)
library(stringr)
library(ggpubr)
library(tidyr)
setwd("/home/sridevi/inkwell03_sridevi//metadevorganoid/werneranalysis/DevTime_gitub_repo/") #change to the working directory
final_common_genes<-readRDS("models/commongenes.rds")#list of com... |
4d859883af50e309442d11c138a749d1935c8614f9dba95b69ebe5c33790b42d | R | 1,721 | 43 | #' @title smooth Repli-seq assay
#' @description Calculate the smoothed count matrices of a Repli-seq assay
#'
#' @param rs_assay a dataframe for a Repli-seq assay loaded with readRS()
#' @param smooth_factor the factor to apply to the scale (going from 1kb to 50kb gives smooth_factor = 50 ; from 50kb to 100kb : smoot... |
05667f4c02e0cad32650bbee935c40c87cdaa5ab08008f0e224a17ae9accfdc7 | R | 1,725 | 70 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_aescatter_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL),
wi... |
63b7ee1a971b6d6bbef5ed0fb180cbf0a8b041a8d6eaaa14c4e93520eecb5acc | R | 1,737 | 73 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_MTrelationships_ui <- function(
id,
title = "",
label = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
... |
325d80c556b1167d7f3e39588d8b10c6751e842bf40a5c0a1eeec56fa18d80bf | R | 1,740 | 67 | dir.base <- "."
dir.data <- file.path(dir.base, "datasets/combp")
dir.results <- file.path(dir.base, "analysis_results")
dir.results.combp <- file.path(dir.results, "DMR")
dir.results.meta <- file.path(dir.results, "meta_analysis")
dir.data.aux <- file.path(dir.base, "../DATASETS/Aux_Sync")
for(p in grep("dir.",ls(),va... |
6f31c87314107483f543f1d7b26ca81ba996eed4b2c6c27369a19ba30405ecc3 | R | 1,743 | 36 | # # GWAS Locus Browser Evidence Script
# - **Author** - Frank Grenn
# - **Date Started** - September 2019
# - **Quick Description:** simple script to merge the evidence files generated by the other scripts. This output will be used in the "Evidence Per Gene" table in the browser.
# - **Data:**
# input data obtained ... |
08b20236c4452ece43ea8097f323c2748a16a122b2afb3bddb8cf713104d806a | R | 1,747 | 75 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_lasagna_network_ui <- function(
id,
title = "",
info.text = "",
info.methods = "",
info.references = NULL,
info.extra_link = NULL,
caption = info.text,
label = ""... |
467702124666aa7ad56e5168102da99d4e699d24a081cd9edb92fbc25737a040 | R | 1,749 | 37 | #' @title Write BigWig files of Repli-seq assays
#' @description writes one BigWig file per fraction in the provided Repli-seq assay
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx (or S0)
#' @param path_file a path to the files to write
#' @param samp... |
886ed0c3aabee822598798199172c7d728daee6d77bd0744b20c749592db87fb | R | 1,753 | 70 | library("rvest")
library("tidyverse")
library("stringr")
library("data.table")
library("httr")
genes <- fread("$PATH/genes_by_locus.csv")
gene_names <- unique(genes$Gene)
completed_genes <- NA
if(file.exists("GeneCardDescriptions.txt"))
{
description_df <- fread("GeneCardDescriptions.txt",sep="\t")
completed_gen... |
aca1ea1c530f3bf8d886228bfb50d38b5909e18794e56c6c5f9718a235d62df0 | R | 1,758 | 51 | finemap<-list()
finemap$id <- "finemap"
finemap$title <- "Fine-Mapping of Locus"
finemap$loadData<- function(){
#finemapping data
finemapping <<- fread("www/finemapping/fineMappingFilteredData.csv")
colnames(finemapping) <<- c("Locus Number", "SNP", "Chr", "BP", "Ref", "Alt", "Frequency", "P-value", "Prob", "... |
2e07abe31536b7c219cd8f8dbf393a0fd9e5c7f1eb02c5f7c66bcbc7254272b1 | R | 1,759 | 67 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
# Building a Prod-Ready, Robust Shiny Application.
#
# README: each step of the dev files is optional, and you don't have to
# fill every dev scripts before getting started.
# 01_start.R s... |
1aa99815096cb03ab3de67d027098afb28db303592460a73fe41d25597e3e087 | R | 1,760 | 77 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_module_barplot_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400,
...
