sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
e23dfb9800aee2daf283ea401b236e90334f6f2a3d710c185eb818121c1005d7 | R | 11,005 | 361 | ##
## 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_markers_ui <- f... |
b75a16cfe2f51bf874bdc9917ed34a2ccfbc3d868691485e2c549e0dd21b4396 | R | 11,011 | 333 | ---
title: "Figure S1B-C: Intergenic Read Distributions and UTR Length Comparison"
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$set(root.dir = dirname(dirname(rstudioapi::ge... |
47fd148f776653fc5629b4aeade133cd1b684087b1056e68c025afaf0f5907d2 | R | 11,043 | 276 | suppressMessages(library(data.table))
suppressMessages(library(assertthat))
suppressMessages(library(stringr))
source("workflow/scripts/arbigent_utils/mosaiclassifier_scripts/mosaiClassifier/mosaiClassifier.R")
source("workflow/scripts/arbigent_utils/mosaiclassifier_scripts/mosaiClassifier/haploAndGenoName.R")
#' Der... |
53fc2a73ab7598a30fff8466ede4070b2f948a7ff820a0fb6b1cd4a2a0f413a1 | R | 11,111 | 323 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
1f8cd2e0a3778f1e29c05d4271b26f25013aff5c3d2c2ad15d058bcdb60001fb | R | 11,169 | 403 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
compute_enrichmentmap <- function(pgx, qsig = 0.05, ntop = 120, wt = 1, contrast = NULL, plot = FALSE) {
meta <- playbase::pgx.getMetaMatrix(pgx, level = "geneset")
#
F <- meta$fc
... |
369b9c5425b4dee731463ae841b5094865cea1b7be7c9b2d701983699a653722 | R | 11,172 | 283 | set.seed(1)
################## EIB Accuracy Analysis — CORnet
################## Conditions: Inhibitated (α=0.5), Balanced (α=1.0), Excitated (α=2.0)
# ============================
# Packages
# ============================
if (!require(jsonlite)) install.packages("jsonlite", repos = "https://cloud.r-project.org")... |
50ff17f34f68379143d8b767edb84dd0d29fae29816cd0d4d44b71306ff19579 | R | 11,190 | 336 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
loading_table_datasets_public_ui <- function(
id,
title,
info.text,
caption,
height,
width,
delete_button = FALSE,
load_button = FALSE
) {
ns <- shiny::NS(id)
tagList(... |
f4239f5c6a3d72a76a52a92e54e3c53e8e8e25c8a9be66858764d38c37e9355f | R | 11,214 | 187 |
#########################################
### Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
### Cis_DTMR.R requires 2 input files
### An Exposure GWAS
### An Outcome GWAS
Exposure_GWAS <-
Outcome_GWAS <-
### Column sh... |
958b2f84f60383b05e4b7b34b5d859c4030107fb2d29191e0b9b97ccbb19aa66 | R | 11,215 | 371 | ---
title: "HUDECA — Figure 4: Transcription factors (TFs) activities in olfactory sensory epithelium"
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 set... |
5db739662401b039d8f4a5134845919d5f94b23947066f973ca558bc89cd33b1 | R | 11,264 | 351 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
create_user_dir_if_needed <- function(user_dir, pgxdir) {
if (!dir.exists(user_dir)) {
dir.create(user_dir)
example_file <- file.path(pgxdir, "example-data.pgx")
if (file.ex... |
8412144eb5def2416ff3397f0b840d0c2c66d97ce89e576a872132bef47a90b3 | R | 11,284 | 308 | ---
title: "TRUST Patient Data Imputation"
output: html_document
date: "2024-10-31"
---
```{r setup, echo =F, warning=F, message=F}
knitr::opts_chunk$set(echo = F, warning = F, message = F)
# delete all variables
rm(list=ls())
# clear RAM
gc()
library(kableExtra)
library(Hmisc)
library(tidyr)
library(tidyverse)
lib... |
f0bfb765c4779c879f37f20fcc38254ef6d67bfa010013d759b088195ef3a640 | R | 11,285 | 228 | #!/usr/bin/env Rscript
suppressMessages(library(dplyr))
suppressMessages(library(readr))
source("utils.R")
pipeline_align = function(path_metadata, path_fastq, alignment_mapq=40, trim_quality=22, trim_minlength=40, path_database, path_output, threads=1, SAMPLE_NUMBER)
{
path_output = R.utils::getAbsolutePath(path_o... |
aea0f28f6296246eb6d26d1638a99a825249f99afb8aee130b30f30ab55992c2 | R | 11,289 | 236 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
