sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
197f49e2e36bb081fc419bf63e8dbed616184644fafedbb8523408745df05eae | R | 965 | 31 | sink(snakemake@log[[1]])
library(data.table)
library(assertthat)
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/mosaiClassifier.R")
system("LC_CTYPE=C")
# Currently read files from the Snakemake pipeline
counts <- fread(paste("zcat", snakemake@input[["counts"]]))
info <- fread(snakemake@input[["info"... |
1af7cbb3f704189d5db9144463800058d537f5cc1af9f2555ca2dc6acc23704d | R | 968 | 26 | library(data.table)
source("/g/korbel2/weber/workspace/mosaicatcher-update/workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/makeSVcalls.R")
probs <- readRDS("/g/korbel2/weber/MosaiCatcher_output/MosaiCatcher_output_sample_KG_dryrun/mosaiclassifier/haplotag_likelihoods/RPE-BM510.Rdata")
llr <- as.numeric(4)
use... |
3c9d177ce176d95b4d169bb029fea3d7eb9759bb1b1c74419d01d156456032d1 | R | 969 | 46 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_dummy_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL),
width = c("auto", "100%")
) {
ns <- shiny:... |
30e6a6636e7ea6ca1736f49a7d2d09ea49dea2aa15bf56e7f5566f23fdd359c9 | R | 974 | 43 | plsnipal_R <- function(x,y){
my <- nrow(y); ny <- ncol(y)
if (ny > 1){
ssy <- round(colSums(y^2));
ymax <- max(ssy); yi <- which.max(ssy)
u <- y[,yi];
} else {
u <- y[,1];
}
conv <- 1;
told <- x[,1];
count <- 1.0;
# Specify the conversion tolerance
while (conv > 1e-4){
count <- count + 1;
w <- t(t(as.matr... |
9efe94ad4b3df837bfc898b587c5cf57ef7bf2afa37fa150a5379a7407e77943 | R | 985 | 25 | #!/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... |
90adc75b70880bc9aaa555f8b57023634b97f4bc08543e9204eb3806cb9861ef | R | 993 | 34 | get_first_passage_density = function(pars_list, dt=.01, ...){
density = do.call(ddm_integral_fpt, c(pars_list, dt=dt, ...))
rownames(density) = seq(dt, dt*nrow(density), dt)
density
}
get_rt_liks = function(dat, density_list, min_p=1e-10){
min_p = as.numeric(min_p)
#get time bin for each response
tve... |
150514973fa20005fd52565b51a7f17d29e48c72c77ef270ddb40e87f7e4c1b2 | R | 1,010 | 34 | ##
## 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... |
fb27beb76f9089c4764764fd7ff078a8b24cf3f14f1ed3c248f5acaf5a7d4cd5 | R | 1,017 | 41 | bestCandidate<-list()
bestCandidate$id <- "bestcandidate"
bestCandidate$title <- "Best Candidate"
bestCandidate$loadData<- function(){
}
bestCandidate$generateUI<- function(){
fluidRow(
column(htmlOutput("bestCandidateOutput"), width = 12)
)
}
bestCandidate$serverLogic <- function(input,output,session,re... |
61b0e84e4d7ab2c61b6537ab1ce3de190e112668c3fb58a20a3c630d23242189 | R | 1,027 | 39 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
UserProfileUI <- function(id) {
ns <- shiny::NS(id) ## namespace
div(
class = "row",
boardHeader(title = "User Profile", info_link = ns("board_info")),
shiny::tabsetPanel(... |
f59b719fd3a960be23b7684444e752b4a12f59c1d6a6237e043d9b0d69420651 | R | 1,036 | 24 | #' @title double the values of X chr (for human male samples)
#' @description Calculate Repli-seq assay count matrices after doubling the values of chrX windows
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx (or S0)
#' @param chr level of chr to doubl... |
02fe19d50b6bdd10a6c5e1d03f7f100db12faa5c41156663459422a9f11c568f | R | 1,037 | 37 | # For calculating TSS enrichment
library(GenomicFeatures)
library(GenomicAlignments)
library(rtracklayer)
args <- commandArgs(trailingOnly = TRUE)
bam_file <- args[1]
gtf_file <- args[2]
score_file <- args[3]
upstream <- as.numeric(args[4])
downstream <- as.numeric(args[5])
# Read GTF and extract TSS
txdb <- makeTxDb... |
72b55e1da47cab109e3202ec6f1eb2c5c6ef6487cfed8e085b904a6a36e919a7 | R | 1,041 | 42 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
show_upgrade_modal <- function(timeout.min = 40) {
require(shiny)
msg <- HTML(paste0("<center><h4><b>Ditch the ", timeout.min, "-minute limit</h4>
Upgrade today and get advanced analy... |
3d37ce61ba542f8efad13e2ea21d7023c9f2b943f339545516d94adeeeddf23f | R | 1,044 | 30 | ##
## Write license file of the used/installed packages
##
# This file is supposed to run from the root Playground folder
if (basename(getwd()) != "omicsplayground") {
stop("Please run from the OmicsPlayground root folder")
}
## packages used in omicplayground
renv1 <- renv::dependencies(path = "components", r... |
24d26edf28db0dbf28d29f388aa8bf26c10904101ed82cae6ca37ec7b7574b98 | R | 1,045 | 44 | #' Open a URL using JavaScript in a Shiny App
#'
#' This function opens a given URL in a new browser window or tab using JavaScript
#' within a Shiny app. This is particularly useful when using a Docker container,
#' as the `browseURL()` function may not work as expected.