) {
ns <- shiny::NS(id)
options <- s... |
a562001c080ce970466da8554cc1ae828b493b1ac2c59093a93b784a5c91ca20 | R | 1,763 | 78 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_sampletree_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- ... |
8777b44608dd8d55bf9e6f826355e73f293a6fb48d22966d672d64f1be4c6cab | R | 1,787 | 30 | args=commandArgs(trailingOnly=TRUE)
data1_resize<-read.table(args[1], sep = '\t', header=T, comment.char = "")
data1_resize$chr <- 0
data1_resize[data1_resize[,1]=="chr1",ncol(data1_resize)] <- 1
data1_resize[data1_resize[,1]=="chr2",ncol(data1_resize)] <- 2
data1_resize[data1_resize[,1]=="chr3",ncol(data1_resize)] <-... |
88bf24ad6af718ad1734c0a1b726bc4385d04ef873fe16b6b35d0157ab55b2bf | R | 1,802 | 71 | # =========================================================
# PCA analysis (no plotting)
# =========================================================
library(data.table)
# -----------------------------
# 1. Paths
# -----------------------------
# PCA输出目录（analysis层）
output_dir <- file.path(results_analysis_dir,... |
8d9b63c685d41762432414940a84081c8c71bcfa685ddb81d1dbae9cee2bd76b | R | 1,802 | 87 | #
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MODULE.wgcna <- list(
module_menu = function() {
c(
wgcna = HTML("Standard WGCNA"),
consensus = "Consensus WGCNA",
preservation = "Preservation WGCNA",
mwgcna ... |
369f81fd38a3dba4e8dfd1272e5123c9255ee5de1d8f64cba40e37cb8ff00d03 | R | 1,814 | 81 | ## make as R6 class?? e.g. add documentation, initialize object,
## object id.
MODULE.enrichment <- list(
module_menu = function() {
c(
enrich = "Geneset enrichment",
sig = "Test geneset",
pathway = "Pathway analysis",
wordcloud = "Word cloud"
)
},
module_server = function(PGX, la... |
22af675ab05046675eeb4fbd592191aa5f6826c52c48cf664c1c6309f2cf0370 | R | 1,819 | 70 | #
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
UpgradeModuleUI <- function(id) {
ns <- shiny::NS(id)
shiny::actionButton(
ns("action"), "Upgrade",
width = "auto", class = "quick-button"
)
}
UpgradeModuleServer <- function... |
86bef0b1bd8b765c7185d94691a68235d8df247c55c81ff8dbf6470df5130a9f | R | 1,820 | 75 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_dendrogram_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tagLis... |
51c98105bdbed79b2c3ccaa917b6210a940cfd9e4e31fe1ffcfc112bd0286780 | R | 1,821 | 44 | log <- file(snakemake@log[[1]], open = "wt")
sink(file = log, type = "message")
sink(file = log, type = "output")
library(data.table)
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/makeSVcalls.R")
# probs <- readRDS(snakemake@input[["probs"]])
# llr <- as.numeric(snakemake@wildcards[["llr"]])
# use.... |
efbb61cd2b8c8689e769d40475d0af6c9f675ba6ddc90714a4a0c85075eaf4a3 | R | 1,831 | 58 | # Step 1: Install and load RSQLite
library(RSQLite)
# Step 2: Create a new SQLite database and establish a connection
connection <- dbConnect(RSQLite::SQLite(), dbname = "etc/user_details.sqlite")
# Step 3: Create a table with the specified fields
dbExecute(connection, "
CREATE TABLE IF NOT EXISTS users (
usern... |
08e6e7b2c452b3255a2cae392402bd4b43df620f799412334a07c529a8d33f54 | R | 1,838 | 73 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_snfgraph_ui <- function(
id,
...
