sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bbc40d2f3218e4d34bf5d5ef83321a6ce0db55e7a77f69c27c82c0f8e95156c2 | R | 3,969 | 87 | #################
### 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$opdir,'processed/pathdata.RData',sep='')) # load path da... |
e0106317a65915a0a612e7219a2798aa742cc941caa5c755fce055c997a1e7bc | R | 3,973 | 80 | set.seed(1)
##EIB part
mydata<-read.csv("EIB_inactive_neurons_results.csv",header = T, na.strings = "NA")
colnames(mydata)[1]<-"Sub_ID"
mydata$Sub_ID<-as.factor(paste0("Sub_",mydata$Sub_ID+1,"_",mydata$Slope))
mydata$Slope<-as.factor(mydata$Slope)
require(rstatix)
sink(file = "/Users/lchen4/Documents/Research/LCCN re... |
fa883dd4ca87cc69f6eee837fd9b4ad36aa0c03dd145403d3da7462ecfd58ee4 | R | 3,973 | 119 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## =====================================================================================
## ===================== NORMALIZE GADGET UI ===========================================
## ======... |
d7c161636eb42b8650982d1568b427c66f4dc2885c123f698cf8a658982bfba4 | R | 3,974 | 166 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_go_actmap_ui <... |
de7a721e31d6d7ba6726407b79e969b5919525b36af799a627c404861bf48273 | R | 3,975 | 166 | ---
title: "Initial Analysis of Cultured hGPCs and Human Cells out of Shiverer Chimeras"
author: "John Mariani"
date: "12/6/2022"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, mes... |
159da06444bcf862e1c6b60f11600a0a53593ae9781202495d6ea62454858736 | R | 3,998 | 112 | #### Differential Expression Analysis of scRNA-seq Data - 01 - Create Design Matrix and Filtering Genes ####
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis")
stopifnot(suppressMessages(sapply(packages, require, character.only=TRUE)))
setwd(glue::glue("... |
850b24ae887a63c7435b7b4ed6668a23491cf25be86befc90e208dbf10c42477 | R | 4,002 | 148 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_table_crossgenes_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
... |
6ac313502873f4524e2c31eb89f36f0fd664d84fe862933bb0d4eb86b762a47e | R | 4,007 | 112 | #### Differential Expression Analysis of scRNA-seq Data - 01 - Create Design Matrix and Filtering Genes ####
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis")
stopifnot(suppressMessages(sapply(packages, require, character.only=TRUE)))
setwd(glue::glue("... |
902e5eb84c40e93b08da8cec6d0454a4c1ffdaae89534d375255699fd482b88c | R | 4,015 | 112 | #### Differential Expression Analysis of scRNA-seq Data - 01 - Create Design Matrix and Filtering Genes ####
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis")
stopifnot(suppressMessages(sapply(packages, require, character.only=TRUE)))
setwd(glue::glue("... |
b4b916dd43deb9a8e02085db0372d21bb645b56d8b0c72fba2b3df6a2ca79188 | R | 4,018 | 116 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
QA <- list(
"What are my top genes?" = "Your top differentially expressed genes across all comparisons are: {topgenes}.",
"What is a 'meta-q' value?" = "The meta-q value is a aggregat... |
f2e55249ba8e05ac0c13c24ef55ed5ae1bda2c63603d0453052508d19836d9f1 | R | 4,025 | 137 | ---
title: "Figure S1E-F: Compare Genes and UMIs across Opossum Genome Versions and Mouse"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudi... |
82284ddb6fb96d3e6498fc84a46f5f8c1902047d6946027cad4bbeceecbb045c | R | 4,029 | 104 | ## ================================================================
## Script: neonatal_FOCA_GAM_analysis.R
## Purpose:
## Model age-related trajectories of internetwork FOCA (Adversarial Connectivity)
## during the early postnatal period using mass univariate GAMs.
##
## Description:
## - For each pair am... |
053a740d8018b3966ab1bc701808b5fd8f5b56d0357c6b813db38fc80d4a6f03 | R | 4,038 | 153 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_plot_modulenetwork_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options ... |
42d69c5abd31bf25b0123ea3d215c421ba03a23fca18705eaef7c8ceda43c383 | R | 4,044 | 163 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
2a3c61079e23f642dd6ad6cb60699401315e36f6b07684973ade3e1a06a92755 | R | 4,048 | 107 | ## Hyperparameter
InputFolderName = "./MIBI-TNBC_Input/"
Sys.time()
#Create an outer folder to collect all images.