#'
#' @param url A character string representin... |
3f66aa56fef475880b5f39cbcb76b7b55a5dd56f30d51243c942133ceb3b20bf | R | 1,065 | 37 | ##### Summary of scRNA-seq DEG Analysis #####
library(openxlsx)
library(glue)
library(tidyr)
library(ggplot2)
library(viridus)
cell_types = c("Astro", "L2_3_IT", "L4", "L5", "L6", "Lamp5", "Non-neuronal", "Oligo", "Pvalb", "Sncg", "Sst", "Vip")
list <- vector(mode="list", length=length(cell_types))
list <- lapply(c... |
adc9d214f278e6ced705516d5fdfca550534fe42f1aee5532b9828ab7723a31c | R | 1,068 | 19 |
library(devtools)
load_all("/g/korbel2/weber/Gits/Rsamtools/")
load_all("/g/korbel2/weber/Gits/GenomicAlignments/")
source("utils/haplotagTable.R")
# tab <- getHaplotagTable2(
# bedFile = "/g/korbel2/weber/MosaiCatcher_output/MosaiCatcher_output_sample_KG_chr21/haplotag/bed/RPE1-WT/100000.selected_j0.1_s0.5_sce... |
998dc7cb3825d1891a130caae7d76e08c159e13901e86760ebb1180c29086ed9 | R | 1,074 | 33 | library(ggplot2)
library(reshape2)
library(scales)
args = commandArgs(trailingOnly=TRUE)
x = read.table(args[1], header=F, na.strings=c(".", "NA"))
colnames(x)[1] = c("cnv")
x = melt(x, id.vars=c("cnv"))
x = x[!is.na(x$value) & x$value != -1,] # drop missing / invalid RDCN (-1 sentinel)
x$cn = round(x$value)
if (su... |
4539a2248f9eb69a056d8e1f05da6b33ceb1de3fb8d4540bc9af71440ded1e9f | R | 1,078 | 29 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
header_infotext <- "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exerc... |
54638d1e7ae53abca04379c32281fbfc1f988c04158be4a628687c76054ed946 | R | 1,081 | 48 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_module_graph_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),
... |
2eb9923d385c418d93742524528a0982112609781c7e9e1fbe6b32df30c8eba0 | R | 1,083 | 32 | file_path <- file.choose()
file_directory <- dirname(file_path)
file_list <- list.files(path = file_directory, pattern = "\\.out$", full.names = TRUE)
num_files <- length(file_list)
results_list <- list()
pb <- txtProgressBar(min = 0, max = num_files, style = 3)
for (i in seq_along(file_list)) {
file <- file_list[i]
... |
bc14bcf2fda2cc613dc56ffeab4e524184880306e9c61d31b8d70ac0f02ad43f | R | 1,085 | 63 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
GOOGLE_BASE_URL <- "https://firestore.googleapis.com/v1/projects"
google_base_url <- function() {
sprintf(
"%s/%s/databases/(default)/documents/users",
GOOGLE_BASE_URL,
Sys.... |
5888f06a8f1d700f91b1661ebf12719209e795ad65a2377a1e554f30adccc5dd | R | 1,087 | 32 | file_path <- file.choose()
file_directory <- dirname(file_path)
file_list <- list.files(path = file_directory, pattern = "\\.out$", full.names = TRUE)
num_files <- length(file_list)
results_list <- list()
pb <- txtProgressBar(min = 0, max = num_files, style = 3)
for (i in seq_along(file_list)) {
file <- file_list[i]
... |
94584e0970b03fd0dc7751e784dadcef05057b4e29dad6b01ccddf500cf501aa | R | 1,103 | 26 | #' @title Calculate noise ratios
#' @description Calculate noise ratios of a Repli-seq assay versus a Repli-seq control
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
#' @param rs_control a Repli-seq control assay (data.frame) loaded with readRS() and... |
c02d138c5d9057f0c21b139c7939afd6892e026312fab1b7ef85ab2f4b47aa8d | R | 1,125 | 51 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_factorcorheatmap_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotModuleUI(
... |
0f601d2981c33b66152a29fa711bb2059a6a00e37555cef30e46e3549f4280a8 | R | 1,132 | 51 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_summaries_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotModuleUI... |