) {
ns <- shiny::NS(id)
options <- tagList(
shiny::selectInput(
ns("labeltype"),
"Label type",
choices = "none"
... |
c9fa824fabd82aa3e14ff894f4fa836a01b0468dea9c6357827215e90535a9e9 | R | 1,862 | 42 | ### Differential Expression Analysis of scRNA-seq Data - 00 - Splitting Seurat Object ###
# Splitting Seurat Object by Activated and Unactivated Neurons
# set up
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat")
stopifnot(suppressMessages(sapply(packages, require, character.only=TRUE)))
s.obj.name =... |
8ef0054b3559c2709287a84a5ba5ffcca3e79cfd9c912d8fbc25d600b10356b4 | R | 1,878 | 68 |
## from https://gist.github.com/Swarchal/b938933ae9ded94b3c14d6485b27cf69
## Requirements and library loading
# install.packages(c('platetools', 'ggplot2', 'viridis', 'dplyr'))
library(platetools)
library(ggplot2)
library(viridis)
library(dplyr)
## collect ASHLEYS prediction and count files
# prediction_file = li... |
52dde753fc4364d518d0c24773d96abcfbdb264038f890a44444c74f0c25f7dc | R | 1,889 | 76 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_mgsea_ui <- function(
id,
title = "",
info.text = "",
info.methods,
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- ta... |
7b7981dc8d5eaebfc74f0d57b8a9a12b21aac12a85694d4fe4acfc0d5df82964 | R | 1,893 | 64 | rm(list = ls())
library(Seurat)
library(harmony)
set.seed(1234)
# The data with format required by Harmony are available at:
# https://drive.google.com/file/d/1g763Z7ClovTDn7aQXj4hJs6cxLFjvQAS/view?usp=sharing
# load data
data_path <- "data_for_R"
load(paste0(data_path, "/DLPFC_4slices.RData"))
obj.list <- SplitOb... |
e1407627e967d6a64e42db0fa0c97df6ed26d12a8e7aed6dfdacc60c3f56081e | R | 1,897 | 51 | library(ggplot2)
library(reshape2)
# cellwise <- "cell" %in% names(snakemake@wildcards)
if (("cell" %in% names(snakemake@wildcards)) == TRUE) {
wc_cell_row_plate <- snakemake@wildcards[["cell"]]
type <- "Cell"
} else if(("row" %in% names(snakemake@wildcards)) == TRUE) {
wc_cell_row_plate <- snakemake@wildc... |
955d32f60298b5fb758fa97ff1083db709e531d227b63c715de21f233628f865 | R | 1,901 | 59 | # Manhattan plot
dir.base <- "."
dir.results <- file.path(dir.base, "analysis_results")
dir.results.meta <- file.path(dir.results, "meta_analysis")
dir.data.aux <- file.path(dir.base, "../DATASETS/Aux_Sync/")
dir.results.combp <- file.path(dir.results, "DMR")
dir.plot <- file.path(dir.results, "plots")
source(file.pa... |
d0bca429c943a271ff581d0f204e39199d6b12941f7486ae346d777087204890 | R | 1,905 | 76 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_eigengene_heatmap_ui <- function(
id,
label,
title,
info.text,
caption,
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::checkboxIn... |
febb9f280100523d8f1f14b6d70f8b18c2748caec7817714251b0ed1ca58e5a8 | R | 1,911 | 85 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_dendrograms_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- sh... |
8dadfb9fb882c27441aebde6e817f4d1ce1a98bd28fc81f709c8c73f5cc6ede1 | R | 1,915 | 48 | searchTabs <- function(board) {
tabs <- list(
biomarker = c("Feature selection", "Feature-set ranking"),
dataview = c("Gene overview", "Sample QC", "Data table", "Samples", "Contrasts"),
clustering = c("Heatmap", "PCA/tSNE", "Parallel"),
featuremap = c("Gene", "Geneset"),
exp... |
c2f7a3ebae2f47d84bff05f7711651a4fbfbf09908d2e3d5a0932941c2e530a2 | R | 1,934 | 48 | #!/apps/lab/aryee/R/R-3.2.3/bin/Rscript --vanilla
# Usage example using test data from the circleseq repository:
# ./site_pvalue.R ../test/U2OS_EMX1_counts.txt ../test/U2OS_EMX1_counts_pval.txt
# Usage example using a larger test dataset on erisone:
# ./site_pvalue.R /data/joung/CIRCLE-Seq/complete_analysis/160122... |
38ccb24070eac751063f4c3603bc8dc4b5735b30697702dfdb548b3780a3b415 | R | 1,935 | 47 | Script_IGV_generator_v1.0 = function(){
#Test
snapshot_folder = paste0("\\\\l2export\\iss02.corti-corvol\\analyse\\genetique\\Resultats_genetique\\Exomes\\Tiers\\", Run, "\\bam_capture\\T1")
bam_folder = paste0("\\\\l2export\\iss02.corti-corvol\\raw\\genetique\\Exomes\\PF_GS\\", Run, "\\BAM")
Script <- vector... |
61dd803e8bfe73411241dddfbdb10afc4bffe5d64d95a9ef681144f5b06c6994 | R | 1,935 | 47 | Script_IGV_generator_v1.0 = function(){
#Test
snapshot_folder = paste0("\\\\l2export\\iss02.corti-corvol\\analyse\\genetique\\Resultats_genetique\\Exomes\\Tiers\\", Run, "\\bam_capture\\T2")
bam_folder = paste0("\\\\l2export\\iss02.corti-corvol\\raw\\genetique\\Exomes\\PF_GS\\", Run, "\\BAM")
Script <- vector... |
d667807c123b014a1c02e4720b971b58439a2c9b0a4ebd8eb4dc16a54940d4ca | R | 1,941 | 67 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