downloadButton2 <- function(outputId, label = "Download", class = NULL, ...) {
aTag <- shiny::tags$a(
id = outputId,
class = paste("btn btn-default shiny-download-link", class),
... |
2bf64e8c247fdd120052ea3aa667030f02024c9f00869712856943df1fa40ca2 | R | 11,322 | 373 | ##
## 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_scattercorr_ui <- func... |
8425ebd1bcc4e37d023f7b51f9b2d4b218c73b9d6d2e701f2caccf40fbeea9a7 | R | 11,336 | 227 | args <- commandArgs(trailingOnly = TRUE)
## Extract clonal copy-number variation based on MosaiCatcher result for normalization purpose
# 0) Separate sv_call result into subclones (by default, strict callset was used)
output_filename <- args[1]
subclone <- read.table(output_filename, sep = "\t", header = T)
sv_call... |
11f502598b40cc439131cfd84e03bef4a09adb4766325508ef3e64c286d42ece | R | 11,412 | 390 | ##
## 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... |
5c57f4d9e0c1d6b2a62ef037f9c90f411ff50e71fd027dfba109ef601562cfa0 | R | 11,427 | 375 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Single cell plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#' @param width
#'
#' @export
singlecell_pl... |
2725a197fcac0d7d66f94424df3e8e2be4f0bbce3c81b48e3d51be86576d81b1 | R | 11,504 | 217 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PathwayInputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
withTooltip(
shiny::selectInput(ns("fa_contrast"), "Contrast:",
choices = NULL
... |
9827dfc6498f524510cdd4181063ef068a9d5dcc4cd8a7d75f1ff2bc85430f73 | R | 11,519 | 461 | ---
title: "Aging analysis"
author:
- Wei Zhang^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r Sys.Date()`"
output:
rmarkdown::html_document:
highlight: pygments
theme: yeti
toc: true
number_sections: true
df_print: paged
code_download: false
toc_float:
collap... |
215a818e525079cac55ecba5b66c8105a84412222b802bf489218beb1780b567 | R | 11,529 | 330 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
dataview_plot_expression_ui <- function(
id,
label = "",
height,
title,
caption,
info.text
) {
ns <- shiny::NS(id)
options <- shiny::tagList(
shiny::radioButtons(
... |
17cf0a3ab4381f0ae040fe343e233e15f7fd7ea00164cd2d6dad98bfc1ba45f9 | R | 11,535 | 367 | #' @noRd
#' @importFrom foreach %dopar%
ddm_rtdists_nll = function(pars,
dat=NULL,
min_p=1e-10,
transform_pars=F,
check_constraints=F,
debug=F){
### check constraints
checks =... |
40a1d7b7e60ed5b86780f619368372bfff502a934c8093bd738b8fdb33fd7515 | R | 11,543 | 308 | #########################################
### Taylor-Bateman et al., 2025 - Repurposing drugs for the prevention of vascular dementia: Evidence from drug target Mendelian randomization
### SNPColoc_DTMR.R requires 2 input files
### An Exposure GWAS
### An Outcome GWAS
Exposure_GWAS <-
Outcome_GWAS <-
### Colum... |
8e7d3f1d3d309fb05a1b05ec5f7ff1635f1c5d9c0a67fe5baa92b301dfde6f7f | R | 11,566 | 285 | library(tidyverse)
library(patchwork)
library(png)
library(ggtext)
library(tidyverse)
library(ggimage)
source("subscripts/load_and_clean_data.R")
# 1=NCD 0=F
# 2=CD 1=M
metadata[metadata$Visit!= "",] %>%
mutate(Visit = str_remove(Visit, "Visit "),
Coffee_Type = coffee_group) %>%
mutate(Coffee_... |
f2777758eb6f3d76b66f9892107462c7eacaccee7e733582fc8df19a6cd25e6c | R | 11,674 | 339 | source("workflow/scripts/arbigent/probability_helpers_2.R")
library(ggplot2)
library(ggbeeswarm)
library(reshape2)
library(dplyr)
# TODO NEEDS DESCRIPTION
ggplotColours <- function(n = 6, h = c(0, 360) + 15){
if ((diff(h) %% 360) < 1) h[2] <- h[2] - 360/n
hcl(h = (seq(h[1], h[2], length = n)), c = 100, l = 65)
}
... |
d933e1274b14c8da053d883c1861586f30ff91c8b0592156bf8165382558de41 | R | 11,689 | 451 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Expression plot UI input function
#'
#' @description A shiny Module for plotting (UI code).