4a876c41c0388d2fc8b3f1369dbe785a36ef75dbce11f33ac75acfd9168b669f | R | 1,134 | 37 | library(coloc)
options(stringsAsFactors=F)
library(stringr)
library(dplyr)
library(data.table)
cell<-commandArgs(trailingOnly = T)[1]
chunk<-commandArgs(trailingOnly = T)[2]
n<-sample_n # number of samples
chunkfile<-read.table("/path/to/chunkfile.txt")
colnames(chunkfile)<-c("chr","gene")
data="ROSMAP"
res<-data... |
456101204a4791d840898d82a1e6d360096302072365297abf4040145366d839 | R | 1,142 | 50 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_MMvsGS_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),
title... |
e90cf598782b5f04b16e293a67059a5f67b9bebf857002b26b599fe890fb1864 | R | 1,168 | 26 | #' @title Write Bedgraph files of Repli-seq assays
#' @description writes one bedgraph 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 ... |
ba8ead6d1a3ce88e2193f2fca06cdaa5100c1e263b4b5ea4a9c4dc94094c41f5 | R | 1,169 | 52 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_heatmap_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"... |
3d093f77a925688fef517d3fbb315c0ff1e8595c681f43d39ab3f4e786f6ab3b | R | 1,170 | 32 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
RDIR="../R"
FILES="../lib"
PGX.DIR="."
dir.exists(PGX.DIR)
source(file.path(RDIR,"pgx-functions.R"), local=TRUE) ## pass local vars
source(file.path(RDIR,"pgx-api.R"), local=TRUE) ## pa... |
ebbdda19ab47df6a90a7379ddeefbbc3720c40132b223bc433155ba8e6fc4642 | R | 1,185 | 49 | ## make as R6 class?? e.g. add documentation, initialize object,
## object id.
MODULE.clustering <- list(
## MODULES[["multiomics"]] <- list(
module_menu = function() {
c(
clustersamples = "Samples",
clusterfeatures = "Features"
)
},
module_server = function(PGX, labeltype = NULL) {
inf... |
defbc91f69d9f96495b88890926fdc8c598971bf6e3f6a532ae043f693d51f87 | R | 1,192 | 40 | library(optparse)
library(ChIPseeker)
library(GenomicFeatures)
library(rtracklayer)
# Parse command line arguments
option_list <- list(
make_option("--peaks", type="character", help="Comma-separated list of peak files"),
make_option("--output", type="character", help="Output file path"),
make_option("--gen... |
a3a4a34242f0a57112c182d1c02da7cf68b326d2754a8a5762a325c9518f3093 | R | 1,198 | 47 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
# Sass code compilation
sass::sass(input = sass::sass_file("inst/app/www/custom.sass"), output = "inst/app/www/custom.css", cache = NULL)
# Sass code compilation
#sass::sass(input = sass:... |
889415d1948bf8eee8e8f88627e5410f7d83fec68e643e4057176dd4d806a91d | R | 1,200 | 35 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DropdownMenu <- function(..., size = "default", status = "default", icon = NULL, circle = TRUE, border = "default", width = "") {
id <- bigdash:::make_id()
bslib::popover(
tags$a(
... |
84a15f87f6387d0ba5a24e2b326870a82e8ee0d2f882d570d8a9958143011044 | R | 1,203 | 33 | drawPriorGamma <- function(data, col=NULL, xlim=c(-3,1.5), ylim=c(0,3)){
nn <- length(data$gamma.bar)
if (is.null(col)){
col <- 1:nn
}
gamma.hat <- data$gamma.hat
t2 <- data$t2
gamma.bar <- data$gamma.bar
normal_data <- lapply(1:nn, function(i){rnorm(1000000, mean=gamma.bar[i], sd=sqrt(t2[i]))})
plo... |
4e64c32f26fad438f0458427f02fbe16cef61f92e705e4f92876672fe36005e8 | R | 1,211 | 48 | library(data.table)
library(dplyr)
library(LDlinkR)
args = commandArgs(trailingOnly=TRUE)
if (length(args)==0) {