compare_table_corr_score_ui <- function(id, width, height) {
ns <- shiny::NS(id)
info_text <- "In this table, users can check mean expression values of features across the conditions ... |
edbd4ead44a1f5160f81e31c2233a5ee42a3d17ed3a0591a3f99ccc7f95bbabf | R | 1,945 | 69 | #RUN LOCALLY
#nohup R CMD BATCH GenerateWordCloudPlots.R output_wordcloud.log &
#check progress with "jobs"
#get jobid with "ps -ef | grep WordCloud"
#and kill with "kill [PID]"
library(data.table)#to store the search results and other data in data tables
library (dplyr)#to select specific columns from data frames
lib... |
9905f1903151d37e6e054180952ac33f1cf368bd34fe2c299f931ab29e24fa94 | R | 1,947 | 47 | Script_IGV_generator_v1.0 = function(){
#Test
snapshot_folder = paste0("\\\\l2export\\iss02.corti-corvol\\analyse\\genetique\\Resultats_genetique\\Exomes\\Tiers\\", Run, "\\bam_capture\\T2plus")
bam_folder = paste0("\\\\l2export\\iss02.corti-corvol\\raw\\genetique\\Exomes\\PF_GS\\", Run, "\\BAM")
Script <- ve... |
6e9f8789b7cd5eeaeea3a8ff259c7c8c72da8f5eba4e3d025f5722dacca008a7 | R | 1,954 | 33 | count_add_peakind <- function(inputfile){
data1_resize<-read.table(inputfile, sep = '\t', header=T, comment.char = "")
data1_resize$chr <- 0
data1_resize[data1_resize[,1]=="chr1",ncol(data1_resize)] <- 1
data1_resize[data1_resize[,1]=="chr2",ncol(data1_resize)] <- 2
data1_resize[data1_resize[,1]=="chr3",ncol(data1... |
bdaebe8e56a7767e4481fb101292d085e15259a6159132d0fa777d628e85952e | R | 1,960 | 59 | library(data.table)
library(dplyr)
library(ggplot2)
genes <- fread("genes_by_locus.csv")
scdata <- fread("expression/Nigra_Mean_Cell_GABA_type.txt")
merge <- merge(x = genes, y = scdata, by.x = "GENE",by.y = "Gene", all.x = TRUE)
final <- merge[complete.cases(merge),]
final <- final %>% select("GENE","Astrocyte","D... |
1449548c9f1aa77c9e1ff4a130e96fccdcb8e031407d97c111c6c869062b08a8 | R | 1,969 | 74 | # -----------------------------------------------------------------------------------------------------------
# For reproducible research, please install the following R packages
# and make sure the R and BiocManager versions are correct
# Session Info ------------------------------------------------------------------... |
28a05320d820035ff73a984402fa5c833456ba55c012886b9c87d2d85d9d57ba | R | 1,969 | 65 |
library(shiny)
library(shinyjs)
library(googledrive)
library(data.table)
library(shinydashboard)
library(shinydashboardPlus)
library(DT)
library(dplyr)
library(openxlsx)
library(shinyWidgets)
library(stringr)
library(htmlwidgets)
library(plotly)
library(shinyanimate)
library(shinyhelper)
library(httr)
#current versio... |
810883cbaf117001db45ff4681423aaef24dd90ad94446c7d464269a27f7e79f | R | 1,984 | 46 | #' @title rescale Repli-seq assay
#' @description Calculate the count matrices for a lower resolution ( larger genomic windows )
#'
#' @param rs_assay a dataframe for a Repli-seq assay loaded with readRS()
#' @param scale_factor the factor to apply to the scale (going from 1kb to 50kb gives scale_factor = 50 ; from 50... |
c13200fd082c499e05383770d17033beadf5d3887dfd79225cd870d05b16f393 | R | 1,987 | 51 | manuscriptPalette <- c("In Vivo" = "red2",
"In Vitro - GPC Stage" = "#2E30FF",
"In Vitro - PSC Stage" = "mediumseagreen",
"NPC" = "magenta",
"GPC1" = "forestgreen",
"GPC2" = "darkorange",
... |
b9418b0d3bcc280b2230558ac5e04df7ad4e21c83a7223646921743652accc7d | R | 1,989 | 76 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_clusters_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL),
wid... |
6cc8ae96e2528059daae3608fa1af95d2818944f346c1a6ee707f4a834a6d1f6 | R | 1,990 | 72 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_variance_ui <- function(
id,
title = "",
info.text = "",
info.references = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
Pl... |
c0448ae617b3b957f0759c97957bb12cdfdc927562894d4e8fa2dbedc800b1ee | R | 2,001 | 77 | library(peer)
dataset = commandArgs(trailingOnly=TRUE)[1]
celltype = commandArgs(trailingOnly=TRUE)[2]
meta<-read.table("meta_info.n424.selected.txt",header=T,sep="\t")
colnames(meta)[19]<-"RID"
pcs <- read.table("pca.n424.evec")
pcs <- pcs[,c(-1,-13:-23)]
colnames(pcs)<-c("IID",paste0("PC",1:10))
pcs <- pcs[, 1:6 ]... |
bc05f6df9c6a321ed8fe3ee07e4eab0010ef3e25e295957ed40eec3f127ad34e | R | 2,003 | 82 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_module_heatmap_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
opts <- shiny::tagList(
shi... |
2a2bead2895bc38fafc5867207f9609e35787e37560d51799b5ba7a2f6bcb8e1 | R | 2,012 | 68 | rm(list = ls())