#'
#' @param id
#' @param label
#' @param height
#'
#' @export
pcsf_gsetpanel_networkplot_ui ... |
da0a1d903775d9ae39ca36abfeab16f4ec82de4b52711dba0d800256b279053f | R | 11,735 | 349 | ---
title: "Prepare changeO files for scRepertoire"
output: pdf_document
date: "`r format(Sys.time(), '%a %d %B')`"
params:
run: "D1"
datapath: "data/D1_concat/Immcantation/"
---
```{r setup, include=FALSE}
# silence the warnings
knitr::opts_chunk$set(warning = FALSE, message = FALSE, echo=F, fig.path = "images/... |
27b98e60ad3d53a83053651d2849b0ab884186b55f0b07f1300c6beaf6642c6e | R | 11,745 | 374 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## ACCESS_LOGFILE = file.path(ETC,"access.log")
## unlink(ACCESS_LOGFILE)
pgx.record_access <- function(user,
action,
comment =... |
9e0858ed988dfa7ab703ff703ad58b48eaadcad9af29b6310efb11935a6ea862 | R | 11,777 | 342 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
message("\n\n\n")
message(" ___ _ ____ _ _ ")
message(" / _ \\ _ __ ___ (_) ___ ___| _ \\| | __ _ _ _ __ _ _ __ ___ ... |
c81969227d37fada3951a62f0d588563b06be1e29cbea45d8cc6e150c231aa18 | R | 11,852 | 332 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
7ea7970addf571150f0c2d9b48a4d8ee0d3730586b7eee189436e60eb43a131c | R | 11,914 | 310 | # Script to generate volcano plots from DESeq2 results
# with specific thresholds: 50 reads, FC > 0.5, FC > 1
# Uses the same styling as the original generate_volcano_plots.R
library(tidyverse)
library(ggrepel)
# --- Configuration ---
RESULTS_FILE <- "results/DESeq2/DESeq2_results_all.csv"
OUTPUT_DIR <- "results/volc... |
e4d4dd7ba9c70b040b3f3a8db6f7fb8331d1f10d98404602ef4ed93f2341e760 | R | 11,927 | 282 | sumStats <- list()
sumStats$id <- "sumstats"
sumStats$title <- "Summary Statistics"
sumStats$loadData<- function(){
#dataframe holding links for the other summary stats table
other_gwas_info <<- data.table(ID=c("aoo","gba_aoo","gba_mod","lrrk2","asian","META5","ad","als","latam","male","female","lbd"),
... |
2259a4ae787e5d9bcaa3090c1fb55fe6544c6cc243439f7fd55455cabd908447 | R | 12,183 | 263 | # heatmap
# Final Version
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
library(ComplexHeatmap)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
path <- "~/Desktop/NIMH Research/Photometry/fLME_methods_paper/d... |
483453e071148d64753c1dd7a25d8a8fa37242e1b8ff414bf66e646ecf16571e | R | 12,187 | 350 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
message("\n\n\n")
message(" ___ _ ____ _ _ ")
message(" / _ \\ _ __ ___ (_) ___ ___| _ \\| | __ _ _ _ __ _ _ __ ___ ... |
51e8272137f5efe52180de045e3d8c0b0f6777d82290374c0355c921417dc6aa | R | 12,230 | 334 | library(data.table)
library(susieR)
library(coloc)
library(SNPRelate)
library(gdsfmt)
library(knitr)
## ----------------------- Inputs -----------------------
fer_file <- "Ferritin_AF0p005.mr_ready.tsv.gz" # <-- set to your ferritin GWAS (GRCh38)
del_file <- "Delirium_AF0p005.mr_ready.tsv.gz" # delirium G... |
1f34882266b1cfd0424c43d841b215e338421f68883bbb0b7da83199fafcacdb | R | 12,322 | 287 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
SingleCellBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 750 ## full height of panel
imgH <- 680 ##... |
d5b0e51c7b12a71823260a17470654f87d7b420540ba5e33e13e21026ff76996 | R | 12,362 | 295 | # ============================================================
# Script 05: Figure Generation
# Candrea et al. - Gut Microbiota Comparative Analysis
# Biomedicines 2025
# ============================================================
# Description:
# Generates all manuscript figures (Figures 1-3 and 6).
# Note: Figure 4 ... |
b8e9cb8ae9898a52e686c958191d537c7f48641a1a037125ebd310cb051d0bce | R | 12,383 | 306 | library(Seurat)
library(dplyr)
library(scCustomize)
library(patchwork)
library(glue)
library(limma)
library(ggplot2)
library(ggrepel)
library(edgeR)
##################
## Load samples ##
##################
base_path <- '/Users/osman/Documents/GitHub/snRNA-seq-pipeline/scripts/09_mosiacism_analysis/'
load(glue('{base_pa... |
9f683ec5ea305ec151a8c765564c6371c896cafc6a377c18174e41d5012e2767 | R | 12,409 | 294 | #' A subsetted version of mouse 'pancreas' datasets
#'
#' Mouse pancreatic endocrinogenesis dataset from \href{https://doi.org/10.1242/dev.173849}{Bastidas-Ponce et al. (2019)}. A total of 1000 cells were downsampled to form the \code{pancreas_sub} dataset.
#'
#' @format A \code{Seurat} object.
#' @concept data
#' @sou... |
74cb8ef4fe9f241ff922ca935743c16c09fc561818c75dea479230ff5b798ac5 | R | 12,460 | 160 | ---
title: "Photometry FLMM Guide Part III: Association with continuous variables -- akin to FLMM version of a correlation"
author: "Gabriel Loewinger, Erjia Cui"
date: "`r Sys.Date()`"
output:
html_document:
df_print: paged
toc: yes
pdf_document: null
vignette: "%\\VignetteIndexEntry{fastFMM Vignette} %\\Vig... |
6de5a817bcecb511b6968304510c2a73af9b102102e810a8c63e8e3395a5780c | R | 12,477 | 277 | # 1=NCD 0=F
# 2=CD 1=M
metadata %>%
mutate(Visit = str_remove(Visit, "Visit "),
Coffee_Type = coffee_group) %>%
mutate(Coffee_Type = case_when((visit %in% c("V2") & coffee_group == "CD" ) ~ "Coffee",
(visit %in% c("V2") & coffee_group == "NCD") ~ "NCD",
... |
9cc6866bf27c91666be64eb5704fa4a5f4280d5f553be0a15fab84a02ee0d72e | R | 12,495 | 465 | ##
## 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
pcsf_genepanel_networkplot_ui ... |
ee8f02be25803bda04373929354d501cd21eaf4b852de4f3f434ad753c2c9aa3 | R | 12,497 | 290 | # Whoeps, 9th March 2021
#' @param pg_f
#' @author Wolfram Hoeps
#' @export
#'
calc_new_logllhs_singlecell <- function(pg_f){
print('Re-calculating likelihoods after read count normalization. This will take up to several minutes.')