ThisStep_OutputFolderName <- "./Step3_Output"
if (file.exists(ThisStep_OutputFolderName)){
unlink(ThisStep_OutputFolderName, recursive=TRUE) #delete the folder if already exists.
}
dir.create(ThisS... |
553ca866d28207b4110ab0e26e477f4d307d5972a14263e5c7c52bf996484c85 | R | 4,052 | 104 | library(data.table)
library(coloc)
## 0) Inputs
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
pqtl_path <- "prot-a-2958.vcf.gz"
chr_met <- 17L # <-- REPLACE if METTL25 is on a different chr in GRCh38
start_met <- 42900000L # <-- REPLACE start (e.g., TSS-250kb)
end_met <-... |
631bc22a00a7860428cf00989bd5d0434500fbb80f4a03183034214092f70c17 | R | 4,101 | 134 | ---
title: "Visualize Spatial Columns: Subclass Distribution and Density Profiles (Mouse)"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudio... |
14cfe61309992ffd78c81ffb756e5b5f2d83ecbcc73feb8c8cec66b328e9b08c | R | 4,103 | 143 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Heatmap plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
biomarker_plot_heatmap_ui <- func... |
a560be93121b4f0838064cbdfecc54b98b4d34aab5f132d17c4d9744204e4873 | R | 4,111 | 134 | ---
title: "Visualize Spatial Columns: Subclass Distribution and Density Profiles (Opossum)"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstud... |
8eb45e8b85114a4bdf0b6b05b11d223af6bc32381e4109768c613ccdfac4b180 | R | 4,150 | 89 | library(Seurat)
library(dplyr)
library(caret)
library(readr)
library(ggplot2)
library(stringr)
library(ggpubr)
library(tidyr)
#data is downloaded from
#'https://data.nemoarchive.org/biccn/grant/u01_devhu/kriegstein/transcriptome/scell/10x_v2/human/processed/analysis/Herb_2022_Hypothalamus/SeuratObj/HypoSamples_AllCell... |
e2339e1fdf17a2fba1b0986203ebd346c9ece1ec4fa45c2b90163be0693ace29 | R | 4,159 | 136 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Word Cloud Plot UI
#'
#' @description
#' Creates the UI for the word cloud plot module.
#'
#' @param id Module ID string
#' @param title Plot title
#' @param label Plot label
#' @param... |
f107dad01c2fdf8b886ddc880c8d90eb879840c05845ed3d7e57edbdcaadc3c7 | R | 4,164 | 149 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics Sagl. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_reactome_gra... |
9a55387230c2828b9a765d1a66fcae07a722bbff27f8db3a6ff987da6cbe7ddf | R | 4,165 | 106 | library(dplyr)
library(shiny)
library(dqshiny)
library(sortable)
library(shinycssloaders)
ui <- shiny::fluidPage(
shinyjs::useShinyjs(),
shiny::titlePanel("HTGTS postprocess"),
shiny::HTML("<style>
.tlx-group .shiny-file-input-progress { margin-bottom: 1px !important; }
.tlx-group .shiny-file-input-progress... |
555a482212ce01d26593e862aad6385103c5cb7d1c83bf6dd36025845276a681 | R | 4,177 | 168 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_html_module_summary_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- tagList(
shiny::... |
bf9fddaa708e0b1db74692dbc0dfdfa36e9458f62d8550990f8d31b00a6b819f | R | 4,183 | 118 | #Useful R subroutines
library(tools)
# first argument is a start and end coordinate pair defining a span
# second argument is dataframe with Tstart and Tend columns
# returns the number of basepairs in the span covered by the dataframe
bedIntersect <- function(x,df) {
df <- df[df$Tend >= x[1] & df$Tstart <= x[2],]
... |
43ca398bf0c1cc25a802c0d94893d947a3a5d2585587ce796a5ea904ffb2c2ad | R | 4,193 | 128 | #' The application server-side
#'
#' @param input,output,session Internal parameters for {shiny}.