library(readxl)
library(jmvcore)
library(jmvReadWrite)
library(GAMLj3)
library(ggplot2)
### Select the Monkey and Load the table ###
##
tableStatBehav <- read_excel(".../Human_Behavioral_Data/Human_Behavioral_Data_Analysis3.xlsx")
column_name <- paste("ParticipantA", sep = "")
tableSta... |
df430339228412a364f97677f4ce476c5afcfb9684d4da27ec38494a660e2ad5 | R | 2,015 | 62 | rm(list=ls())
basedir <- '~/Dropbox/Neurodegeneration/MouseDiffusion/connectome_diffusion/'
setwd(basedir)
opdir <- 'asyndiffusion3/'
dir.create(opdir,recursive = T)
params <- list(basedir=basedir,
opdir=opdir,
matlab.path='/Applications/MATLAB_R2018b.app/bin/matlab',
grps =... |
be8324aed1b15e3e96c3196d7c9f7f303389e7bab223d979f4a8b5300f4eb8d1 | R | 2,018 | 86 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_lasagna3D_ui <- function(
id,
title = "",
info.text = "",
info.references = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
o... |
9b467723d2fb4f11eff1587297b28152ec17227da60b380ff668425843fd4d6f | R | 2,026 | 85 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_sampletree_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shi... |
a37bd80459d52b4a3c80254b28e52e30462d86ce2d6ff01fca7a103124725032 | R | 2,027 | 52 | # add bar labels to indicate time periods
interval_label <- function(fig,
x_interval_list = list(c(-2,-0.5), c(-0.5, 1)),
x_interval_text = NULL, #list(c(-2), c(-0.5)),
text_list = list("Baseline Period", "Reward Period"),
... |
5d7728d94aa6679423a6809298dcdd1fdb1dd0d11acf125505ba3ab4a98ed58b | R | 2,032 | 84 | # =========================================================
# Utility functions for reproducible workflow
# =========================================================
# -----------------------------
# Safe directory creation
# -----------------------------
dir_create_safe <- function(path) {
if (!dir.exists(p... |
8cdefd8dd81c483b004bca0152de053d4a0fc4a5679f79ed7f8f70002cde5483 | R | 2,034 | 58 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'G20vsNTG/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load path da... |
c6a9ecc228a8a50b76c4a3fa18958d0399ac2c110323353575923687815bc44a | R | 2,035 | 67 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
QUESTIONS.ANSWERS <- list(
c("Would you recommend Omics Playground to your colleagues?", "no|maybe|yes|sure|definitely!"),
c("What is your favorite fruit?", "banana|apple|pear"),
c(... |
5c66cba1f5d7de6a5ec8281a2de75e65b3681a47511292e848a57be5a09de991 | R | 2,065 | 42 | data_error_modal <- function(path, data_type) {
con <- file(path, "rb")
text_raw <- readBin(con, "raw", n = 1000)
close(con)
is_bin <- tryCatch(
{
paste(rawToChar(text_raw), collapse = "")
},
error = function(w) {
NULL
}
)
if (!is.null(is_bin)) {
shinyalert::shinyalert(
... |
6839fec9c0a6c782ff557a93ae2a593706b95801c1e7050e76f55b3f400bae10 | R | 2,069 | 78 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_weights_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagList(
shi... |
b2c1d62a22bea76f94e1bce3c6316cde91f03ee03bbda67ab1141eaf2e55baac | R | 2,071 | 84 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_diagram_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny:... |
51a9e78017331f1d12e398b05c5333a50b8648d804f8fbc3cf11f0ece1173187 | R | 2,075 | 83 | #' ============================================================================
#' Project: PCB Exposure and Gene Expression in Mouse Brain (snRNA-seq)
#' Script: [SCRIPT_NAME]
#' Purpose: [ONE LINE DESCRIPTION OF WHAT THIS SCRIPT DOES]
#'
#' Author: Osman Sharifi
#' Date Created: 2024-10-31
#' Last Modified: 2024-10-... |
212d46fd11a28b2272a0ca53ed0366724ee20595c0d7f484580f835daa8a7fff | R | 2,081 | 50 | #' @title Weighting phases
#' @description Using a simulation of the S-phase (active forks in function of the percentage replicated genome), this function calculates a normalization factor for each phase based on the FACS gates and G1/G2 peaks
#'
#'
#' @param G1_peak aproximate position of the G1 peak
#' @param G2_pea... |
6f9aea2124803cb5ba0b213a754af3c2fcd978ce960f42dff13d97d332c3a6b3 | R | 2,088 | 83 |
pbmc3k.sce.logcounts <- local({
callcheck <- 'resave_data_others' %in% unlist(lapply(
X = sys.calls(),
FUN = as.character
))
if (!isTRUE(callcheck)) {
return(NULL)
}
# Check required packages
pkgcheck <- requireNamespace('rprojroot', quietly = TRUE) &&
requireNamespace("stats", quietly = T... |
998cd468e98eee775f2b3d2b6363c407f343b86029aa4e1f43a946013414624a | R | 2,093 | 72 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_lasagna_clustering_ui <- function(id, ...) {