# With new 'expected number of reads', recalculate dispersions W and C. Step 1... |
8fe470640c74938af0506837c02e7048b6145a1b20973c74ee6a42e610cfbbde | R | 12,585 | 338 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
IntersectionBoard <- function(
id,
pgx,
selected_gxmethods = reactive(colnames(pgx$gx.meta$meta[[1]]$fc)),
selected_gsetmethods = reactive(colnames(pgx$gset.meta$meta[[1]]$fc))
) {... |
070a929b238fd50bf9ee38945ca832f351c81c675abfdc303ab890e97347bfca | R | 12,757 | 377 | #=========================================================================================================
# Main for project: Genetic influences on missing data across experimental measures in infancy
#
# used to prepare data for subsequent twin analysis
#
# author: Giorgia Bussu
# project: BT missing data
# v... |
427db5e008bcfcbbdc1f0af63fc4d4bce502df9e7b7d47d8ae23535864cab47a | R | 12,784 | 406 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
intersection_plot_venn_diagram_ui <- function(id,
title,
caption,
... |
2e3a79f23a522e9dc2776c4fc2fe6a889ed66bd455090be8fecc655eb12e04f7 | R | 12,803 | 325 |
unstim <- read.delim("raw/cytokines/cytokines_unstim.csv", sep = ",")
stim <- read.delim("raw/cytokines/cytokines_stim.csv", sep = ",")
unstim_df <- unstim %>%
pivot_longer(!c(Screening.ID, Group, Coffee.ID, Timepoint)) %>%
mutate(Legend = case_when(Group == 1 ~ "NCD",
Group... |
2bee5fe64c7393598fcc4db55c99bff2d4abb27aa055dba9ef90d0ce5130efd4 | R | 12,804 | 321 | library(data.table)
library(coloc)
library(arrow)
Ferr <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
# GTEx v10 sQTL — Liver (for TF, ±250 kb)
liver_sig <- read_parquet("Liver.v10.sQTLs.signif_pairs.parquet" )
liver_genes <- fread("Liver.v10.sGenes.txt.gz")
# GTEx v10 sQTL — Brain (Cortex) (for TOMM40 a... |
866e72e4850131cc863a43caa70a36d9a3cd3fd9a3942a371c9f615d8267a6da | R | 12,811 | 389 | ###################################
# Spine March 2024
###################################
library(lme4)
require(lmerTest)
library(car)
library(pbkrtest)
library(MuMIn)
library(sjPlot)
library(ggplot2)
library(modelr)
library(gridExtra)
library(cowplot)
# mixed effects model without interactions
mod... |
adf4706ac95681579c8d28f5a6f0dd5bee5dea590d3d5eaf4aa76df74e1dfd6b | R | 12,819 | 265 | # Lick aligned Experiment 1
# Final Version
library(data.table)
library(dplyr)
library(parallel)
library(lme4)
library(mgcv)
# fGLMM code
source("/Users/loewingergc/Desktop/NIMH Research/Photometry/code/existing_funs.R") # for time align functions
source("~/Desktop/NIMH Research/git_repos/fast_univ_fda/code/fui.R") #... |
4aafaa058cd1755669c58db775e1fedbca6881910f687af4e191c4218bba32bc | R | 12,823 | 298 | library(minet)
library(GENIE3)
library(simone)
library(paletteer)
library(ggplot2)
library(ROCR)
library(hash)
for (N in 5:9)
{
#ground_truth_path = "insilico_testbed/in_silico_GRN9/Ground_Truth_AM.txt"
#input_attractors_path = "insilico_testbed/in_silico_GRN9/Alpha_Attractors_9.txt"
#genalg_results_path... |
2790297990daf9d70cdfc8ba064e6a30895f905ea18450358fcd80311fe3f68c | R | 12,867 | 329 | #####################################
# Helper functions for evacc model object
evacc_chisq_obj <- function(pars,
dat=NULL,
n_sim=1,
transform_pars=F,
check_constraints=T,
debug=F... |
fba57337758c4a6ea43fc2001850456111d0b1939ae60b245287819c0fe2245e | R | 12,871 | 301 | library(tidyverse)
library(Seurat)
library(extrafont)
library(cowplot)
library(ggrepel)
library(ggplotify)
loadfonts()
setwd('~/Dropbox/share_paper/paper_Visium_DCN/')
set.seed(2023)
# A: UMAP of DCN inhibitory neuron cell type
# B: UMAP of expression of Kit, Zfhx4, Piexo2
# C: Barplot showing number of CD vs HC, TN ... |
b91ad4da8926f3139250d30761e1da539e9c28771db0a78189c65e5c4f811961 | R | 12,887 | 426 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DeepNetBoard <- function(id, pgx) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 700 ## full height of page
rowH1 <- 250 ## row ... |
38c451fb11b46d4f057b4a4e49f0f3c20de326142c33f9bdc0dbbd18ec00f350 | R | 12,905 | 310 | urmet <- read.delim("raw/urine_reclustered/urine_metabs_classified.csv", sep = ",", header = FALSE)
urmet <- urmet %>%
separate(V1, into = c("visit", "ID"), sep = "_", remove = FALSE) %>%
mutate(visit = toupper(visit),
ID = case_when(visit == "SAMPLE" ~ "ID", .default = ID),
ID = case_when(I... |
91c576567abeb369386ec508be0bbcb02ee3e3f1cdbbbc7c1f92e43c235ac56a | R | 12,913 | 344 | # Whoeps, 10th Feb 2021.
