sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
98cc720b1a646d4d06ebe5ab7ee72020e0a7a117d7fc2d951d376746ad8cdc1b | R | 5,258 | 177 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
featuremap_plot_gene_sig_ui <- function(
id,
label = "",
title,
caption,
info.text,
info.methods,
info.extra_link,
height,
width
) {
ns <- shiny::NS(id)
PlotModuleUI... |
990c5fbd1c135b0d0a153dfe5dad92fd5b286d4aa9432f246e6ce728aac18ca1 | R | 5,271 | 133 | #
# # GWAS Locus Browser Expression Scripts
# - **Author** - Frank Grenn
# - **Date Started** - June 2019
# - **Quick Description:** get average expression data per gene
# - **Data:**
# input files obtained from: [Single Cell SN Data](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140231), [GTEX Data](https:... |
f3cb8d617739f3d4fe354c9b46f6bd1307522e70eb09462f8d245d7a84c85c1d | R | 5,285 | 138 | #https://www.genenetwork.nl/
pathways<-list()
pathways$id <- "pathways"
pathways$title <- "Gene Network Pathway Data"
pathways$loadData<- function(){
}
pathways$generateUI<- function(){
div(id = "pathwaysSection",
fluidRow(
column(div(uiOutput('pathwaysSelectUI'),class="geneselect"),width =2)... |
6bea1fe6f91af3349e99c64aa33ade0d43133de79d6eced7d6e4a825f76bdf16 | R | 5,297 | 182 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##' TimeSeries board server module
##' .. content for \details{} ..
##' @title
##' @param id
##' @param pgx
##' @return
##' @author kwee
TimeSeriesBoard <- function(id,
... |
df65d047b0497729d6761e1f62936f5215f9933b9a369a9d162989ec4f2baf8e | R | 5,297 | 121 | # functions for photometry data pre-processing
# written by Gabriel Loewinger
# time aligning
time_align <- function(time_truth, data, name = "timestamps", save_time = FALSE){
# time_truth - is a vector of timestamps for the (usually photometry) timepoints to align to (ground truth)
# data - is the dataset with t... |
5ef7f81ed68ce4875b14df1c5f73f1b4b496f514cdba84947d6f7232ee004a6f | R | 5,307 | 171 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
enrichment_table_enrichment_analysis_ui <- function(
id,
title,
info.text,
caption,
width,
height
) {
ns <- shiny::NS(id)
gseatable_opts <- shiny::tagList(
withTooltip... |
93cd78cc7f81d47be26314cb79eec9d700fe014313b8e7a19139499357fb2df6 | R | 5,331 | 150 | library(data.table)
library(susieR)
library(coloc)
library(SNPRelate)
library(gdsfmt)
## ---------- inputs ----------
del_file <- "Delirium_AF0p005.mr_ready.tsv.gz"
pqtl_file <- "prot-a-131.vcf.gz"
## APOE ±500 kb (GRCh38)
chr_apo <- 19L
start_apo <- 44421094L
end_apo <- 45421094L
## sample siz... |
d38c8a446ec8869fefb2a64364b496693b8b0f6d99574b26fa03af975437c09a | R | 5,360 | 178 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
epigenomics_plot_methylIdeogram_ui <- function(id,
label = "",
title,
... |
896ff2838a4bf969029dc03e8bb575f3249013e322f7f50a3c66eb95c75c53f0 | R | 5,361 | 122 | library(ggplot2)
axisTitleSize <- 24
axisTextSize <- 18
labelFont = 18
titleFont = 22
tagSize = 26
## Make SCA for DE
makeSCA <- function(seurat, cellFractions){
DefaultAssay(seurat) <- "RNA"
data.use <- GetAssayData(object = seurat, slot = "data")
fdat <- data.frame(rownames(x = data.use))
colnames(x = fdat)... |
3ccdc11b06ab6ab7a4e46b7e2c769b2cbf33eaabd022bea60513197d47fe8deb | R | 5,371 | 188 | ##
## 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
compare_plot_cum_fc2_ui <- fun... |
bedcc6e20af298310b513fb0abdbe411c878b64a97a2d998facbf0035762e7c4 | R | 5,386 | 146 | library(data.table)
library(coloc)
Ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
pqtl <- fread("prot-a-131.vcf.gz", sep = "\t", header = TRUE, skip = "#CHROM", showProgress = FALSE)