stop("enter path to a file with columns 'RSID' and 'POP' (EUR, EAS, ALL, etc) for each variant you want proxies for, and then the r2 cutoff value", call.=FALSE)
} else if (length(args)==1) {
file = a... |
0f09c01ddf8b7b6ce26df4b0311bd46ad7dd494a234c1cfcc14b2fb37ba51d98 | R | 1,215 | 44 | sink(snakemake@log[[1]])
library(data.table)
library(assertthat)
e <- fread(snakemake@input[["phased_states"]])
e
d <- fread(snakemake@input[["info"]])
d
g <- fread(snakemake@input[["initial_states"]])
g
d$bam <- basename(d$bam)
# Handle empty phased_states: ensure bam column is character type
if (nrow(e) > 0) {
... |
dc01607d2d515fbf36f9fcc87f812d59871e8ca12234a1779f8c1938a99f1463 | R | 1,223 | 18 | ######################################################################################################quote
### test_regions_BED.R: make bed file with regions including
### on-target site, 2 off-target sites without variants,
### 2 off-target sites with variants, and 1 region wi... |
da39759586255f71542172919c58c0431ef29396c9b723aaa24014fdcc5ef063 | R | 1,240 | 25 | #' @title Normalize Repli-seq assay
#' @description Calculate Repli-seq assay count matrices after normalizing (dividing counts by ratios)
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
#' @param norm_ratios an array with the ratios in the order of rs... |
a8f606f832436555645f452b7b8bbd623d2822817e32bc07a22e57638ec52470 | R | 1,246 | 37 | rm(list = ls())
library(Seurat)
library(PRECAST)
set.seed(1234)
# The data with format required by PRECAST 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@meta.data$row <... |
03b3c9bc8cb365bde3513c0e269a7adaea2b5a35ade386be6d354e35f6f3a4dd | R | 1,253 | 24 | #' @title remove Noise
#' @description Calculate Repli-seq assay count matrices after substracting noise
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
#' @param rs_control a Repli-seq control assay (data.frame) loaded with readRS() and formatted as c... |
30aa60f19a93c648f9cb4c578a58a66ee9977fe8b82f3812ac8f912c39a2861e | R | 1,255 | 42 | library(dplyr)
library(data.table)
install.packages("gwasrapidd")
library(gwasrapidd)
##get top SNPs
top_vars<- "file containing lead variants to be queried"
var_list<- top_vars %>% dplyr::select(rsID) %>% distinct(rsID)
var_list_array<- var_list$rsID
# Initialize list to hold results by rsID
results<- list()
se... |
6588bd08f34d6c6e7e0b637bed529a2d19e6b0d13c3b3ca7495a45a03e4f029c | R | 1,263 | 60 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_covariate_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tagList... |
c537b55d3e1a40b809673590d8de6a7e19d1e17c357c7dcdfe83a3bb7386fe76 | R | 1,266 | 34 | #' @title Read Repli-seq assay data (bedgraph format).
#' @description Bedgraphs with a one line header and with similar organization (same length and sorted)
#'
#' @param paths_data list of paths to repliseq fractions files
#' @param fractions list of fractions names
#'
#' @return a dataframe composed of genomic coord... |
e0ab7dae65f5da6e220ac4093701514ef73b34aec2b39f36ea151c2cffaa3eab | R | 1,283 | 37 | #' @title Calculate S50.
#' @description Calculate replication timing S50 values from Repli-seq assay (data.frame)
#'
#' @param rs_assay a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
#'
#' @return a dataframe composed of genomic coordinates plus S50 : chr,start,stop,S50
#... |
9ed3a7570b943c7b7f7df631cebf93c516cbea506fa0449431a76caf215c54a5 | R | 1,290 | 33 | #
# Copyright (c) 2018 German Cancer Research Center (DKFZ).
#
# Distributed under the MIT License (license terms are at https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows).