# This is the main script for step three of the regenotyper Snakemake.
# Take an all.txt and turn it into a series of vcfs.
# Filtering and testing will, i think, be done by another file.
library(ggplot2)
library(reshape)
library(dplyr)
library(tibble)
library(optparse)
source("workflow/scrip... |
188d1d9e1159b50ceebb59873c0f2f48ff75e26d4f05a503b07593f894eac6e1 | R | 12,994 | 343 | args <- commandArgs(trailingOnly = TRUE)
## ---------------------------------------------------------------------------------
## DESeq after filtering out NE from deepCNN
## ---------------------------------------------------------------------------------
library(matrixStats)
library(DESeq2)
library(Rtsne)
library(uma... |
5ddbd7b3e6c901861252368176758b80968f351e44b349f49649baf0a3dbd859 | R | 13,038 | 405 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/getStrandStates.R")
source("workflow/scripts/mosaiclassifier_scripts/mosaiClassifier/getCountsPerSegment.R")
source("workflow/scripts/mosaiclassif... |
602f17d4b20245cef9e31c4226bf3e6e65462d33cdfda36e34b2887640517950 | R | 13,109 | 203 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
PreservationWGCNA_Inputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
shiny::selectInput(ns("splitpheno"), "Split dataset by:", choices = NULL),
# s... |
f3b9c68c03af0ed18eafe1a061f2592a51fa59a6f202c8c3b99e0061dbe67993 | R | 13,118 | 330 | ###################
## Load Packages ##
###################
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Glimma", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis", "RColorBrewer", "BiocParallel", "DEsingle", "enrichR", "DMRichR", "org.Mm.eg.db", "AnnotationDbi")
stopifnot(suppressMessages(sapply(pa... |
1a2c0b6921c3e8e60bb01c882a9d5bdda0b404c488ffea3ccee54a6ae3aca9b3 | R | 13,133 | 330 | ###################
## Load Packages ##
###################
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Glimma", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis", "RColorBrewer", "BiocParallel", "DEsingle", "enrichR", "DMRichR", "org.Mm.eg.db", "AnnotationDbi")
stopifnot(suppressMessages(sapply(pa... |
47a207569c625ba9e676e754f09dded2c9905c4d08e017d50c18c9c84275063b | R | 13,141 | 330 | ###################
## Load Packages ##
###################
packages <- c("tidyr", "openxlsx", "glue", "magrittr", "Glimma", "Seurat", "limma", "edgeR", "ggplot2", "ggpubr", "viridis", "RColorBrewer", "BiocParallel", "DEsingle", "enrichR", "DMRichR", "org.Mm.eg.db", "AnnotationDbi")
stopifnot(suppressMessages(sapply(pa... |
91c0785eb107c14e2afa4d212547e1138ea6ff4cf8ead296f2988a85ed64e5f2 | R | 13,288 | 329 | fecmet <- read.delim("raw/urine_reclustered/faecal_metabs_classified.tsv", sep = "\t", header = FALSE)
fecmet <- fecmet %>%
separate(V1, into = c("visit", "ID"), sep = "_", remove = FALSE) %>%
mutate(visit = toupper(visit),
ID = case_when(visit == "SAMPLE" ~ "ID", .default = ID),
ID = case_w... |
d71d5e96859c0edd69c0fa1e8c5a67377830a6ca66b76597c16c2f1f862f0108 | R | 13,339 | 489 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
wgcna_html_report_ui <- function(
id,
label = "",
title = "",
info.text = "",
caption = "",
height,
width
) {
ns <- shiny::NS(id)
options <- tagList(
shiny::radioBut... |
b75eeb7ac24a40f33f7cf9883d9972ff37aaf2f7926d654d14c73925880b8061 | R | 13,375 | 425 | ##
## 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_connectivity... |
8ee136a86a7c8cc025e9495575791c649a29252ad34de93f4a2e4b757627b7a2 | R | 13,383 | 450 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#########################################################################
## ##
## Utility Functions for Om... |
eb8f871b64b653987b452f12c76f080236e62d2709db3c0d238429899f56d580 | R | 13,423 | 394 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
##===================================================================
##================ Script to build PGX object =======================
##==============================================... |
5917721fcc6d4c9e6d057d651100fc575b56bdf15b1217fa139c1541e89d21dc | R | 13,509 | 354 | suppressMessages(library(dplyr))
suppressMessages(library(data.table))
suppressMessages(library(assertthat))
source("workflow/scripts/arbigent_utils/mosaiclassifier_scripts/mosaiClassifier/getStrandStates.R")
source("workflow/scripts/arbigent_utils/mosaiclassifier_scripts/mosaiClassifier/getCountsPerSegment.R")
source(... |
15e48588fe1759a4778ffbe40a2ab8085ee4a32695ff174a2cd003139099c6ba | R | 13,593 | 296 | # Whoeps, 30th Nov 2020