setnames(pqtl, sub("^#", "", names(pqtl)))
# ---- Define APOE window (GRCh38) ----
chr_apo <- 19L
start_apo <- 444099... |
20d3aae2f045e002218dd0874274ee08a4bfff74a6ff73b94bf2eb28859e7f8b | R | 5,413 | 134 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
UploadUI <- function(id) {
ns <- NS(id)
body <- div(
style = "overflow: auto;",
bslib::as_fill_carrier(),
bslib::layout_columns(
fill = TRUE,
div(
styl... |
93142476c77a1e3fbabf9f1e475b0fb6d2583b439b9646502cabf23591666c9b | R | 5,417 | 188 | ##
## 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
compare_plot_cum_fc1_ui <- fun... |
9f74ffb9818dc7ee75bbad63f6da360ecee848616bfd5232e2fc2a7a4bb7eea5 | R | 5,421 | 137 | library(ggplot2)
library(dplyr)
library(showtext)
library(hrbrthemes)
# Add Google fonts
font_add_google("Outfit", "title_font")
font_add_google("Cabin", "body_font")
showtext_auto()
title_font <- "title_font"
body_font <- "body_font"
# Function to calculate summary statistics
calculate_stats <- function(df, column)... |
e93d1cc3c2f20970d24a2be355a8103d322d4942f53e2f457e9acce76cae2bc7 | R | 5,431 | 203 | #' ============================================================================
#' Project: PCB Exposure and Gene Expression in Mouse Brain (snRNA-seq)
#' Script: SoupX Ambient RNA Correction
#' Purpose: Remove ambient RNA contamination using SoupX
#'
#' Author: Osman Sharifi
#' Date Created: 2024-10-31
#' Last Modifi... |
284494121eadd2715f2622b36124d81c75bb37819258a7bfcd34d74291920f35 | R | 5,433 | 134 | # This program adds Mecp2_allele counts back to the PEBBLES seurat object
####################
## load libraries ##
####################
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Seurat", "dwtools", "devtools", "dplyr", "patchwork", "scCustomize")
stopifnot(suppressMessages(sapply(packages, require, char... |
e74b21208e3df79584d61413555186469e5e2c0cc820a775495901a45a0adc23 | R | 5,439 | 140 | ---
title: "Figure 1F: Opossum-Mouse Integrated All-Cell Co-Clustering Heatmap (By Subclass)"
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$set(root.dir = dirname(dirname... |
36fe3394439fce165077e1c1baaeefab897c658f5fee5d589186afd4fe8d34e7 | R | 5,442 | 193 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
TimeSeriesBoard.parcoord_plot_ui <- function(
id,
label = "label",
title = "title",
info.text = "Parallel line plot displaying the average expression per time point of features map... |
d2df6e08cc485123f1fd6e6f8104aa58575d3ea125915bd3ba021ab514193967 | R | 5,444 | 180 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
a481b43008082bfd1efcbb31c21693a86ad9ec8c99f5a3143bd2159dc58383f0 | R | 5,499 | 166 | ---
title: "scRNA-seq_Mecp2e1_genotype_diffExp_02_females"
author: "Kari Neier"
date: "12/6/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir="/Users/karineier/Documents/scRNA-seq/Genotype/noDreamWeights/Females")
```
## Setting up
Loading li... |
b1610fe6789c86d43e19a79919545b89f8fcaf4db05bc908df47158744aee4a5 | R | 5,520 | 176 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
preservationWGCNA_table_modulegenes_ui <- function(
id,
label = "a",
title = "Title",
info.text = "Info",
caption = "Caption",
height = 400,
width = 400
) {
ns <- shiny::NS... |
eb0a11d4d7549ca87324a4cc80bc6dd5143e23e88984e3cfdd3e6e990cb932be | R | 5,542 | 177 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
3a6206f87efbf6e66a36e400fe5d0948efab513009a36a3c24418b736b354e19 | R | 5,549 | 138 | set.seed(1)
################## EIB NRS Barplot — CORnet
##################
################## Reads nrs_within_between.csv (pre-extracted by extract_nrs.py)
################## NO .npy loading in R. Instant, crash-free.