#
# Rscript ${TOOL_INSERT_SIZE_PLOT_SCRIPT} ${FILENAMED} ${FILENAMEP}_qcValues.txt ${FILENAMEP} "PE insertsize of ${FILEINFO} (rmdup)"
# Rscrip... |
b8740229589e0fdf7d68041ad365caee8f4e1818f3c182e03e91e59a8c49fd16 | R | 1,292 | 47 | library(DiffBind)
library(tidyverse)
library(BiocParallel)
# Get the experiment name and number of threads from Snakemake
experiment <- snakemake@wildcards[["experiment"]]
threads <- snakemake@threads
# Set up parallel processing
register(MulticoreParam(workers = threads))
# Read sample sheet
# Set DATA_DIR to your ... |
bc943ea0303800232a67aea6aad60065cf89830072fb07a85547cd5bd949bb91 | R | 1,294 | 55 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_eigengene_clustering_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- shiny::tagList... |
87356d215aecedc4c0989451cb7deca93239fbc0f1ad98274bc9bc70d88de43c | R | 1,323 | 32 | #' Get response time quantiles
#'
#' @param dat data.table; choice and response time data
#' @param qs numeric; vector of quantiles
#' @param rt_var character; name of rt variable in data table
#' @param conditions character vector; vector of columns indicating the conditions in which to calcluate rt quantiles
#'
#' @... |
213daf534f8274051a12166da41bbaa522cb152ca25ed5941c6eae2de4403df7 | R | 1,330 | 28 | #!/usr/bin/env Rscript
library( optparse )
# Command line arguments
pArgs <- OptionParser( usage = "%prog [options]" )
pArgs <- add_option( pArgs, c("-i","--input_matrix"), type="character", action="store", dest="str_input_matrix", metavar="Input_matrix", help="Input genotype matrix to visualize." )
pArgs <- add_optio... |
3ecef2e384574acc03bf878c3ea5d550b581bbd3c8a19bbbe3b5b26ff172c2da | R | 1,340 | 55 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
plot_deepnet_lossplot_ui <- function(
id,
title = "",
info.text = "",
info.methods,
info.references,
caption = "",
label = "",
height = c("100%", TABLE_HEIGHT_MODAL),
wid... |
068c12e087a0dfea6ad51a0b2f9b751e0c3174915b378a5162788ab1a6e9fb16 | R | 1,341 | 55 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_loadingheatmap_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns... |
5aaba68a749ef0767ee1e158e1dcbf6492e016117104c61cb2d7ab17cd52672f | R | 1,342 | 53 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ui.startupModal <- function(id, messages, title = NULL) {
if (length(messages) == 0) {
return(NULL)
}
header <- sapply(strsplit(messages, split = ":::"), function(m) m[[1]])
m... |
58641e9189787edb30435b5b4cfcd746a3f4de61427b8cdeba3cf9e263cc0c86 | R | 1,352 | 38 | file_path <- file.choose()
file_directory <- dirname(file_path)
file_list <- list.files(path = file_directory, pattern = "\\.out$", full.names = TRUE)
num_files <- length(file_list)
results_list <- list()
pb <- txtProgressBar(min = 0, max = num_files, style = 3)
for (i in seq_along(file_list)) {
file <- file_l... |
5cab346d59dc887d4a84fd3770dc5f37f07f829e3b70f2a474505040cb88a62c | R | 1,358 | 38 | library(diceR)
## Hyperparameters
Image_Name <- "1_-0.14"
#Import data.
LastStep_OutputFolderName <- paste0("./Step2_Output_", Image_Name, "/")
NodeMask <- read.csv(paste0(LastStep_OutputFolderName, "Run1/NodeMask.csv"), header = FALSE)
nonzero_ind <- which(NodeMask$V1 == 1)
#Find the file names of all soft TCN as... |
9675d4246cf6e3874e383b73d1d7a6581b0370ed249a845252e227803799b3ae | R | 1,358 | 60 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_gdendogram_ui <- function(
id,
title = "",
label = "",
info.text = "",
caption = "",
height = 400,
width = 400,
...