# Flip vcf labels!
library(stringr)
library(ggplot2)
library(optparse)
library(data.table)
library(dplyr)
make_nophasing_list <- function(phases_proc_rename_f, blacklist_f, blacklist_lower, blacklist_higher){
#print(phases_proc_rename_f)
samples_no_phasing = phases_proc_rename_f
samples_... |
d43a0f408170e7a530ee06682fe52514ee4f793d1f945f2e6311b545d93f3bb6 | R | 13,661 | 336 | library(data.table)
library(TwoSampleMR)
library(MRPRESSO)
exposure_raw <- fread("Ferritin_AF0p005.mr_ready.tsv.gz")
outcome_raw <- fread("Delirium_AF0p005.mr_ready.tsv.gz")
# Map to TwoSampleMR expected names
exp_dat <- copy(exposure_raw)
setnames(exp_dat, c("effect_allele","other_allele","beta","se","eaf... |
ad23b8ba1f7119b47669e6cd0ae2f637a753a2fa2b8fa44f5f8150493a71e06a | R | 13,677 | 552 | ---
title: "Find DMR using coMethDMR"
author:
- Wei Zhang^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r Sys.Date()`"
output:
rmarkdown::html_document:
highlight: pygments
theme: yeti
toc: true
number_sections: true
df_print: paged
code_download: false
toc_float:
... |
e4ac4db3c3a2e75cabeab9d4adc2f35401fbcfd5d3de0dfe92d51ded005603cb | R | 13,830 | 496 | ---
title: "Figure 2K-M: Cross-Species WGCNA Module Preservation"
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::getSourceEditorConte... |
a885d1e3fbab4530595cf45b7def6ae1a2c03d9ef1b0134e3ec01fdb0a29f23e | R | 13,839 | 296 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' Function to generate color palettes
#'
#' @param hex Hex code for main color as string
#' @param discrete Reorder for categorical data to place main color first
#' @return A set of thr... |
1b35ddef0c748938e648a0e93c20dbeafb7706d55d0f01b280ee9c4ee904e4c3 | R | 13,869 | 320 | #library(ggalluvial)
library(modelsummary)
library(tidygraph)
library(ggraph)
# df_long_cog
# df_long_MB
# df_long_MX
df_tot <- df_long_MX %>%
dplyr::select(c(ID, Coffee_Type, visit, name, value, caffeine)) %>%
filter(Coffee_Type != "NCD") %>%
group_by(name) %>%
mutate(value = c(scale(value))) %>%
ungr... |
791868322ac3def9c1286f70e9f37acbc0383becbc7732aa1f282c0f9ded5bfa | R | 13,876 | 443 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
## ================================================================================
## ================ AUTHENTICATION_MODULE UI FUNCTIONS ============================
## =================... |
cb4bd8943914a7b37f804bd2cbbf75c4d175948078513a927ebbecc31ed23366 | R | 13,905 | 366 | #!/usr/bin/env Rscript
if (commandArgs()[1] != "RStudio") {
ARGS <- c(
"tlxfile", "character", "",
"output","character", "file path to plot to"
)
OPTS <- c(
"binfile","character","","write bin info to file",
"binsize","integer",2500000,"bps per bin",
"assembly","character","mm9","genome... |
f86c13d1e3c481a06bd21d397e5ed9b5491b4f7af2bfddb44847c3856d9bbb93 | R | 13,979 | 379 | ---
title: "Figure creation for xenium data"
author: "John Mariani"
date: "09/08/2025"
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(Seura... |
2a7fdac45f98bd39b2d3861463c4e9bfb22d7a431aff11a6d8acd6f930b98f02 | R | 14,023 | 305 | SNAPSHOT_THRESHOLD <- 25
test_that("example data loads with no error",{
# source aux functions
source("aux-test-functions.R")
# Parallelization config
n_workers <- getOption("test.workers", 3) # Default 3 workers, configurable
base_port <- 8080
# Check if parallel execution is supported (Unix only for m... |
608fa857fbf77b18b23d008e3b738ceb8db1d88a1c64f0b170d5f23bdf1df49a | R | 14,040 | 451 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
TableModuleUI <- function(id,
height = c(400, 800),
width = c("auto", "100%"),
info.text = "Table",
... |
66139eb78d9068fef0791d1ba1a7fd6faa18bfc2dad21d19144fe2fdada8c344 | R | 14,073 | 348 | group_na_summary <- function(data) {
grouped_data <- split(data, data$Group)
mark_na_columns <- function(df) {
na_ratio <- sapply(df, function(col) mean(is.na(col)))
na_ratio <= 0.2
}
na_marked <- lapply(grouped_data, mark_na_columns)
na_matrix <- as.data.frame(na_marked)