ns <- shiny::NS(id)
options <- tagList(
shiny::radioButtons(ns("colorby"), "Color by:",
c("foldchange", "correlation")... |
c00410e8d64ab3eefedaa4180d47c7aca4cd53cb6f4c0fe02e557006c740b88b | R | 2,095 | 60 | ##this script is to prep file for MTAG run
##while running from command line give your input filename as first argument
library(data.table)
library(dplyr)
library(stringr)
library(stringi)
library(scales)
args <- commandArgs(trailingOnly = TRUE)
##assign arguments
filename<- as.character(args[1])
prefix<- paste(st... |
af429202a15843f58e9c3a89ad66b46b7b1997aea7a021e22f9862ff977334cc | R | 2,108 | 73 | #' chisquare objective function
#'
#' @param rts list of simulated response times for different conditions
#' @param rt_qs matrix of response time quantiles for each condition (condition x rt quantile value)
#' @param p_q vector of probabilities corresponding to response time quantiles
#' @param n_rt vector with the n... |
4e7bd94d2dcee0a9393a5c87439379a5099a9350daa6f4c4fa9825a2c653d29c | R | 2,109 | 88 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_membership_v_trait_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
... |
087581207ddf188b63034f75efa3e3362237610807033e0b8c036e2c2cfadb04 | R | 2,126 | 60 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
# This file is supposed to run from the root Playground folder
if (basename(getwd()) != "omicsplayground") {
stop("Please run from the OmicsPlayground root folder")
}
if(!require("re... |
174a2069e7da8d9991aa3a97eda019b3781a218fc13924b706d5e24eb4cb2dcf | R | 2,129 | 68 | # ============================================================
# Script 01: Data Preparation
# Candrea et al. - Gut Microbiota Comparative Analysis
# Biomedicines 2025
# ============================================================
# Description:
# Prepares input CSV files from the raw Excel dataset for use
# in LinDA, ... |
885270f4e795a44e4474d209f7272b6c6cca09e7a318e8e335e53d669337f510 | R | 2,129 | 68 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##appdir="~/R/golem/omics.app";wd="packages/board1"
get_appdir <- function() {
wd <- strsplit(getwd(),split='/')[[1]]
root.files <- c(".gitignore",".dockerignore")
chk <- rep(... |
064c65cde9dad07fbe1654cc53c597a1eb3dcf8bc8702b3f6d5923663052ac02 | R | 2,131 | 32 | rm(list = ls())
library(TwoSampleMR) #v0.6.21
library(ieugwasr)
ab42_input <- read_exposure_data('Summary stats file with rsID', sep = '\t', snp_col = 'rsID', beta_col = 'Beta', se_col = 'SE', effect_allele_col = 'effect_allele', other_allele_col = 'other_allele', pval_col = 'P')
##try to subset to genome-wide varian... |
651396baced54172943776cc78f8dc0cbc01b84f7c7f16d83d716b120fde860e | R | 2,136 | 58 | #RUN LOCALLY
#nohup R CMD BATCH pubmed/pubmedHitData.R pubmed/output_pubmedhitdata.log &
#check progress with "jobs"
#get jobid with "ps -ef | grep HitData"
#and kill with "kill [PID]"
library(data.table)#to store the search results and other data in data tables
library (dplyr)#to select specific columns from data fra... |
c047a7078c1c1116113aa05dc3e844a01228457afa033704017ef8d1db6234f4 | R | 2,137 | 68 | # =========================================================
# Master script for full reproducibility
# =========================================================
cat("Starting WGBS methylation analysis pipeline...\n")
# -----------------------------
# 1. Load setup
# -----------------------------
cat("Loading... |
eb8cd37f404c5c6835b89bb9f9ef2bccf73829189f7fa505d62add6ebb3dedc9 | R | 2,149 | 73 | rm(list = ls())
library(readxl)
library(jmvcore)
library(jmvReadWrite)
library(GAMLj3)
library(ggplot2)
### Select the Monkey and Load the table ###
##
mk=1
tableStatBehav_mk_Opt <- read_excel(".../Monkey_Behavioral_Data/Monkeys_Behavioral_Data_Analysis3.xlsx")
column_name <- paste("Session", sep = ""... |
3d9950a84afbdd1dc12ec3af61cfa4fc061bdc75c24ecdae27baf3200ada83c6 | R | 2,174 | 82 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_correlation_network_ui <- function(
id,
title,
info.text,
caption,
label,
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),
title = title... |
7c9c43360c11ff8e03f42d56145f7fdd11c15532b37370716e6e7600697a6bc6 | R | 2,177 | 47 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'sncamodel/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load path d... |
b83b846ddddd5dbd5dfef29f3bd37ab3343af1e997c6994a4716181c97c0367b | R | 2,200 | 83 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Decisiontree plot UI input function
#' @description A shiny Module for plotting (UI code).