) {
ns <- shiny::NS(id)
options <- shiny... |
195d1e7e819085b434c0890ba53d205b5996e0c5e820e83e997c97cff34fe05b | R | 1,373 | 45 | ##
## 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... |
73b2953d605f79a5220a85a22dcd50db0913b222697211a5189c08710f9f317f | R | 1,377 | 44 | rm(list = ls())
library(Seurat)
set.seed(1234)
# The data with format required by Seurat 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 <- SplitObject(obj, split.by... |
af785f4aee3027c3d3254999f43ec9fda4f289c4da37b792b9569d61a57e948a | R | 1,398 | 49 |
pbmc3k <- local({
# Check that we're running during package build
callcheck <- "resave_data_others" %in% unlist(x = lapply(
X = sys.calls(),
FUN = as.character
))
if (!isTRUE(callcheck)) {
return(NULL)
}
# Check required packages
if (!requireNamespace("Matrix", quietly = TRUE)) {
return(... |
91855cf3b7c14ad2494f018920c982b6b7e9a18f754ef862d96dd94df4b94536 | R | 1,408 | 45 | dist_matrix = function(x, by.row = FALSE) {
# Create a matrix and transpose if by row
x = as.matrix(x)
if (by.row == FALSE) {
x = t(x)
}
# Make distance matrix
m = matrix(nrow=nrow(x), ncol=nrow(x))
diag(m) = 0
colnames(m) = rownames(x)
rownames(m) = rownames(x)
... |
c21abf9462ac0891b64580e4260cfb06228a9318d23ed7eaf693b6b3720dd8c6 | R | 1,413 | 42 | rm(list = ls())
library(Seurat)
library(rliger)
set.seed(1234)
# The data with format required by LIGER 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@meta.data$row <- a... |
2fe73c8956eb969152e06ebb350f18027db2a652d29661fb193ac6cb0dd2aad9 | R | 1,427 | 25 | rm(list= setdiff(ls(),c('params','grp')))
#####################
### Test accuracy ###
#####################
tp <- c(1,3,6)
tf = 0.5
load(file = paste(params$opdir,'diffmodel/traintest/',grp,'testfits',tf,'.RData',sep=''))
n.reps <- length(r.SC)
test.accuracy <- t(do.call(what = 'cbind',args = r.SC))
load(file = paste... |
e372b7126aa32f667c5f00252efb815a3cc85d296c20b9c25a24c7aa9f0a1627 | R | 1,428 | 53 | # =========================================================
# Environment setup for WGBS analysis
# =========================================================
cat("Initializing environment...\n")
# -----------------------------
# 1. Load packages
# -----------------------------
required_pkgs <- c(
"tidyver... |
07b6766cdb1d6b181f9faa34822ddbd264ed1fc25a1c54f290dc3448f97d46fa | R | 1,433 | 63 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_TOMheatmap_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400,
...
) {
ns <- shiny::NS(id)
PlotModuleUI(
... |
bad3349b521d7ddb13195f11406e707c5d2f904b387ec796e778baa7d0ed74f3 | R | 1,434 | 76 | #
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MODULE.systems <- list(
module_menu = function() {
c(
drug = "Drug connectivity",
tcga = "TCGA analysis",
cell = "Single cell",
pcsf = "Protein networks"
)... |
f025ce36371187786b8b3f031fe3a6b7177e19c3d9c89a1da3549be6a239258f | R | 1,457 | 50 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfile", "character", "",
"bedfile","character","",
"output","character", ""
)
OPTS <- c(
)
source_local <- function(fname){
argv <- commandArgs(trailingOnly = FALSE)
base_dir <- dirname(substring(argv[grep... |
2df406f8e75d67caff358d93d6788a03c9607db3e7a2345e408ae27bda511764 | R | 1,463 | 43 | #!/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... |
96540d3fb8c4e219226b1e68a4c897cf1da507120eddfe677da59db0557e78b0 | R | 1,468 | 53 | # !/usr/bin/env Rscript
## #!/usr/bin/env Rscript
# Sys.setenv(Renv='PWD')
# Rscript version updated according to README 30-Mar-22 commit 69c9fb4
# Long time execution : ~20 min
# install.packages("devtools", repos = "http://cran.us.r-project.org")
library(devtools)
# if (!requireNamespace("BiocManager", quietly=TR... |
c98b84f97dcb5684182a5132db234541b8508d7194aa8f67f50fec8c841b440b | R | 1,493 | 66 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_snf_heatmap_ui <- function(
id,
title = "",
info.text = "",
info.methods = "",
info.references = "",
caption = "",
label = "",
height = 400,
width = 400
) {
n... |
582b0e2b81ae0d20410261305d58ab7f63c996ba3cf4e7aeb331832f2af315ec | R | 1,498 | 61 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_centrality_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("pl... |
84069e5a3923c5254f40f51ae48ea855a57976b456ebf9439dab7b9c45b7b3d0 | R | 1,499 | 34 | # sink(snakemake@log[[1]])
library(data.table)
library(assertthat)
source("utils/mosaiClassifier/mosaiClassifier.R")
# Currently read files from the Snakemake pipeline
counts <- fread(paste("zcat", "/g/korbel2/weber/MosaiCatcher_output/Mosaicatcher_output_singularity_LCL-TALL/counts/H2NCTAFX2_GM20509B_20s000579-1-1/H... |