#' DO NOT REMOVE.
#' @import shiny
#' @noRd
app_server <- function(input, output, session) {
setUserOption(session, "llm_model", "")
# list functions in global
board = options()$board
authentication = option... |
dd469822f28f134745d124ffad3fc7b1f97d237a807b920fb92aa95db234d161 | R | 4,201 | 175 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ui.showSmallModal <- function(msg = "Please wait...", timer = 0) {
shiny::showModal(shiny::modalDialog(
title = NULL,
shiny::HTML("<br><center><p>", msg, "</p></center>"),
fo... |
f4716f801c1d2b8da70205bfd0dad399373722c4c857006e51b05b60e5606c89 | R | 4,241 | 103 | ###############################################################################
# Title: Multi-organ split workflow — filter by organ, impute, and run stats
# Author: Yumi Kim
#
# What this script does
# 1) Loads helper functions from `R/MultiOrgan_Total_Split_Function.R`
# (expected to provide `group_na_summary... |
1473dac076a3964123cda7fe1b0e7b78f31602f24de7babc54097ab646941dcb | R | 4,248 | 149 | #' ============================================================================
#' Utility Functions for PCB snRNA-seq Analysis
#' ============================================================================
#' Load and Validate Seurat Object
load_seurat <- function(file_path, required_metadata = NULL) {
if (!file.e... |
29afe39cbca7249b39f6d7ec03d126992a7e68f91f4bca6a7e16fe17b6f49100 | R | 4,256 | 162 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_table_contrasts_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
opts <- shiny::tagList(
withTooltip(
shiny::radioB... |
3b71ead5290198c38e77f8022cf69715f2b9a7af1368625a832f60ec886365b7 | R | 4,275 | 130 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfiles", "character", "comma-separated list of files or dir and will grab all *.tlx",
"outdir","character", "file path to plot to"
)
OPTS <- c(
"meta","character","","",
"by.percent","character","0.02,0.05,0.1","",
... |
0aad135a4c8dae4646398e22bde160d4ab77f80dbd9ff4c912c5552f12b5a5ca | R | 4,336 | 157 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
contrast_correlation_ui <- function(
id,
title,
info.text,
caption,
label = "",
height,
width
) {
ns <- shiny::NS(id)
ctcorrplot.opts <- shiny::tagList(
## "Show cor... |
133b2fceb7640163d0e1787587787d71bac7093c0ca71b2df901e7697e7883aa | R | 4,345 | 147 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' UI code for table code: expression board
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
expression_table_fctable_ui <- function(
id,
title,
info.te... |
9ca9069a4f757762f7a42288add861f67c722d97a58a5480150d0076f959c74d | R | 4,345 | 92 | rm(list=ls())
library(ggplot2)
library(reshape2)
library(stringr)
library(gridExtra)
library(cowplot)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("brain_FA.normalized.csv", row.names = 1)
info <- read.csv("brain_FA.info.csv", row.names = 1)
info <- info[info$species != "Q... |
7afe3b835934ef5eb58732f96e48cc84bdfa0f47c54d7164d69151837318f8b0 | R | 4,347 | 150 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
setwd("~/Playground/omicsplayground")
rfiles <- dir("components", recursive=TRUE, patter=".*[.][rR]$",full.names=TRUE)
## scan all function declarations
func.defined <- c()
f <- rfiles[1... |
4a5915d9c667b23d637cdfe7787f617d895f374e9d8e84744775ccdb4df2c42d | R | 4,364 | 137 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
user_table_resources_ui <- function(id) {
ns <- shiny::NS(id)
bslib::layout_columns(
col_widths = c(4, 4, 4),
height = "100%",
TableModuleUI(ns("timings"),
info.text... |
a742c4e76cdd6ff3163fea5ae585c1bba62bf1bbcbe53bf6dc39545e3a93eaf4 | R | 4,401 | 145 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_table_genes_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- tagList(
shi... |
6d0a422de8c50e66e5d2a3d5625f780811b7087ff84020dca948b0904376757e | R | 4,402 | 143 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
TimeSeriesInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
settings_taglist <- tagList(
withTooltip(
shiny::selectInput(ns("module"), "Select module:",
choi... |
7f7869110b1cba8a28d532256bd35e022c64f562d7a7cb1edc4b84049f818d6e | R | 4,429 | 98 | suppressMessages(library(dplyr))
suppressMessages(library(reshape2))
suppressMessages(library(readr))
suppressMessages(library(smoother))
calc_bamsizes = function(i)
{
source("utils.R")
suppressMessages(library(dplyr))