##################
################## Produces:
################## A: Train RSA barplot (within vs... |
b98d172ad8edfbcb3642f3daedbde212d5cbb9689777fac86a666ba879e0fc96 | R | 5,551 | 116 | library(ggplot2)
library(dplyr)
library(tidyr)
library(scales)
library(scico)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
tdp_data=read.table("data/pTDP43_levels.txt", header=T, sep="\t")
summarySE <- function(data, measurevar, groupvars,
na.rm = FALSE, conf... |
54d035b257cab2ffb175de1229ee95c86840942cdbdec155c3435e955aa07ac8 | R | 5,566 | 172 | #!/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(
"metafile","character","","explicitly set breaksite, otherwise guess",
"b... |
a3572aff295da8330a9bf104520b32db373b8bdc29957b4a72deeb0a9a71050d | R | 5,573 | 193 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
6bafbdc1cad60ab9db39ab12d862337c67ed1767282af4de2e9b0916733751d7 | R | 5,574 | 135 | expression<-list()
expression$id <- "expression"
expression$title <- "Expression Data"
expression$loadData<- function(){
#read the average expression data for the brain and substantia nigra and single cell data
expressionData <<- fread("www/expression/ExpressionData.csv")
colnames(expressionData) <<- c("GENE"... |
a646154ca62dd054ffaa09113a65b9dce7ec0858d720fb8eb5f4bff1f703fc89 | R | 5,577 | 179 | #!/usr/bin/env Rscript
suppressPackageStartupMessages(library(argparser))
suppressPackageStartupMessages(library(magrittr))
parser <- arg_parser("mark duplicate juntions",
name="TranslocDedup.R") %>%
add_argument("tlxfile",
"",
type="character") %>%
add_a... |
eb1f6e2f91c36f799e8b5900ca2b174737a54de274218cc231eb0698dbe1d8e6 | R | 5,617 | 202 | ##
## 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
expression_plot_maplot_... |
ee7e87c154ad6cb5b7710d361faeb4e0e078d6e1fbb433076a9b26abe725c44a | R | 5,668 | 186 | ## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
epigenomics_plot_boxplot_beta_ui <- function(id,
label = "",
title,
... |
15c1021ef6df0088b9a587955c4c07bea95600df57d25c315dcda1ace57a3f53 | R | 5,675 | 178 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
e0fcbe8aab95131c2b32d73fee2455fa72ad64b7710608d9f12a8f484cbdf402 | R | 5,686 | 186 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
featuremap_plot_gset_sig_ui <- function(
id,
label = "",
title,
info.text,
info.methods,
info.extra_link,
caption,
height,
width
) {
ns <- shiny::NS(id)
info_text <-... |
aef0f7464a6554dcc2c426d6361403cce1b95a3f2a5ff4476eaf2aaaf7cc5f5e | R | 5,698 | 211 | #Combination
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 1190,
c_COM = 25,
u_remission = 0.85,
u_response = 0.72,
u_nresponse = 0.... |
b7b8b83685f2f7f4136f21aa75ea3a5e1a8a14bd940cdb338d37d68364f836f9 | R | 5,735 | 88 | library(dplyr)
library(Rsamtools)
library(IRanges)
library(tidyr)
analyze.offtargets = function(sequences, genomes_path, model) {
#
# Find primers position in genome
#
# TODO: Find multiple alignments
# bwa index -b 100000000 mm10.fa
# bowtie-build --threads 30 mm10.fa.gz data/mm10/bowtie1/mm10
# bwa me... |
cc1240ec0ac91b485a8bffdf921a0a07d6c50068ea5d9a84aba027a54b856ea6 | R | 5,744 | 195 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
19b9cfbc56c536c0138a603f8fd07d8fe857ea06e2391ee9e6615a60fa5eb52f | R | 5,750 | 168 | ---
title: "scRNA-seq_Mecp2e1_genotype_diffExp_02_females"
author: "Kari Neier"
date: "12/6/2021"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir="/Users/karineier/Documents/scRNA-seq/Genotype/Females")
```
## Setting up
Loading libraries, settin... |