b39d9bec69f7f9b1a81aad360edfe49b7349cf50ee4879f6d5ee32db246d4cc8 | R | 1,499 | 24 | options(warn = 2) # treat warnings as errors, otherwise script can fail silently if a package fails to install
InstallPackageFromArchive = function(packageName, packageURL) {
# make sure to use http not https as this will give an "unsupported URL scheme" error
if (!(pack... |
cb4ee2f964464808ddf43ad3960c87f50c7a744cc8f48f73743eb71476e1dca3 | R | 1,499 | 58 | #' returns the hapotyoe name
#'
#' @param hap.code The haplotype coding
#' @author Maryam Ghareghani
#' @export
#'
get_hap_name <- function(hap.code)
{
hap.codes <- c("1010", "0010", "1000", "0000", "0110", "1001", "0101", "2010", "1020", "2020", "1110", "1011")
hap.names <- c("ref_hom", "del_h1", "del_h2", "del... |
81002bbe7d8bb4f204f2ef2e1f080932117d6dc4ebca450a0e4004a7daf62194 | R | 1,512 | 64 |
pbmc3k.seurat.counts <- 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 = ... |
ece7efdc117bda65fc6afa3898672d7095847827c61b0db688ea106544056e1e | R | 1,514 | 69 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MODULE.compare <- list(
module_menu = function() {
c(
isect = "Compare signatures",
comp = "Compare datasets",
cmap = "Similar experiments"
)
},
module_ui =... |
2c138947e6918fc5f5876400f836b42e51d5fbf29ed24f508b598b3b22b0f6e5 | R | 1,520 | 67 | # ==========================
# 0. Libraries
# ==========================
library(dplyr)
library(data.table)
# ==========================
# 1. Paths
# ==========================
# 输入（processed data）
dmr_file <- file.path(data_processed_dir,
"DMR_full_results.tsv")
# 输出（analysis层）
ou... |
d952095e86a5bc1b4ac14a902b7d92763030eee9785e6333283a0279a2cc4a29 | R | 1,521 | 68 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
admin_module_info_ui <- function(
id,
label = "",
title,
height,
width = c("auto", "100%"),
caption,
info.text
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("mod"),
... |
0e90fa6d268e98b558983f6dee4d2df812f565c2bd998b4ad062204dd5f8dc1c | R | 1,522 | 57 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_correlation_network_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height,
width,
...
) {
ns <- shiny::NS(id)
PlotModuleUI(
n... |
1f485f1ca6eee66f01940d04d13781f5cc880c05d4319ee4748a0aebf16eb3d2 | R | 1,523 | 39 | # https://scholar.google.com/scholar?q=%22fiber+photometry%22&hl=en&as_sdt=0%2C21&as_ylo=2014&as_yhi=2014
years <- 2014:2022
t <- 1:length(years)
refs <- c(6, 27, 71, 137, 240, 372, 532, 614, 879) # 549
add_nls <- nls(refs ~ a*exp(r*t),
start = list(a = 20, r = 0.5)) # estimates are very stable for re... |
a369772664a5aac87a11405173a3b54ca36d18f9c092f7f2aa63847d0b0ad89a | R | 1,524 | 68 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_dendrograms_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <-... |
9a9f5a36aa49e77790e0e05b054acabe20a29c6302e2c2dc450f6d87dc22c62c | R | 1,537 | 66 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_sampledendrogram_ui <- function(
id,
title = "",
label = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),... |
5739eb721930156e80dadf774b891567d36657c8a842d254281db615e7376e04 | R | 1,541 | 72 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_topgenes_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot"),
ti... |
33450af05ea29e1b42c0595494d200fb7a6124eb5b6ff7de4301820ce196ca73 | R | 1,544 | 73 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_overlap_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
## options <- ... |
5b3c01f7d631e3b949a80f3b0bcb85cf4eb80bba7d94803871b7da6174c21fd4 | R | 1,563 | 44 | #' Get simulated responses and rts from first passage time density
#'
#' @param fpt matrix; 2 X time points matrix with first passage time for upper and lower boundary crossings
#' @param dt numeric; size of time bins used to calculate first passage time density, default = .01
#' @param n integer; number of trials to ... |
5a7c8bd8f4af100ad1d8847c866643d3649c8865e518a11ca1e2d461d47df9d1 | R | 1,601 | 70 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
admin_module_status_ui <- function(
id,
label = "",
title,
height,
width = c("auto", "100%"),
caption,
info.text
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("mod"),
... |
377456d3f6cf3c1dc255f48f9f60b48e7b90bd660b2e63f688753fcd0b2396f3 | R | 1,609 | 76 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_traitsignificance_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options... |
52625a1473c3a6b5d4d89fe238f8bc07ba2467a0ef7e7c129e507ac80cb2bd76 | R | 1,616 | 53 | ##
## 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... |
2f27a94b1e69d05ccca575d70107617996326c46ed45e92045aec5966b69a331 | R | 1,618 | 58 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
if(interactive()) {
library(shiny)
