sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
036f0a930d8655b652fb852c0de2f87c9a3a7ea28b15f93376ae4e9e0bcb20a0 | R | 28,111 | 368 | #' Function to prioritise genes given a list of seed SNPs together with the significance level (e.g. GWAS reported p-values)
#'
#' \code{oPierSNPs} is supposed to prioritise genes given a list of seed SNPs together with the significance level. To prioritise genes, it first defines and scores seed genes: nearby genes, e... |
c839ca9e372b578112090f876d0c4dfc0f500610e703648debd3ef7b02c9f591 | R | 28,165 | 659 | #Generate the anatomical overview Video1 of the Platynereis 3d connectome paper
#Gaspar Jekely 2021-2023
# load nat and all associated packages, incl catmaid
source("code/Natverse_functions_and_conn.R")
#create temp dir to store video frames
mainDir = getwd()
dir.create(file.path(mainDir, "videoframes"), showWarning... |
2f707731a32375b6ecfb6047a533085428c1a9cb71cde55ca9d584889ac70b20 | R | 28,213 | 760 | #*******************************************************************************
# Filename : tmiic.wrapper.R Creation date: 24 march 2020
#
# Description: Data transformation of time series for miic
#
# Author : Franck SIMON
#*******************************************************************... |
33832022c4d0b13d2d0d3f4bd86d780e98a840bc16c2c0cec760da9a0bbd19cf | R | 28,298 | 830 | context('Test helper functions')
VCD_AVAILABLE <- requireNamespace("vcd", quietly = TRUE)
.skip_if_vcd_not_available <- function() {
if (!VCD_AVAILABLE) {
testthat::skip("Optional testing dependency 'vcd' not found.")
}
}
float_tolerance <- 5e-6
# disable some tests for 32-bit environment
flag_32bit ... |
63fd72419d9ff986ff54fa9473dd52ba3d361b941a5ee22223b9bbca52da2c29 | R | 28,490 | 648 | ---
title: "Single-cell based analysis of Tha astrocyte subpopulations"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
```{r libraries and functions, message=FALSE}
library(tidyverse)
library(ggplot2)
library(dplyr)
library(Seurat)
library(Matrix)
library(viridis)
#library(randomForest)
#library(ranger)
... |
c2bacb994d624453424e4262c46935a7835734d06335a9815d1201862e985a5f | R | 28,929 | 746 | ---
title: "SV2A_propagation_simulation_example_output"
output: html_document
---
# load libraries
```{r message=FALSE, warning=FALSE}
library(psych)
library(reticulate)
library(corrplot)
library(lm.beta)
library(boot)
library(plyr)
library(tibble)
library(lme4)
library(lmerTest)
library(NbClust)
library(zoo)
library(g... |
6caf89a1fcee0ef7e20f0eeb49007cd8c7757a3d515737eb99af4a95b292e7db | R | 29,342 | 615 | #### load packages ####
targetPackages <- c('tidyverse','arrow','ggtext','patchwork')
newPackages <- targetPackages[!(targetPackages %in% installed.packages()[,"Package"])]
if(length(newPackages)) install.packages(newPackages, repos = "http://cran.us.r-project.org")
for(package in targetPackages) library(package, chara... |
d876caaf3937fbf76e947eb9705e0b2f265dacc79bd097b3e847290ca8e93bbb | R | 29,372 | 616 | ---
title: "Single-cell Pseudotime Trajectory Astrocyte Preprocessing"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
```{r libraries and functions, message=FALSE}
library(tidyverse)
library(ggplot2)
library(dplyr)
library(readr)
library(Seurat)
library(monocle3)
#library(Matrix)
library(viridis)
source... |
6f502a93a34a786b4c2e5a6446dbb7eaa118d6a7042fd8caab6c4b8f52972efb | R | 29,439 | 719 | #Generate Video of head neuropils for the Platynereis 3d connectome paper
#Gaspar Jekely 2021-2023
rm(list = ls(all.names = TRUE)) #will clear all objects includes hidden objects.
gc() #free up memrory and report the memory usage.