f48c1dfa57c4d2e80728fb0cc6623260f9100da374e2ee0fc462f486e3c8034b | R | 5,754 | 189 | # set arguments
input_path <- snakemake@input[["counts_scaled_gc"]]
save_path <- snakemake@output[["counts_scaled_gc_vst"]]
chosen_transform <- "anscombe"
plot <- TRUE
rescale <- TRUE
# PRE-PROCESSING DATA
# open count file
counts_raw <- data.table::fread(input_path)
# force cell column to factor
counts_raw$cell <- a... |
6f23e48e9bcc4b92b1339070e7fdc3a0aa6cc2999a8eb584ac952e2e64b3e0f7 | R | 5,762 | 174 | library(edgeR)
library(ggplot2)
# fetch arguments
args = commandArgs(trailingOnly = T)
filter <- ifelse('filter' %in% args, TRUE, FALSE)
chosen_transform <- ifelse('anscombe' %in% args, 'anscombe',
ifelse('laubschner' %in% args, 'laubschner', 'anscombe'))
# open count file
counts_raw <- d... |
e099ded3c87c3e3bd7abdbeb8e587a9bd315df8ba8825e04eca7faadbef1e858 | R | 5,782 | 101 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
WordCloudInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("wc_contrast"), "Contrast:", choices = NULL),
"Sele... |
293299a537a060f3cf1f52730b7f841657d170e477b2268974161f8239f8ed65 | R | 5,787 | 203 | ---
title: "HUDECA — Extended Data Figure 10. Analysis of the expression of the olfactory receptors (ORs) in individual INPs and OSNs"
author: "Mbouamboua Yvon <yvon.mbouamboua@inserm.fr>"
output:
html_document:
toc: true
toc_float: true
number_sections: true
date: '`r format(Sys.Date())`'
---
## Goal
Fi... |
7361423af099489cdce10c3997c476e258f173ad52a59d3b131fceabc22b2fe2 | R | 5,800 | 202 | ##
## 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
signature_plot_overlap_ui <- f... |
2e4b84935e4e722b109148dcd1f824a4536a6ab008d84cf48b53d7d1f19f3778 | R | 5,807 | 194 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_totalcounts_ui <- function(
id,
label = "",
height,
width,
info.text,
caption,
title
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::radioBut... |
a16837114edabac86a213404a2acb4afc27d683edce525770bed46982909859f | R | 5,828 | 221 | #Psychotherapies + AD
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 4760,
c_AD = 12.5,
c_PSY = 12600,
u_remission = 0.85,
u_response ... |
0958886587b383d7416f06cda446160d22fc5d79240abfcdbca3b90775a788a9 | R | 5,832 | 150 | ---
title: "Figure 2D-F: Opossum-Mouse Cross-Species Mapping Confusion Matrices"
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::... |
6c4a9c9ceb57dd38f073e64509af0dcd6f7deb08fc925bc6f0ee952939e58e16 | R | 5,840 | 225 | #Psychotherapies
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 4760,
c_PSY = 12600,
u_remission = 0.85,
u_response = 0.72,
u_nrespons... |
5d282f761759f0a2e9c769746618b950630459fb4111a578ba931454d9ad8e8d | R | 5,859 | 161 | ###############################################################################
# Title: Visualization workflow — group comparisons, volcano plots, and PCA
# Author: Yumi Kim
# Purpose:
# - Run two predefined group comparisons on a metabolomics-like dataset
# - Visualize results as boxplots and volcano plots
# - ... |
02171399439569ea822ab0efe2661613b03da9054a52770565a0a833a5366cad | R | 5,871 | 132 | ---
title: "2c. Mouse, Label Nonneuronal"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
knitr... |
aface80ff70adb024394a07046f40f3cddee1ff8feead8b6a8ac27472a4d0a22 | R | 5,890 | 191 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
08f4f213dc6db961fa71bb4f54ba3a0a5357f5cf1b90f36a0b4e3f8d35bc53a7 | R | 5,906 | 186 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## textInput <- function(inputId, label, value = "") {