## RUN FROM root folder!
source("shiny/global.R") ## global variable
source("shiny/modules/plotModules/examplePlotModule.R") ## exampl... |
36b21ee9ad253852191119243add1b8d40e0a7912b97a35e0c8bcf24ffc3cb02 | R | 1,619 | 71 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_factortrait_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tagLi... |
6895055873755b5ef78f6d31f75e738b00f2152c059c297e3fde50dbf25eb874 | R | 1,620 | 56 | library(pracma)
library(progress)
library(foreach)
library(doParallel)
# vip_null_R <- function(x, y, perm, lv_for_vip) {
# m <- nrow(y)
# n <- ncol(y)
# tmp1 <- matrix(0, ncol(x), perm)
# for (i in 1:perm) {
# ind <- sample(m, m, replace = FALSE)
# X1_r <- x[ind, ]
# result_pl... |
9b5549485cda9f7d43a4765db537a545b044259364c1effe4a5adb8f8db21a94 | R | 1,620 | 75 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_traitsignificance_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
opti... |
14f3dd5b8e8cff05806b96e06aae77158883c845b4aecf60fa6456847e5e2c03 | R | 1,631 | 67 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_module_significance_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("plot... |
be72ff4285cab0fdb0915642dd6e02c9e752eb3c59872505c76f9fef070819bc | R | 1,644 | 70 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_plot_gclustering_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400,
...
) {
ns <- shiny::NS(id)
options <- shin... |
666cef0a6fd5fd214d4a6573231d5b2fea21cbbcbcca127456a0229d77b1bb4f | R | 1,651 | 73 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_plot_power_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::tagLi... |
1b7c6944309711331741b90a9aa565414c00afa81c378ce974df576e68af8ef4 | R | 1,657 | 40 | #' @title calculate URI
#' @description Calculate the under replication index of two compared Repli-seq assays
#'
#' @param rs_x a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,stop,S1,...,Sx
#' @param rs_y a Repli-seq assay (data.frame) loaded with readRS() and formatted as chr,start,sto... |
270a584d2e1f8826c88d17dba1627820e5cfe858944c9eca034abafb0a290e46 | R | 1,657 | 46 | rm(list=setdiff(ls(),'params'))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'processed/',sep='')
dir.create(savedir,recursive=T)
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load path data and ROI names
#####################################
### Tract tracing connectome onl... |
24c3f30a3cff9e18bf81aafc9e2021c6b464a47c46eac636e5bcaaf35403d347 | R | 1,671 | 74 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_power_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny::t... |
06a70e15eca67318edcf01f3e06ccf0c81a5f8a89b35aa7a76a52457a54fa024 | R | 1,683 | 75 | ## make as R6 class?? e.g. add documentation, initialize object,
## object id.
MODULE.expression <- list(
## MODULES[["multiomics"]] <- list(
module_menu = function() {
c(
diffexpr = "Differential expression",
timeseries = "TimeSeries",
corr = "Correlation analysis",
bio = "Find biomark... |
34a9cefb22d6fee65354c462b391772188d43351524fc5e741bde08d001e4e6b | R | 1,683 | 74 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_power_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- shiny... |
d60166e6da478e5eb5a4f2399fff45c002700cd31fc8682ace10f472e1bf1b9b | R | 1,688 | 72 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
mofa_plot_factorgraph_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagList(
... |
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