Sys.setenv('R_MAX_VSIZE'=8000000000)
# load nat and all associated packages, incl catma... |
417b3d04b5639e3d1233cbbfa467026e604e47cb85add4381e127167589f637e | R | 29,482 | 778 | #
# This file is for the low level reusable utility functions
# that are not supposed to be visible to a user.
#
#
# General helper utilities ----------------------------------------------------
#
# SQL-style NVL shortcut.
NVL <- function(x, val) {
if (is.null(x))
return(val)
if (is.vector(x)) {
x[is.na(x... |
b2a45cba039e3aed304a55f547bddd2532e72da394b526329bfd674be2540276 | R | 29,529 | 497 | ###### This scripts plots the output from the population genetics model for 2 clones. It produces
###### - For each patient the model fit vs data and the posterior probabilities of the parameters
###### - A summary of the 80%HDI estimates across the population
###### ###### ###### ###### ###### ###### ###### ###### ###... |
644c6ec6d9d823835364ab37abbe4f3a9fe1004732129665de4a14149be01419 | R | 29,750 | 393 | library(data.table)
library(Biostrings)
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg38)
library(stringi)
run_all <- function(args){
args <- as.list(args) # making the list
repeatmasker_bed <-args[1]
transcripts <- args[2]
features <- args[3]
is_umi <- args[4]
is_ambiguous <- args[5]
for (i in 6:l... |
a4d54afc8bf69ff454dccfd8a9fbd967f307bc177e929ba0101fd30f8b767448 | R | 29,754 | 142 | # R script to download selected samples
# Copy code and run on a local machine to initiate download
# Check for dependencies and install if missing
packages <- c("rhdf5")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
print("Install required packages")
source("https://bioconductor.org/bio... |
d2030ba6146bb96213e6c8fd898c28b80c8e227801ca6afef8d5b8c8e92ecfd9 | R | 30,136 | 1,015 | # code to generate Figure 4 (cell types graph) of the Platynereis connectome paper
# Gaspar Jekely 2023
# load natverse and other packages, some custom natverse functions and catmaid connectivity info
source("code/Natverse_functions_and_conn.R")
# network plot - read all skids based on cell type annotations ---------... |
5bd00d1598cd0d18406e91b8b6d9226e89c85cbab0d39f11cb712ec3c5be9ddf | R | 30,302 | 533 | suppressMessages(library(Seurat))
suppressMessages(library(dplyr))
suppressMessages(library(tidyr))
suppressMessages(library(caTools))
#--------------------------------------------------------------
# Load own modules
source('modules/utils.R')
source('modules/global_params.R')
source('modules/seurat_methods.R')
sourc... |
ca567158d4a8817fd86a98e30204c57ff31f42fb5008f12b98281938e94d7d46 | R | 30,383 | 752 | library(JuliaCall)
options(JULIA_HOME = "/Users/roman/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/bin/")
#julia_executable <- "/Users/roman/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/bin/julia"
julia_setup(JULIA_HOME = "/Users/roman/.julia/juliaup/julia-1.10.2+0.aarch64.apple.darwin14/bin/")
# color... |
73cdb075c1216a026d3c16c47bf92ce531df8d1d0daaccfcb4dad2c49f230dd6 | R | 30,526 | 746 | ### ST Functions
### Aunoy Poddar
### Written Monday Dec 12th to summarize separate functions written throughout
### the course of analysis, which were started in May 2022
### Define the groups that each image is in
post_TC_MS = c('TC_15', 'TC_14', 'TC_13', 'TC_12', 'TC_11', 'TC_10', 'TC_9',
'TC_8', '... |
8f6de2a63bd7c766f1259c88f846fa98e95046be8b44df55c3711d844384d409 | R | 30,562 | 726 | source("./Settings.R")
######################### ######################### ######################### ######################### #########################
library(cdata)
# define where output is to be stored
study.directory <- paste0("./data/Model_fits/Simulated_data/")
sample.info <- read.xlsx(paste0(meta.data, "/Sampl... |
d99bc1f8d7585cb490af802b93feb8b366b1e7b959d80c4c78506367b2df83c7 | R | 30,698 | 585 | ---
title: "Seurat Microglia Basics Plotting"
author: "Arpy"
date: '2024-11-12'
output: html_document
---
Neuron and Astrocyte Cytokine/Chemokine Production
Gregory C. 04/2025
```{r load libraries and source, echo = F}
library(tidyverse)
library(Seurat)
library(Libra)
library(patchwork)
source("/Users/chingr/OHSU Dr... |
ac749580e3010ce18ad86f6f587ee1cf82f06e951a125359a2132de9d3768ffa | R | 31,708 | 589 | library(Seurat)
library(ggplot2)
library(dplyr)
#Merge all datasets
hyp <- merge(GSE74672_seu, y = c(GSE87544_seu, GSE146692_seu, GSE132355_se, GSE125065_seu, GSE126836_seu, GSE93374_seu, GSE139923_seu, GSE113576_seu, Anderson_seu),
add.cell.ids = c("GSE74672", "GSE87544", "GSE146692", "GSE132355", "GSE... |
719eacae8ae8b1045bf55e277a548037190485a59b5496e108d19f0ac347c552 | R | 31,743 | 531 | ---
title: "Simulation and parameter estimation of mutation accumulation with SCIFER"
author: "Verena Körber"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Simulation and parameter estimation of mutation accumulation with SCIFER}
%\VignetteEngine{knitr::rmarkdown}
%\Vign... |
533961cd9c3577f6268f9bc87d2273b98b6053d69610320722b7224e0aa3012b | R | 31,958 | 829 | ---
title: "st_physical"
output: html_notebook
---
Written by Aunoy Poddar
July 9th, 2022
# Process the puncta quantified raw data
```{r eval=FALSE}
current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_fil... |
e7a45e76f6fa7770d07e9c713aa49da5c7f8803e5b6c77fac744b7476c67d65c | R | 32,026 | 644 | #' Run impute on the specified inputfile
#'
#' This function runs impute across the input using the specified region.size.