trans_data <- as.data.fram... |
ebea02b2e8889e51219d02abca27cc734a8994bd7d9fe270c2d6d34c77e52c81 | R | 14,074 | 202 |
# simplest GT assignments imaginable
add_gts <- function(tab, bias_factor, cutoff) {
tab$GT <- "UNK"
tab[tab$confidence_nobias_over_hard >= bias_factor, ]$GT <- tab[tab$confidence_nobias_over_hard >= bias_factor, ]$pred_nobias
tab[(tab$confidence_nobias_over_hard >= bias_factor) & (tab$confidence_hard_over_seco... |
fe8d0cc033e0f49dc6c8bb582df3f1d8798c545a2d351c4f54f8a0f75806c5c2 | R | 14,095 | 194 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
ConsensusWGCNA_Inputs <- function(id) {
ns <- shiny::NS(id) ## namespace
bigdash::tabSettings(
shiny::selectInput(ns("splitby"), "Consensus by:", choices = NULL),
shinyjs::hidd... |
04a26a875ce9945f284ca83e09f9d38f23ae023af1cfa14bc619e358a66c708e | R | 14,108 | 384 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
FeatureMapBoard <- function(id, pgx, labeltype = shiny::reactive("feature")) {
moduleServer(id, function(input, output, session) {
ns <- session$ns ## NAMESPACE
fullH <- 800 ## ... |
3f0096de97d5e2064357815169ad4da558ce93b10b6356c586790a6bb2b5a5ec | R | 14,118 | 412 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
#' DataView module server function
#'
#' @description A shiny Module (server code).
#'
#' @param id,input,output,session Internal parameters for {shiny}.
#' @param pgx Reactive expression... |
ba81c4da86df761a355fd093e780973ac7ea18ab256b460f84fe0fc1fbb16b39 | R | 14,150 | 419 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
intersection_scatterplot_pairs_ui <- function(
id,
title,
label = "",
info.text,
caption,
height,
width
) {
ns <- shiny::NS(id)
scatterplot_pairs.opts <- shiny::tagList(... |
6d8295b4f9976590f5b7caf2f6909a7d1f5303c7acd5f9e15fe070441d8db769 | R | 14,280 | 442 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
clustering_plot_clustpca_ui <- function(
id,
label = "",
height,
width,
title,
info.text,
info.methods,
info.references,
info.extra_link,
caption,
parent
) {
ns <- ... |
619bf2f0b1e1e4d22887ae74b3517096aedd99137d2b43f6f5d719084a989864 | R | 14,363 | 549 | ---
title: "scATAC-seq Analysis of WA09 GPCs"
author: "John Mariani"
date: "11/21/2024"
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
knitr::opts_knit$set(root.dir = rprojroot::find_rstudio_root_file())
```
```{r, echo = TRUE, message=FALSE, warning=FALSE}
library(Seurat... |
fab5b331bf9e45245ef0aff67248a7e472419cd5b57a1abd2498694560018c4a | R | 14,394 | 188 | ---
title: "Photometry FLMM Guide Part IV: Testing effects of factor variables -- akin to ANOVA"
author: "Gabriel Loewinger, Erjia Cui"
date: "`r Sys.Date()`"
output:
html_document:
df_print: paged
toc: yes
pdf_document: null
vignette: "%\\VignetteIndexEntry{fastFMM Vignette} %\\VignetteEncoding{UTF-8} %\\Vig... |
1f5f64d65cdc40bdf69394c1e8d94d92c72648b65ae1e42bbee29c09cb4ca68d | R | 14,471 | 411 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
DatasetReportUI <- function(id) {
ns <- shiny::NS(id)
shiny::actionButton(
ns("show_report_modal"),
label = "Generate report",
icon = icon("file"),
class = "btn btn-out... |
7d1668af518b923a118886fe5ee7e6e8f250935130221686e300f5521983020b | R | 14,495 | 322 | # cue aligned Figure 6
library(data.table)
library(dplyr)
# NOTE: days for each animal taken from:
# https://github.com/namboodirilab/ANCCR/blob/master/analysis/fig6/backpropagation_pavlovian.m
# and https://docs.google.com/spreadsheets/d/1pmpQ5JFhg4Q7h18DQYifjNrW17HtaoPHBt2vJF4mxiU/edit#gid=0
# Note: sub-HJ-FP-F2_se... |
f8bedfff37260de6a256124ee9f28f4bfc1b1d958a3fdb7ac648077c173d8403 | R | 14,552 | 399 | # Genotypes QC
# plot 1
library(ggplot2)
library(dplyr)
#theme_set(theme_classic())
#tab2 = tab
tab=tabp
tab=tab[!(tab$pred_hard=='./.'),]
tab$simple = 'ccomplex'
tab[tab$GT %in% c('0|0', '1|0', '0|1', '1|1'),]$simple = 'asimple'
tab[tab$GT %in% c('noreads'),]$simple = 'zeroreads'
tab[tab$GT %in% c('noreads'),]$simp... |