#' @param id
#' @param label
#' @param height
#' @export
biomarker_plot_decisiontree_ui <- fun... |
6bd4fc1d57ad2001d2cc8a5ebc877a7dc0aa542e0e729e6dc7a3c17a9c70ca12 | R | 2,201 | 63 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## DEAN ATTALI code recommendation:
## example of how a board module should be written (TcgaBoard)
##
## https://github.com/bigomics/omicsplayground/pull/20/commits/bd943d84d316d76dca9140f... |
f777d46372cf176fed7f6009aec96d59d451c7c62cec76d285dd553dcb92626f | R | 2,211 | 79 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wordcloud_table_enrichment_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.tex... |
2e6b921528843a53d8407b20b84b7ea9fba17523983df4d8c280b15787ee8d8d | R | 2,220 | 49 |
phenoVars<-list()
phenoVars$id <- "phenovariant"
phenoVars$title <- "Associated Variant Phenotypes"
phenoVars$loadData<- function(){
#read in phenotype variant data
phenotype_ld <<- fread("www/phenovars/PhenotypeVariantLD.csv")
phenotype_variants <<- fread("www/phenovars/PhenotypeVariantData.csv")
phenotyp... |
6baf1c67b84e1358605ad24038b9da47bf5c0707775786c193910ed454a9d543 | R | 2,222 | 87 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_table_samples_ui <- function(
id,
width,
height,
title,
info.text,
caption
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
width = width,
heig... |
6223de8f5eca0dce2df4df9e7ffd5edfdcf2798234b8f24a2fe8357e20d6ceb6 | R | 2,242 | 60 | options(stringsAsFactors=F)
library(stringr)
library(dplyr)
library(data.table)
res<-data.frame()
for(data in c("ROSMAP_BulkRNA","ROSMAP")){
all<-fread(paste0("stats/",data,".FDRsig_eGenes.snps.bed.gz"))
base<-all %>% group_by(V6) %>% summarise(allPIP=sum(V5))
colnames(base)[1]<-"gene"
for(categ in c("trans... |
2c86c5ddaf8d0384b7a65af045a4864b758ebf71d154928b9618395e2e1bd245 | R | 2,249 | 92 |
pbmc3k.seurat.norm <- local({
callcheck <- 'resave_data_others' %in% unlist(lapply(
X = sys.calls(),
FUN = as.character
))
if (!isTRUE(callcheck)) {
return(NULL)
}
# Check required packages
pkgcheck <- requireNamespace('rprojroot', quietly = TRUE) &&
requireNamespace('Matrix', quietly = TR... |
96a07c357555a061a466cf3c712d395b11fdd1662fef766709cd4406d1376e5f | R | 2,258 | 88 | pls_R <- function(x, y, lv) {
out <- 1
mx <- nrow(x)
nx <- ncol(x)
my <- nrow(y)
ny <- ncol(y)
if (nx < lv) {
cat("No. of LVs must be <= no. of x-block variables")
}
p <- matrix(0, nx, lv)
q <- matrix(0, ny, lv)
w <- matrix(0, nx, lv)
t <- matrix(0, mx, lv)
u <- matrix(0, my, lv)
b <- matr... |
243bfb22afecec71514f26f0f2b9ee45898138c01ca1ec1f6cb634d5258a4d3d | R | 2,280 | 79 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PcsfBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns
fullH <- 800
tabH <- "70vh"
pcsf_info <- div(
"This PCSF anal... |
91ce80aee19c1118e07b24377f0af64ace1239902ecf540ef4b3adfce1e42cff | R | 2,291 | 69 | log <- file(snakemake@log[[1]], open='wt')
sink(file=log, type='message')
sink(file=log, type='output')
library(data.table)
library(assertthat)
source("workflow/scripts/arbigent_utils/mosaiclassifier_scripts/mosaiClassifier/mosaiClassifier.R")
# The following function converts the bed format to the segs format, which... |
b05286bbed7d25c49c835826d183fbd4b2621473d8b31ac910d57e3f14c4259d | R | 2,296 | 109 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_preservationDendro_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotMo... |
800e72e28d65f4458004c0d89e5e764f73ae4c0add124433bcb32dd65ebceb28 | R | 2,297 | 91 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
drugconnectivity_table_cmap_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.t... |