path_bamsize = file.path(path_bam, stringr::str_glue("{bam}_size.txt", bam=basename(binned_ar... |
cf93ef5b4b60241ab0a445f158b59846d6d8d6589132a30325114777fac8c0f8 | R | 4,466 | 100 | set.seed(1)
##################EIB part
#read in the data
for (i in 0:19) {
if (i == 0) {
EIB_acc<-read.csv(paste0("trainedACC_1000_",i,".csv"),header = T, na.strings = "NA")
} else {
EIB_acc<-rbind.data.frame(EIB_acc,read.csv(paste0("trainedACC_1000_",i,".csv"),header = T, na.strings = "NA"))
}
}
##Extr... |
f59e557213213a3453a073cf68b2b4a5bc79fcd6308db050955aab3e62f69a53 | R | 4,482 | 143 | ---
title: "HUDECA — Extended Data Figure 6. Cell cycle dynamics in human olfactory epithelium cells"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goal
Final figures
## Setup
```{r setup... |
fc61ca005f0ea5b5efc476262f59bad1ccfd9ef8d93f6d229042e5583eef14f1 | R | 4,483 | 139 | #Results.
# First, load all the different bed files, put them together to a df
load_and_annotate_bedtable <- function(){
# Get the different inversions
basedir = '/home/hoeps/PhD/projects/huminvs/mosaicatcher/results_overlord/used_beds/'
invs_hom_link = paste(basedir,'HG00733_hom.bed', sep='')
invs_het_link... |
7199fa537cbba042ced88c193584654184f371748f015c241d10fe154bb698f0 | R | 4,486 | 159 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
20f3373c884df58a99269d07dc38ce7177ead292e69caa97abcdc85eca6e63af | R | 4,488 | 160 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
args <- commandArgs(trailingOnly = T)
if (length(args) != 4) {
print("Usage: Rscript scale.R <count table> <norm factors> <out>")
print("")
print(" Normalize Strand-seq read counts. Divide the coun... |
3fac7c0f4ddb59ceeccb0fd568b59e930e50cd684a63e57a03da53aeb2528330 | R | 4,502 | 142 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfile", "character", "",
"output","character",""
)
OPTS <- c(
"as.filter","logical",TRUE,"set to FALSE to use filters as selectors instead",
"remove.adapter","logical",TRUE,"remove adapter junctions (not when first ju... |
6818012d86eddf08af4a02f715de2bfb013cc3b918b96937d0312f6e1478f8ab | R | 4,503 | 130 | library(data.table)
library(coloc)
library(arrow)
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
pqtl <- fread("prot-a-131.vcf.gz", sep = "\t", header = TRUE, skip = "#CHROM", showProgress = FALSE)
#-------------------------------------------------------------------------------
# Set case–control meta for ... |
d9de533b367fb775d243196fcc101f9bd803d8d1ab76020ab17ff0391f3aa0fd | R | 4,522 | 138 | args <- commandArgs(trailingOnly = T);
refdir=args[1]
datadir <- args[2]
fout <- args[3]
#source('/home/meisl/bin/FunctionLib/Lib/pagodaLib.r')
library(ggplot2)
dgeToSeurat2=function (refdir) {
#refdir='/home/meisl/tools/slide-seq/test/PCA6T/'
dge_file = file.path(refdir, "dge.rds")
raw.data= readRDS(dge_fil... |
a67e20b3b7f81c5e927486c9410f40cd6eee7a8f03d96da8780cba404ad461f3 | R | 4,529 | 97 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/seedspec/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # loa... |
ad2a0293c24b81fac206ed7c39071d0be0b3474099e1a958e8c1c38e608d7120 | R | 4,532 | 135 | #!/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... |
ce00eb50dabac689e1175456c66f4ba71d24413f1929c004d61f81edf9aa321e | R | 4,570 | 139 | library(data.table)
library(coloc)
del <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
eqtlgen <- fread("2019-12-11-cis-eQTLsFDR-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz")
# APOE window (GRCh38): chr19:44,421,094–45,421,094
chr_apo <- 19L
start_apo <- 44421094L
end_apo <- 45421094L
gwas ... |
045221002d5e77af9ecbf3a53291309d16fff4e5649c9094ccafd5fca8f80721 | R | 4,576 | 132 | # ============================================================
# Script 02: LinDA Alternative Differential Abundance Analysis
# Candrea et al. - Gut Microbiota Comparative Analysis
# Biomedicines 2025
# ============================================================
# Description:
# Taxon-level differential abundance anal... |
84a02f9136fb92eca7122526eef39926305da98eb1c05d8664e201f4acb86ce9 | R | 4,586 | 123 | # # GWAS Locus Browser Burden Script
# - **Author** - Frank Grenn
# - **Date Started** - June 2019
# - **Quick Description:** get the minimum burden p value for each gene of interest for imputed and exome burden tests. Bonferroni correct p-values by number of genes in test and assign significance scores to each gene.