225ca3a6ba06779e6254ca5177bfe75b76009726067eb71ccf0c197c2f407de4 | R | 14,591 | 445 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
upload_table_preview_contrasts_ui <- function(id) {
ns <- shiny::NS(id)
uiOutput(ns("table_contrasts"), fill = TRUE)
}
upload_table_preview_contrasts_server <- function(
id,
uplo... |
9d03af4e4cfa17c9d5416de08d971b25744e37648081d481a2d1c3038f4043c1 | R | 14,599 | 332 | #library(ggalluvial)
library(modelsummary)
library(tidygraph)
library(ggraph)
# df_long_cog
# df_long_MB
# df_long_MX
df_tot <- fecmet_df_long %>%
dplyr::select(c(ID, Coffee_Type, visit, name, value, caffeine)) %>%
filter(Coffee_Type != "NCD") %>%
group_by(name) %>%
mutate(value = c(scale(value))) %>%
u... |
26b5e270ab155f82f3398ca7e98e5c81b037ecbbc13d02489a72e7331c6ae48a | R | 14,627 | 336 | #library(ggalluvial)
library(modelsummary)
library(tidygraph)
library(ggraph)
# df_long_cog
# df_long_MB
# df_long_MX
df_tot <- fecmet_df_long %>%
dplyr::select(c(ID, Coffee_Type, visit, name, value, caffeine)) %>%
filter(Coffee_Type != "NCD") %>%
group_by(name) %>%
mutate(value = c(scale(value))) %>%
u... |
6f2e0592d3a92961329ca2ff0293b06cbfb82fe574a9ac5c57fa12f40c0a61cc | R | 14,646 | 359 | library(Seurat)
library(dplyr)
library(scCustomize)
library(patchwork)
library(glue)
library(limma)
library(ggplot2)
library(ggrepel)
library(edgeR)
##################
## Load samples ##
##################
base_path <- '/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/07_mosiacism'
load(glue('{base_path}/PEBBLES_pa... |
29a34251dba831e7d2d08b5feaa8847def49c265c2312fce1a1f29d3a42b0bb2 | R | 14,671 | 328 | # 1=NCD 0=F
# 2=CD 1=M
# #1
# c("Cholic acid", "Piperine", "Pipecolinic acid", "Agmatine",
# "3-(3-Hydroxyphenyl)propanoic acid", "ω-Muricholic acid", "Indole-3-carboxyaldehyde",
# "N1-Methyl-2-pyridone-5-carboxamide", "Tetradecanedioic acid",
# "Indole-3-propionic acid", "2,5-’ or 3,4-Dihydroxybenzoic acid",... |
b0910a06404c5524d00de5efde9c9b05c831002bd9c458604bb63e9768f9e18f | R | 14,688 | 258 | ##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics SA. All rights reserved.
##
style0 <- "font-size: 0.9em; color: #24A; background-color: #dde6f0; border-style: none; padding:0; margin-top: -15px;"
SignatureInputs <- function(id) {
ns <- shiny::NS(id) ## namespac... |
39deb5ea7e988960a15338da674456e8935c520b35da9f7d8a68304f8868f0f5 | R | 14,736 | 343 | ####################
## Load libraries ##
####################
library(magrittr)
library(VennDiagram)
library(grDevices)
library(dplyr)
library(Seurat)
library(glue)
library(scCustomize)
library(edgeR)
library(ggplot2)
library(ggrepel)
library(GeneOverlap)
library(enrichR)
##################
## Load samples ##
########... |
eba15f405343008f74f12505e476395c6a708dcb9aed2e5f42084205ef0542b4 | R | 14,755 | 319 | args <- commandArgs(trailingOnly = TRUE)
browser()
# print(args)
## Extract clonal copy-number variation based on MosaiCatcher result for normalization purpose
# print("HELLO")
TSS_matrix <- read.table(args[1], header = TRUE, sep = "\t")
TES_matrix <- read.table(args[2], header = TRUE, sep = "\t")
Genebody_matrix <- ... |
0c04e56079185c5054a7dc32e998201ed80b7a90c39cedd3e4bbf6e06e562223 | R | 14,882 | 310 | library(UpSetR)
library(dplyr)
library(ggplot2)
# Get a list of all directories
all_directories <- list.dirs(path = "/Users/osman/Documents/GitHub/PEBBLES_mouse_snRNAseq/soupx", full.names = TRUE)
# Create an empty data frame to store the combined data
combined_data <- data.frame()
# Loop through each directory
for ... |
d4156036070fe9b0d914bef2cfd907b75afd39f1a1479ab0941fca3e2e65d202 | R | 15,033 | 336 | #library(ggalluvial)
library(modelsummary)
library(tidygraph)
library(ggraph)
# df_long_cog
# df_long_MB
# df_long_MX
df_tot <- urmet_df_long %>%
dplyr::select(c(ID, Coffee_Type, visit, name, value, caffeine)) %>%
filter(Coffee_Type != "NCD") %>%
group_by(name) %>%
mutate(value = c(scale(value))) %>%
un... |
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