#' @param inputfile Full path to a csv file with columns: Physical.Position, Allele.A, Allele.B, allele.frequency, id ,position, a0, a1
#' @param outputfile.prefix Prefix to the output file. Region... |
35cdea6b30e0ded97cb6447553bcbe1c4064ced9790b3368e45f8d205f9d2b56 | R | 32,148 | 1,014 | # R code to generate the connectome graph images in the 3d Platynereis connectome paper
# Gaspar Jekely March 2022
# load natverse and other packages, some custom natverse functions and catmaid connectivity info
source("code/Natverse_functions_and_conn.R")
# plot graph with coordinates from gephi --------------------... |
99ed7e6fb83481ab8c0f286698102a52208bb1b54023e358c15359c0386099fa | R | 32,266 | 1,180 |
local({
# the requested version of renv
version <- "1.0.3"
attr(version, "sha") <- NULL
# the project directory
project <- getwd()
# use start-up diagnostics if enabled
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
if (diagnostics) {
start <- Sys.time()
profile <- te... |
3cfbe4fc70af95f3df287003cd91529070179ab5a019f4c2a10b0f36b8385f12 | R | 32,370 | 606 | #' Function that plots two types of data points against it's chromosomal location.
#' Note: This is a plot PER chromosome.
#' @noRd
create.haplotype.plot = function(chrom.position, points.blue, points.red, x.min, x.max, title, xlab, ylab) {
par(pch=".", cex=1, cex.main=0.8, cex.axis = 0.6, cex.lab=0.7,yaxp=c(-0.05,1.... |
813421cea5832627403579974264ed163329e3a976b1c77352255d0bd583c2e6 | R | 32,738 | 951 | ---
title: "Pre-processing of host cell expression responses to Tha and Tha2P4M mutations"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
#Libraries and Source Files
```{r libraries and functions, message=FALSE}
library(tidyverse)
library(Seurat)
library(Libra)
source("~/OHSU Dropbox/Saunders Lab's share... |
6154298c4415cd8d661c848861d2226d1f2ac278d46e97153fdf9b4b5da8bbc2 | R | 33,679 | 1,201 |
local({
# the requested version of renv
version <- "1.0.5"
attr(version, "sha") <- NULL
# the project directory
project <- getwd()
# use start-up diagnostics if enabled
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
if (diagnostics) {
start <- Sys.time()
profile <- te... |
589b687e929771393b169bbca4a47d5463b1efff1cddb7b2bcc4231682340731 | R | 34,172 | 602 | ###########################
#I/O
###########################
library(tidyverse)
library(ggplot2)
library(Seurat)
library(fgsea)
library(pheatmap)
library(cowplot)
library(patchwork)
library(scCustomize)
library(CellChat)
library(msigdbr)
library(org.Hs.eg.db)
library(readxl)
library(xlsx)
library(ggrepel)
library(gridE... |
ba13523b95d6289d44f846efba7c60b95dbbc563fd3248fffcdcc8aebf415fec | R | 34,296 | 633 |
#' Run the Battenberg pipeline
#'
#' @param analysis The mode of Battenberg copy number analysis to be undertaken: 'paired' for tumour-normal pair, 'cell_line' for Cell line tumour-only and 'germline' for germline CNV of normal sample (Default: 'paired')
#' @param samplename Sample identifier (tumour or germline), thi... |
b6467a70847c0ae4ec31ce0df6981c393ae1966ddc4fe47243069e1498b3a6de | R | 34,825 | 1,136 | context("basic functions")
data(agaricus.train, package = "xgboost")
data(agaricus.test, package = "xgboost")
train <- agaricus.train
test <- agaricus.test
set.seed(1994)
# disable some tests for Win32
windows_flag <- .Platform$OS.type == "windows" &&
.Machine$sizeof.pointer != 8
solaris_flag <- (Sys.info()["sysnam... |
04fef45f6d67be12fcac31c65bf67aea0495622c9922d6ef3a55ea9490a729cc | R | 34,864 | 1,148 | ---
title: "st_dist"
output: html_notebook
---