myTextInput <- function(inputId, label, value = "") {
#
shiny::tagList(
shiny::tags$label(label, `for` = inputId),
shiny:... |
dbd2b2f680aa1193cd065f84ffd1d183d156698201e174a84cb7877903aa7aaf | R | 5,932 | 88 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
MGseaInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
## data set parameters
shiny::selectInput(ns("contrast"), "Select contrast", choices = NULL... |
62d27bca6cbae0d60635c5400d00b05ccf0b026bc7c63cda551aad03f3806ee8 | R | 5,942 | 198 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_abundance_ui <- function(
id,
label = "",
height,
width,
title,
info.text,
caption
) {
ns <- shiny::NS(id)
menu_grouped <- "<code>grouped</code>"
option... |
34020fc4f94e6ceec31d93041667d66511257364bd04e55ad9ebf432d53836b6 | R | 5,952 | 188 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
WelcomeBoardInputs <- function(id) {
return(NULL)
}
WelcomeBoardUI <- function(id) {
ns <- shiny::NS(id) ## namespace
pages <- list(
'<h1 class="d-block w-100 text-center alig... |
ce8eaaba425ccae17393b2f28f05340bf03e33e9a09c54f70071546cc2be7f82 | R | 5,952 | 142 | ---
title: "1. Opossum, Split Classes"
output:
---
```{r setup, include=FALSE}
# This sets the project root based on the repo structure.
# If you move this file, you may need to set the root manually to find config.R
knitr::opts_knit$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
knitr::op... |
523a82fcd59b92199cb094cb362675e54d5ff3e26210a49cc3cb3c3e9ec76833 | R | 5,980 | 171 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfile","character","file path of tlx file",
"output","character","file path ofoutput plot"
)
OPTS <- c(
"facetscales","character","free","allow free or free_x",
"numbins","numeric",100,"",
"flanks","numeric",... |
07621f10c3d134c5d77352a585357e223cf2b089c1dee83f89f5f9a83809de53 | R | 6,003 | 192 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
1c1f41f09c82150a58ee1540f282b89925f51ac322bb016dbaf4a2d595ae3a85 | R | 6,033 | 132 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'nullmodels/',sep='')
dir.create(savedir,recursive=T)
source('code/fitfxns.R')
load(paste(params$opdir,'processed/pathdata.RData',sep='')) # load path ... |
78b033b1a91d4cc46f0381ccc12692efd98e718e51ceea334bf37d7e66c6ac92 | R | 6,036 | 146 | library(ggplot2)
library(dplyr)
library(gridExtra)
library(scales)
library(ggsci)
PROJECT_ROOT <- "." # put your working directory
setwd(PROJECT_ROOT)
summarySE <- function(data, measurevar, groupvars,
na.rm = FALSE, conf.interval = 0.95) {
length2 <- function(x, na.rm = FALSE) ... |
cfc46dfd010f2c92d69ae568ee28af666cc4171aa9e092e29f854ec7462cae2b | R | 6,054 | 202 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
8074df8b3166b01ef0907feeb854e228c714abaaa98bb1964dd76f24601a292d | R | 6,066 | 206 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_averagerank_ui <- function(id,
label = "",
height,
... |
c2de220ad8030930a1a57157edabfe06a17ac190deb92b0f3e2f22d99c4f31e8 | R | 6,068 | 198 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
42aea4b5b352afb1d825e6b0781b0f4ac78b32916f0409cb54d678cef1083ffb | R | 6,074 | 215 | ##
## 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
expression_plo... |
03d34fd7645a1d529d0792a65cddd38217c25a701343dc3f88aeba9b84b394d8 | R | 6,080 | 210 | ---
title: "PSC vs GPC Figure Assembly"
author: "John Mariani"
date: "12/6/2023"
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, message=FALSE, warning=FALSE}
library(Seurat)
librar... |