684d84fcf1c56cb28da878c798a6c765894005ad762a74bd634ef3ddaa68c61d | R | 2,300 | 70 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## From https://github.com/plotly/plotly.js/blob/master/src/components/modebar/buttons.js
all.plotly.buttons <- c(
"toImage",
"senDataToCloud", "editInChartStudio", "zoom2d", "pan2d", ... |
b6061d4942de972c29d0ed43e4a0c67a2a4a47341610f16e647192aaf0a1f4ac | R | 2,308 | 109 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_preservationDendro_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
Plo... |
90f71a8abc4e05b5cc2cdf18a6dbf6816bc6de2ff517a874cf7ad0fbb7ecfeaf | R | 2,314 | 66 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/forward/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load... |
2e40742d1d74cc1f637a377fb153a1e5d0a44c2999473d9ea08745fb28077b85 | R | 2,334 | 89 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_enrichment_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shin... |
5c8bd847d352012ce9054326b6f86c41435dce7bf648d3f9cee0ba84f8abd426 | R | 2,344 | 94 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_pathwayheatmap_ui <- function(
id,
title = "",
info.text = "",
info.methods = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
... |
57c23038bd8709a190eb4e78a5d30dca010e00de5943b4c48eb97d451530bbfc | R | 2,352 | 73 | ## make as R6 class?? e.g. add documentation, initialize object,
## object id.
MODULE.multiomics <- list(
module_menu = function() {
c(
snf = "SNF",
lasagna = "LASAGNA",
mgsea = "Multiomics GSEA",
mofa = "MOFA",
deepnet = "DeepLearning"
)
},
module_ui = function() {
list... |
9683d1ea9076fa021551e2e69e2d554505e0735b0ac78a6f90bf15886db7b475 | R | 2,353 | 101 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Drug Connectivity plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
drugconnectivity_plot_c... |
876a768bd5a2e7194c7ec946e9047631f656ba3f9c58cc0238258a0d0d4fe639 | R | 2,371 | 46 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
tagsub <- function(s) {
s <- gsub("\\{\\{", "<i>", gsub("\\}\\}", "</i>", s)) #
s <- gsub("\\{", "<code>", gsub("\\}", "</code>", s)) #
return(s)
}
#
a_OMIM <- "<a href='https://www... |
e501e26eac68150c60aad5d2491d34db369635d5c418f114ef88d5d121dc1720 | R | 2,379 | 99 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_plot_dendrograms_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny:... |
1bca473ed3ae460d943ae053fdbcc0cda3150e28cab831a4c4c411b16061d8cb | R | 2,391 | 74 | #!/usr/bin/env Rscript
#
# This file is part of the AlignmentAndQCWorkflow plugin.
#
# This script is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 or 3 of the License.
#
# This script is distr... |
93463c37a9ea3c3ff9e08a606060a293f20d596de6e7724e036c1d666b8241f1 | R | 2,401 | 74 | #functions:
#' This function computes the dispersion parameters for W and C read counts in each segment
#'
#' @param prob.tab a table containing all segments with their states in all cells
#' , combined with all possible haplotypes and the corresponding C and W copy number
#' @param alpha The fraction of background rea... |
0c2683a8e1588a22ce88a68b28c56f85b8e729b5389eadd393292ad2cccda2a0 | R | 2,402 | 85 | # Get desired cookie from all the available ones
extract_cookie_value <- function(session, cookie_name) {
cookie_string <- session$request$HTTP_COOKIE
if (is.null(cookie_string)) {
return(NULL)
}
cookies <- unlist(strsplit(cookie_string, "; "))
user_cookie <- grep(paste0("^", cookie_name, "="), cookies, v... |
eafa4406c445924e218419303ffbe2bb948a1457743c6a51dcef9f068344cd36 | R | 2,405 | 90 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
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