#... |
507cc778d7539c14872f1e9d868bbd22289b1dc4cda0d314903516a13532ad7b | R | 4,595 | 130 | # Author: Jean-Philippe Fortin, fortin946@gmail.com
# This is a modification of the ComBat function code from the sva package that can be found at
# https://bioconductor.org/packages/release/bioc/html/sva.html
# The original and present code is under the Artistic License 2.0.
# Devel branch of combat for matched sam... |
d9bc6f96a39d7e82c00b053c91860eace1da11857fba6f91a868417bcaec7fa4 | R | 4,595 | 127 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
WordCloudBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
wc_infotext <- tspan(paste("This module performs WordClou... |
62d97533ce32727a8dbfc5986ee692ba1b2a50f5ffc621e0fcb49b3e2a1cda8c | R | 4,596 | 115 | #!/usr/bin/env Rscript
suppressMessages(library(dplyr))
suppressMessages(library(readr))
suppressMessages(library(openssl))
suppressMessages(library(foreach))
source("utils.R")
pipeline_checksum = function(path_metadata, path_fastq, threads=1)
{
# path_metadata = "/mnt/sda1/Workspace/B400_RS_002/B400_RS_002_replise... |
2a96fec314142238f5eeed52312824fe3959323591c8a8c17b58d9b69da950b6 | R | 4,612 | 132 | #' Get pulse stimulus
#'
#' @description get full pulse stimulus
#'
#' @param up_sequence string; string timepoint by timepoint evidence to upper boundary
#' @param down_sequence string; string timepoint by timepoint evidence to lower boundary (optional). If NULL, no evidence (zeros)
#' @param pattern string; pattern t... |
d48ec6c1ff230a16715ea315a9b22adb9e65dc500aa6a9841d7c1b3ad5e021f4 | R | 4,660 | 80 | rm(list=ls())
library(ggplot2)
library(dplyr)
library(stringr)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
data <- read.csv("brain_FA.normalized.csv", row.names = 1)
data <- log2(data)
info <- read.csv("brain_FA.info.csv", row.names = 1)
info <- info[info$region!="QC", ]
info$age <- as.nu... |
c1a1f89c29e6ebe2b5a32febbad645fd36e290536115884d494bcc877654f9a0 | R | 4,663 | 170 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
connectivity_plot_cumEnrichmen... |
5878f3b9afb91412ca2ce58f294c15209d635ccb6ba456929d250ab04ab7ba7f | R | 4,675 | 127 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MGseaBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row 1... |
eea880c9df09d03fd1132a36f81ca1f464336154d7bd6cf6022d955684de5302 | R | 4,688 | 61 |
## Ramos
integratedRamos <- readRDS("output/RDS/integratedRamos.rds")
round((prop.table(table(integratedRamos$predicted.id, integratedRamos$cellType), margin = 2)*100),1)
integratedRamos$cellType <- factor(integratedRamos$cellType, c("NPC", "GPC1", "GPC2", "GPC3", "GPC4", "imOL"))
integratedRamos$predicted.id <- fa... |
e7f36de32b3fbb9ad3c9b6677efcc2a34bfac678125ee7160d8d24a69d431fb7 | R | 4,696 | 156 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
7d74d8e90c134c50d66fbab27725f6f9ad26484ae3c5544c53460769a571df77 | R | 4,709 | 152 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
functional_table_go_table_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
TableModuleUI(
ns("datasets"),
info.text = info.tex... |
e9efe09b02f04d34e060660ea7775f46c2bbaddbe45834b8cef3d329aa5674ee | R | 4,731 | 191 | # # GWAS Locus Browser QTL Locus Compare Plots Scripts
# - **Author** - Frank Grenn and Hirotaka Iwaki
# - **Date Started** - October 2019
# - **Quick Description:** code to make locus compare plots from eQTL and GWAS data
#nohup R CMD BATCH plot_qtl_locuscompare.R output.log &
#check progress with "jobs"
#get jobid ... |
402056cd7845a31d9445f3d7386ab7504f25311f119fe10f5bbe1babd14b3503 | R | 4,743 | 143 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_module_shared_ui <- function(id, height = 720) {