0533718f9bfabe072dd38ae1a7a3265a7409345e68ae48fbf7f2d2792bad0244 | R | 6,099 | 140 | ---
title: "1. Mouse, Split Classes"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
knitr::opt... |
47e91b7980a7924f3c3f8cb8398aa51e60fb6de18adb25eb0606637c28211c98 | R | 6,110 | 119 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
SingleCellInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(
shiny::selectInput(ns("samplefilter"), "Filter samples:",
choic... |
8421c388ca11322d80a7cd0cef69872a02612341121686e2dfcdc13d24c8feca | R | 6,111 | 162 | ---
title: "DiffBind & ChIPseeker"
output: html_document
date: "2024-07-12"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
### load library
```{r, warning=FALSE, message = FALSE}
library(DiffBind)
library(tidyverse)
librar... |
54ec957acf1b8d29b9cd17081795002b11981d1643695677f1e2b6581420b175 | R | 6,113 | 152 | #### 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", "scCustomize", "Seurat")
stopifnot(suppressMessages(sapply(packages, require, character.only=TR... |
30b75ecdcb53f92898ec79a3ae349ccac0db462eb2e22ea7b97dfe25c010cec2 | R | 6,117 | 225 | #ECT + AD
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC_ECT = 65520,
c_AD = 12.5,
c_ECT1 = 77760,
c_ECT2 = 38880,
u_remission = 0.85,
... |
7552b42585643d5ce2083acf9e229a069937a29755bd765af17c70b8b7e52cff | R | 6,125 | 197 | ---
title: "HUDECA — Extended Data Figure 4. Hierarchical annotation and transcriptional similarity of olfactory system cell types"
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... |
9b50fea87171cc6731a3005451c98c007e164f4796a59250d4a054766e3808c5 | R | 6,147 | 173 | ---
title: "QC plot for eSet"
output:
html_document
---
```{r include=FALSE}
library(NetBID2)
library(kableExtra)
```
```{r echo=FALSE}
dt <- pData(eset)
if(nrow(dt)<20){
kableExtra::kable(dt,align = "c") %>%
kableExtra::kable_styling(bootstrap_options = c("striped", "hover", "condensed")) %>%
... |
810a5f66a5263272f976bc173adb686da028a1f17f652f6648a441e478ce68b0 | R | 6,184 | 211 | #Augmentation
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
# define parameters
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC = 1190,
c_AUG = 109,
u_remission = 0.85,
u_response = 0.7... |
7c2eb3c547c057605aff3349e71c22f230fc24df64d81f7670036198865fd63f | R | 6,185 | 223 | #rTMS
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_SOPC_TMS1 = 23800,
c_SOPC_TMS2 = 11900,
c_AD = 12.5,
c_rTMS1 = 60000,
c_rTMS2 = 30000,
... |
6817bae8274d0291a5aea4ca7acd595c5de4680df15c45e6b818d91f3e9b0852 | R | 6,191 | 217 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Activation map plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
drugconnectivity_plot_actm... |
d183d23a9ebd8f3c6e64d449eed5f65aabd1718ba80e716547fcfd44398206e5 | R | 6,207 | 136 | ---
title: "2a. Mouse, Label Glutamatergic"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
kni... |
b7dbc6dd39c3e16650da830bc7bea3f52ea7b26fda28c6da80514051f6b0fefa | R | 6,227 | 211 | ##
## 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_barplot_ui <-... |
fe4ad38cefda854e9c6529e7a7331c06f322da5d23be5c53c6a2937e231f99fa | R | 6,233 | 162 | # Whoeps 5th Dec 2020
# Horizontal GT concordance plot for both.vcf
library(ggplot2)
library(optparse)
# Read input
#INPUT INSTRUCTIONS
option_list = list(
make_option(c("-f", "--file"), type="character", default=NULL,
help="vcf file to be checked", metavar="character"),
make_option(c("-s", "--sname... |
fa17047be51eb996b2dd75adbae1cf530d25635c09303456a4a2516dffb7c47f | R | 6,254 | 239 | #ESK S3 Monitor Cost = 100