Written by Aunoy Poddar
Dec 25th, 2022
# Process the puncta quantified raw data
```{r eval=FALSE}
current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_file)
f... |
095fdea7608ac2f639a2613614ff2a6b58203b4ed6c3a50de1d6ff47667bc624 | R | 35,050 | 749 | ---
title: "Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo - RNA-seq Analysis"
author: "Jack Kucinski"
data: "04-10-2025"
---
# RNA-seq analysis - P3F v. CNTL
## make directories
```{bash}
WORKDIR="path/to/working/directory"
mkdir rnaseq
mkdir rnaseq/analysis
mkdir rnaseq/cennypipelin... |
e8278462d6e75db1861118a0e4ebeab947ee795f75cbc56e3af201c2487d1c66 | R | 35,243 | 660 |
#' Helper function to adjust the BAF segmented values. By default the segmentation
#' takes the mean BAFphased for each segment, but that doesn't work very well with
#' outliers (i.e. badly phased regions). This function is then called to adjust
#' the segmented BAF. By default this now takes the median
#' @param baf_... |
b9b576af2d32ace615272e2d0967827dc1d9c109c17113646efff75348ef5901 | R | 35,375 | 916 |
# fNMES Study 6 analyses
# add packages ---------------------------------------------------------------------
library("dplyr")
library("plyr")
library("tidyverse")
library("numDeriv")
library("Hmisc")
library("plyr")
library("lmerTest")
library("ggplot2")
library("ggpattern")
library("cowplot")
library("moments")
lib... |
d68963c9c5b71d83149496be70917f8bef8ed7e9ac2852936d2517a0508d5912 | R | 35,456 | 738 | library(igraph)
library(ggraph)
library(tidyverse)
library(magrittr)
library(tidygraph)
library(sf)
library(ggforce)
library(patchwork)
library(qs)
setwd("~/DATA/BRAIN/STEREO/frequentGraph/plot/")
# 15um ------------
project = "../soma15nn15.network"
wsize = 100
chipID_region <- read.delim("../../cortex") %>% {setName... |
a0ba7146634b5bcd9f871a52b7a394471d9f0d70ac4ee8d214b1d59c1bff32d1 | R | 35,583 | 713 | #### load packages ####
targetPackages <- c('tidyverse','data.table','slider','gtools','sf','arrow')
newPackages <- targetPackages[!(targetPackages %in% installed.packages()[,"Package"])]
if(length(newPackages)) install.packages(newPackages, repos = "http://cran.us.r-project.org")
for(package in targetPackages) library... |
d71e07bd1bdf46c4ed819f5b6340bbb92ff78316d0c779c389484de9a668b9ca | R | 35,876 | 897 | ## ----eval=FALSE-------------------------------------------------------------------------------------------------------------
## current_file <- rstudioapi::getActiveDocumentContext()$path
## output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
## knitr::purl(current_file, output = output_file)
## file.edit... |
96b557a2b9e5cab421daf13cfb97ffd60cd961aeafb5a93a5336c28fd7416763 | R | 35,907 | 889 | # Copyright 2024 Masahiro Ono
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... |
451a0ad988db533e5201dbc854337ce6a01f1008b1fd39d30023cfb4f812100e | R | 36,222 | 1,313 |
local({
# the requested version of renv
version <- "1.1.0"
attr(version, "sha") <- NULL
# the project directory
project <- Sys.getenv("RENV_PROJECT")
if (!nzchar(project))
project <- getwd()
# use start-up diagnostics if enabled
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALS... |
73416faf8b4758fd820cc9d45db09b0159f3d5d1c37b6d2115e0c5e3c8d3ee3f | R | 36,479 | 859 | #' Run all steps of \code{SC3} in one go
#'
#' This function is a wrapper that executes all steps of \code{SC3} analysis in one go.
#'
#' @param object an object of \code{SingleCellExperiment} class.
#' @param ks a range of the number of clusters \code{k} used for \code{SC3} clustering.