ns <- shiny::NS(id)
}
upload_module_shared_server <- function(id,
auth,
... |
13297e71a10ca09ac6edfc409849047fa4d083aad81c4b0a4c3bb2a557fc0314 | R | 4,744 | 126 | library(tidyverse)
library(Seurat)
library(magick)
library(cowplot)
library(ggplotify)
library(circlize)
library(ComplexHeatmap)
library(extrafont)
loadfonts()
setwd('~/Dropbox/share_paper/paper_Visium_DCN/')
# A: Schematic of study
# B: UMAP - color by spatial clusters
# C: Spatial plot of spatial clusters
# D: Hea... |
cf00c9acc019af6b5ca23e9b66187002e9d5000185b7b43e7788d8b8bd5cde1e | R | 4,745 | 171 | ---
title: "Process MagicBlast Output"
author: "Hannah Aichelman"
date: "2025-09-23"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
## Library packages
```{r library packages, message=FALSE, warning=... |
713e99a205b77a180920bb5e66360cc810eeb36e53d23120a7c99c09462695fa | R | 4,758 | 106 | # plot fLME models with random effects
## Figure 4
plot.FUI_RE <- function(r,
fig = NULL,
align,
Hz,
var_name = NULL,
title = NULL,
y_val_lim = 1.1,
ylim = NULL,
... |
83e5e17ad781e3e65dfbd1eac01d8a2d3bf81b085444e8d88c606117cde57f62 | R | 4,805 | 171 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_variationcoefficient_ui <- function(
id,
height,
width,
label = "",
title,
info.text,
info.methods,
info.extra_link,
caption
) {
ns <- shiny::NS(id)
me... |
427bd3b715b3f02d9fca2a17929e3b35f3981783ff05e8925b4434d26869aefb | R | 4,824 | 150 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
dataview_table_beta_ui <- function(id,
width,
height,
title,
... |
58b6672cb5e6f6da968a5a250d5ca5bf8c32e587b7ddf194376c76cf68582240 | R | 4,824 | 166 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_histogram_ui <- function(
id,
label = "",
height,
width,
title,
caption,
info.text
) {
ns <- shiny::NS(id)
PlotModuleUI(
ns("pltmod"),
title = titl... |
c312b55f52e894c402ca3c6cffc68324159151925233e41223f167605f8332dd | R | 4,828 | 84 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
SNFInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
bslib::accordion(
id = ns("data_type_accordion"),
open = FALSE
## bslib::accord... |
7ed5856884003f72cc861811f08af5af92e6d8abedfa99b7101c16cd1ea89244 | R | 4,853 | 130 | library(coloc)
options(stringsAsFactors=F)
library(stringr)
library(dplyr)
library(data.table)
data<-commandArgs(trailingOnly = T)[1]
trait<-commandArgs(trailingOnly = T)[2]
chunk<-commandArgs(trailingOnly = T)[3]
subset_dataset <- function (dataset, index)
{
if (!length(index))
return(dataset)
if (... |
cdf1bee5810e11120e3973dad8a6caa95673a10b159a73184fd456896e5bfaa8 | R | 4,864 | 150 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_table_modulegenes_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id... |
2e5e3d0636b3dc535444187241eba9fd2cd671567224dc3aa66bfc5d62deb55d | R | 4,866 | 95 | library(ggplot2)
library(dplyr)
library(scales)
library(RColorBrewer)
library(maftools)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
blank_theme <- theme_void() +
theme(
axis.title = element_blank(),
axis.text = element_blank(),
axis.ticks = element_blank(),
pa... |
f93d4e9393166c0d8ae260fddb28fed8c2e5fd19c2b444825d1d30e264ff8481 | R | 4,874 | 99 | library(Seurat)
library(limma)
library(glue)
# By Osman Sharifi & Viktoria Haghani
################################################################################
## Variables
## Paths
# data_file <- "~/GitHub/snRNA-seq-pipeline/raw_data/rett_P30_with_labels_proportions.rda"
# data_file <- "~/GitHub/snRNA-seq-pipe... |
8cbedf8f8258320adebbfea137738050b9449c443bb0ef2d902252dd3a27b6cd | R | 4,885 | 131 | # Author: Jean-Philippe Fortin, fortin946@gmail.com