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 3480,
c_ESK_SOPC2 = 1740,
c_ESK_TX1 = 31296... |
115209eb22357488ec7a2e7cef676be226c0a67dd313552e370f2574a7a69655 | R | 6,263 | 225 | ---
title: "Initial Analysis of Mouse Cells"
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, message=FALSE, warning=FALSE}
library(Seurat)
l... |
058761b8f8a735834a08c8c478844af8170d6ca2b204e77a771f734b44b22a51 | R | 6,279 | 130 | #################
### Load data ###
#################
rm(list=setdiff(ls(),c('params','grp')))
basedir <- params$basedir
setwd(basedir)
savedir <- paste(params$opdir,'nullmodels/anterograde',sep='')
dir.create(savedir,recursive=T)
dir.create(paste(savedir,'roilevel',sep=''),recursive = T)
source('code/fitfxns.R')
loa... |
23a14126b354c9a4c4cb8b8b500f8c09a303f0651fa0316f28ab20d99ebd3ef4 | R | 6,314 | 200 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
a3cb47450529f60dbd562b620491a1a53ba98837e9cb28c08c7349c8949c46e3 | R | 6,323 | 202 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
416c13a3c31cca3103c11076748dbdfd5439352ab62f33a5606d584ff5ab5404 | R | 6,338 | 234 | #ESK Basecese
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760,
c_ESK_PDH1 = 10080,
c_ESK_P... |
e1e224318c77dab9a7e83c8ea9eb06023085c2f21fdbd51ce255439adb600524 | R | 6,344 | 145 | ---
title: "2b. Mouse, Label GABAergic"
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$set(root.dir = dirname(dirname(rstudioapi::getSourceEditorContext()$path)))
knitr::... |
a2aea7a0e232383f733dd842e7cedc17f4bbe13b3aae55954740971507113aaa | R | 6,346 | 174 |
## it takes a long time to run this script, thus it is better to run on a super cluster ##
rm(list=ls())
library(dplyr)
library(stringr)
setwd("D://work//skoltech//lipid//writing//GitHub//data")
setwd("/home/wangym/work/skoltech/lipid/writing/GitHub/data")
data <- read.csv("milk_FA.normalized.csv", row.... |
ff8b025dff08ffcc5c410c7c42486b90765b8e0ce722d75f0f4183b8890845b9 | R | 6,347 | 137 | #######################################################################################################
# ===================================================================================================
# Function for meta analysis
# ==================================================================================... |
4dc493253e7db055af21550851f218cf2f3dc336b773f981b28f8d88d2994004 | R | 6,363 | 252 | ---
title: "R Notebook"
output: html_notebook
---
Prepare scRNA-seq reference datasets
```{r}
con=readRDS('/home/meisl/Workplace/Prostate/Oct2020/Data/conos.selected.rds')
ano=readRDS('/home/meisl/Workplace/Prostate/Oct2020/Data/ano.OCT.2020.rds')
allp2=readRDS('/home/meisl/Workplace/Prostate/Oct2020/Data/join.all.Se... |
d6d2d2fcb1f8ea8cfda6d4b107df8b17e06ba4e085a2e0ba7d28dd98d957f03b | R | 6,365 | 230 | #ESK S5 - A 3.5% annual discount rate
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760,
c_ESK_... |
800ef13fdf85872e6a87e400562e31db8d7a3f55433cca71a1a3c14ffe1aa22d | R | 6,366 | 239 | #ESK Cycle Length = 8(Scenario 2)
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 2330,
c_4thOP = 2682,
c_5thOP = 3372,
c_3rdIP = 810,
c_4thIP = 810,
c_5thIP = 1144,
c_AD = 25,
c_ESK_SOPC1 = 14280,
c_ESK_SOPC2 = 9520,
c_ESK_PDH... |
b206f1c3af801ed559510fa81924028297ade8b82bd2a2b9c4f4743512f36d15 | R | 6,369 | 232 | #ESK S6 - A 75% reduction in the esketamine
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_ESK_SOPC2 = 4760,
c... |
d3f81a31c181eca74f05d293423ee95284d22208cabe30e39e93d110fa0c1209 | R | 6,378 | 208 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