# This is a modification of the ComBat function code from the sva package that can be found at
# https://bioconductor.org/packages/release/bioc/html/sva.html
# The original and present code is under the Artistic License 2.0.
# If using this code, make sure you agree ... |
c63cf6294337f4e3d3e1bf8197495ebc3993d3b041f85a8348c63db1fe92031c | R | 4,902 | 196 | # # GWAS Locus Browser QTL Locus Compare Plots Scripts
# - **Author** - Frank Grenn and Hirotaka Iwaki
# - **Date Started** - October 2019
# - **Quick Description:** code to make locus compare plots from eQTL and GWAS data
#nohup R CMD BATCH plot_qtl_locuscompare.R output.log &
#check progress with "jobs"
#get jobid ... |
5bc706c503b5d3436e5a7a8009da1f44a29f206f39a6f48fff101ee2712e6b96 | R | 4,908 | 191 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_reactome_actma... |
352090ca9abf487306e4583aabacd3638a78ea0a80e35ef9441ab77b5391ac70 | R | 4,936 | 196 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
clustering_plo... |
4c34c5a2572a33196c286bd3f14751e6e1dc6404f1340276acd50cb435bbc0b6 | R | 4,960 | 158 | # SET ARGUMENTS
input_path <- snakemake@input[["counts_scaled"]]
gc_path <- snakemake@params[["gc_matrix"]]
save_path <- snakemake@output[["counts_scaled_gc"]]
plot <- TRUE
min_reads <- snakemake@params[["gc_min_reads"]] # <- 5
n_subsample <- snakemake@params[["gc_n_subsample"]] # <- 1000
print(gc_path)
# open files
... |
bcafdef88648d835feb7f7ac0a0cde83ea6151c567fdd7dde7503899458c85fb | R | 4,988 | 169 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## Various Bootstrap goodies.
##
##
bs_alert <- function(text, conditional = TRUE, style = "primary", closable = TRUE,
translate = TRUE, translate_js = TRUE, html = T... |
ccf541f1636af8fcd338055c0eb96cdf37872b6ee131af75cc1572dcf28ae73c | R | 4,993 | 182 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics Sagl. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_wikipathway_... |
27d884caa8452a85e7a0f403d7a1c1a84967374e15913bcb30a469fcce7d4933 | R | 4,994 | 181 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
correlation_plot_cor_graph_ui ... |
7a675ca3f4e83863905f6b6a331d7bc15d78f7025f860ed580dcff868d94289a | R | 5,017 | 92 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'diffmodel/',sep='')
dir.create(savedir,recursive=T)
dir.create(paste(savedir,'roilevel',sep=''),recursive = T)
source('code/fitfxns.R')
load(paste(para... |
58908209eb21bf9fc839dae21f4a0598133f19b089193ae7a1a1ef18dc9b8fec | R | 5,026 | 146 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
app_ui <- function() {
board = options()$board
use_example_data = options()$use_example_data
# handle pgx file input
pgx_file <- ""
pgx_file_opt <- options()$pgx_file... |
fec446adf3b2c2e3c8645a422212f524eeca6f87dcb5cc711e6204f5f55b9827 | R | 5,039 | 178 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
multiwgcna_table_modulegenes_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
... |
f230d7d079394110a33c6ce091ad8132cdccfb4b375f67482f7cd9cdb82699c3 | R | 5,065 | 123 |
rm(list = ls())
gc()
# -------------------------- Load packages & parse command line arguments --------------------------
library(data.table)
library(MASS)
library(sfsmisc)
library(optparse) # Parse command line arguments (install if needed: install.packages("optparse"))
# Parse command line arguments
option_list <... |
a23e53829d44eb7d4b675e34926afde83e72f127bd3e7595d850a20ebff189f6 | R | 5,072 | 148 | TimeSeriesBoard.enrichment_table_ui <- function(