f4541861b5f7504c8916158e83087a63797997b450126d1b7b05c0c64295caee | R | 6,389 | 235 | #ESK S4 - Reduced from three units (84 mg) to two units (56 mg)
install.packages("heemod")
library(heemod)
pacman::p_load(data.table, dplyr)
par_mod <- define_parameters(
c_3rdOP = 1165,
c_4thOP = 1341,
c_5thOP = 1686,
c_3rdIP = 405,
c_4thIP = 405,
c_5thIP = 572,
c_AD = 12.5,
c_ESK_SOPC1 = 9520,
c_... |
45f530f23b90e3f83601fa41504a65b0ca050aa9bf9e1b01b73c3577576e686f | R | 6,407 | 212 | ##
## 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_leadingEdgeG... |
a901a5ef228ee665e48985fc4b09f1a48a388b125e60f00a8542205c52d65c58 | R | 6,417 | 160 | literature<-list()
literature$id <- "literature"
literature$title <- "Literature"
literature$loadData<- function(){
pubmedhits <<- fread("www/pubmed/PubmedHitsData.csv")
#geneCards descriptions
genecards <<- fread("www/pubmed/GeneCardDescriptions.txt",sep="\t")
}
literature$generateUI<- function(){
div(id="... |
73a4035123cae95b90d7710acbb51d1ac84b01e465abbd81cfc4ffe796fa9b61 | R | 6,441 | 201 | ---
title: "Spatial Gene Expression: Layer Markers (Opossum 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$set(root.dir = dirname(dirname(rstudioapi::getSourceEdito... |
3dd944b51f85baece166c3e86d3271b5a6189e0ffd05aac1736b9557dc77ea4c | R | 6,488 | 133 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
IntersectionInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(shiny::selectInput(ns("comparisons"), "Contrasts:", choices = NULL, multiple... |
9b84f0869752ea8fc1e2e9d7f28766bfe33b995283b551f1906b2985243aa740 | R | 6,490 | 235 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Importance plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
connectivity_plot_FCFCplots_ui... |
f8bf10f98e5aa30d155bfed9d70523a669c1ce0d10f83ce16c26f44c5323bef2 | R | 6,491 | 128 | # Manhattan plot
options(stringsAsFactors=FALSE)
library(ggplot2)
library(ggrepel)
library(CMplot)
manhattan_plot <- function(data, # dataframe (columns: 'CHR','POS','Pvalue','label_text')
## genes:
point_colors=c('#44B5AD','#3A948E','#36807A','#2f615d'), # colo... |
498519f19625ccb1d4d41bc411a92a7f6df7eca75051c6e7e77f02f13c46ba4b | R | 6,495 | 161 | ######################
## Overlap analysis ##
######################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(tidyr)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
library(readr)
library(st... |
ab26582c8da70c8b680e41355ca7eff216cdcd3c4739c6c8deae235fd1b1bb75 | R | 6,504 | 171 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
AppSettingsBoard <- function(id, auth, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
dbg("[AppSettingsBoard] >>> initializing User Sett... |
c06b46630a583e72a9ab100a9a2a8e1f7ed37af9a989903ac40cdc0c283772b6 | R | 6,513 | 136 | args=commandArgs(trailingOnly=TRUE)
pdf(args[10], width = 11, height = 10 )
library(pracma)
Deeptool_chr_length <- read.table(args[1], header=TRUE, sep ='\t', comment.char = "")
Deeptool_result_final <- read.table(args[2], header=TRUE, sep ='\t', comment.char = "")
clone_num <- ncol(Deeptool_result_final) - 4
#for ... |
41ca31c6fcb4d0e3871c15e9ce4b58fa21edbeb558f83dca4e87fe5186b578ff | R | 6,518 | 253 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
consensusWGCNA_plot_moduletrait_ui <- function(
id,
title = "",
info.text = "",
caption = "",
label = "",
height = 400,
width = 400
) {
ns <- shiny::NS(id)
options <- sh... |
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