id,
label = "label",
title = "title",
info.text = "Table of enriched genesets. Table reporting the genesets along with the correlation value (rho) and the p.value. ",
caption = "Table of enriched genesets. Table reporting the genesets along with the correlation... |
c4a56f55ec999f36e304f0d329dc3221703c1e07d8593144100eff7114cad979 | R | 5,082 | 179 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
correlation_plot_correlation_U... |
69dc772f09c711c0b6ca4ff0dea17f7af7a9f60f30b364014e7ce02c6c66b8ee | R | 5,090 | 199 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
functional_plot_wikipathway_ac... |
13ece861b6b31394abf742f6df7bede9bc3d1c26b88c7657a38d1d59c3e22691 | R | 5,104 | 167 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_table_gset_enrich_all_contrasts_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
fctable_opts <- shiny::tagList(
withToo... |
925462dc4ad78a62229f81cbcd2647b6a37906540297286ea99a3e8fbc7caac4 | R | 5,106 | 132 | #################
##Jingjing.liu@stjude.org
##2021-07-26
#################
library(NetBID2)
library(optparse)
####input data required####
option_list = list(
make_option(
c("-e", "--expression-set"),
type="character",
default=NULL,
help="File containing gene expression data.",
metavar="charact... |
a6908a0578851d542ee54c54d73a943760c4ca1744aa4af37485cdd33f4125ad | R | 5,119 | 174 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
a8f2c2a06bd20934676ea4b4fcc384384862ea24403d1d46135d2f772cf139a9 | R | 5,124 | 129 | suppressMessages(library(data.table))
suppressMessages(library(assertthat))
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/mosaiClassifier.R")
# source("utils/mosaiClassifier/mosaiClassifier.R")
#' Derives SV type with highest probability according in each cell and segment.
#' Output is a table with... |
b45a64697bdfdb90f02acf0f808ce4ef8ffa8689dbf50411c6fbf693c76eaafc | R | 5,129 | 134 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PcsfInputs <- function(id) {
ns <- NS(id)
bigdash::tabSettings(
withTooltip(
selectInput(ns("contrast"), "Select contrast:",
choices = NULL, multiple = FALSE
)... |
54af3a8f61e5cd07a0c26abce0ef6020074ae70a0a96a0db64b2aee63917f0c7 | R | 5,130 | 101 | library(ggplot2)
library(dplyr)
library(scales)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
val_data=read.table("data/somatic_variant.validation_summary.txt", header=T, sep="\t")
val_data$mipsVAF=val_data$mipsVAF*100
val_data$valseqVAF=val_data$valseqVAF*100
### Fig.3a
ggplot(dat... |
e6f1376f548c97a0a759b0fe10e7300548f7637a27b27df26fbbd6cdc19127f3 | R | 5,149 | 154 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
9f1c21e895e71b5236c54dc99825d0e756843fb3873a26516dc009e53227e168 | R | 5,175 | 149 | # ============================================================
# Script 03: PERMANOVA Beta Diversity Analysis
# Candrea et al. - Gut Microbiota Comparative Analysis
# Biomedicines 2025
# ============================================================
# Description:
# Performs PERMANOVA (permutational multivariate analysis... |
a03b0d9e3abed13be70ccc4353b714430817d36a4577508e0bf454940c79324b | R | 5,213 | 196 | ---
title: "Figure 2B: IT Continuum Diffusion Embedding"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext(... |
1853c71a2f038ae1be0e6413531314d047acca7042b7a48c9893a1e05b00b4ae | R | 5,218 | 186 | ##
## 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_e... |
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