#' Can also be a single intege... |
f2c0e58d9aa55f5e06f7840e112be5f269792dfd0c352613b0fceee6208aafab | R | 36,639 | 908 | ---
title: "Genomic location and exon structure evolution analysis"
author: "Sarah Lower"
date: "`r Sys.Date()`"
output:
html_document:
theme: cerulean
toc: TRUE
toc_float:
collapsed: TRUE
code_folding: hide
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr:... |
9f9369358119257ca89753b1242fdddca42d5484dcb4bc00c3f3bcd9fbe48768 | R | 37,461 | 960 | # scripts for running RCTD and CSIDE method to identify ctDEG
library(spacexr)
library(Seurat)
library(Matrix)
library(doParallel)
library(ggplot2)
library(plyr)
library(data.table)
library(msigdbr)
library(fgsea)
library(data.table)
library(ggplot2)
library(BiocParallel)
library(EnhancedVolcano)
library(viridis)
libr... |
09bce245b99b4b148a3a786b1260936add99aab30cc0239121de8719089803f7 | R | 37,507 | 950 | ---
title: "st_all"
output: html_notebook
---
Written by Aunoy Poddar
July 21st, 2022
# Process the puncta quantified raw data
```{r eval=FALSE}
current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_file)
f... |
c60bd7a17644caf0767309caf4536058c511aad2e20007b8524f19d7d6fe088b | R | 37,696 | 1,049 | ---
title: "st_clumps"
output: html_notebook
---
Written by Aunoy Poddar
July 21st, 2022
# Process the puncta quantified raw data
```{r eval=FALSE}
current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_file... |
bbe35e0a0aee6b6c99395916128b41d02a6eaa14cd257d65b56eceb5d5b8750a | R | 37,838 | 1,105 | ---
title: "IQM measures"
author: "Heejung Jung"
date: "`r Sys.Date()`"
output: html_document
---
Here, we plot the FD means, DVARs and tSNR from spacetop individual tasks.
For FD means, we also plot the UKB task FD values.
```{r include=FALSE}
library(ggplot2)
library(raincloudplots)
library(gghalves)
library(plyr);... |
9c5cac7b39fa81472293f74ce51c39e74b18f16c1f14e12e4ea1e66335b6ee57 | R | 38,997 | 1,139 | ---
title: 'cellranger and kallisto snRNA-seq integration and normalization'
output:
html_document:
theme: united
pdf_document: default
date: 'Compiled: `r format(Sys.Date(), "%B %d, %Y")`'
---
```{r setup, include=FALSE}
all_times <- list() # store the time for each chunk
knitr::knit_hooks$set(time_it = local({
... |
d8766b61234727c01525dda1833021be475c7894ab320cc5fdf462505051103f | R | 39,607 | 1,015 | # Copyright 2024 Masahiro Ono
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... |
bb44abfab0f3efdc9aac78bffe466e122e7b95e84dfb949c157d05145a02a606 | R | 39,695 | 1,171 | # R code to generate the anatomical overview images of the Platynereis connectome in Figure 1 of the connectome paper
# Gaspar Jekely 2021-2023
# load natverse and other packages, some custom natverse functions and catmaid connectivity info -----------
source("code/Natverse_functions_and_conn.R")
# read graph
conn.tb... |
ff73d4fc48bd90e7569118e6fc7745d78b06e08614107d61095abb0e301e4b45 | R | 39,715 | 1,351 | ---
title: "st_nn"
output: html_notebook
---
Written by Aunoy Poddar
July 21st, 2022
# Process the puncta quantified raw data
```{r eval=FALSE}
current_file <- rstudioapi::getActiveDocumentContext()$path
output_file <- stringr::str_replace(current_file, '.Rmd', '.R')
knitr::purl(current_file, output = output_file)
fi... |
ea81d139c5e1296eb911b8916249083285c4ef5ec90d0cf9a9161dd8296d48eb | R | 41,076 | 260 | #' Function to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data
#'
#' \code{oDefineQTL} is supposed to extract eQTL-gene pairs given a list of SNPs or a customised eQTL mapping data.
#'
#' @param data NULL or an input vector containing SNPs. If NULL, all SNPs will be considered. If a input... |
4d61ac4081c4c121e4f28a4351cef5424ae7f7e4e1eaddfa4f549dc7ac8dc216 | R | 41,120 | 516 | library(data.table)
library(seqinr)
library(miRBaseConverter)
library(Biostrings)
library(stringi)
library(GenomicRanges)
library(BSgenome.Hsapiens.UCSC.hg38)
run_all <- function(args){
hybrids <- args[1]
sample <- args[2]
repeatmasker_bed <-args[3]
transcripts <- args[4]
features <- args[5]
mirna_db... |
4001bb435ea1244218277dfd9acebbfb8edda9f3ebaeb74fde04e2598445b3fc | R | 41,408 | 805 |
#' Chromosome notation standardisation (removing 'chr' string from chromosome names - mainly an issue in hg38 BAMs)
#'
#' @param tumourname Tumour identifier, this is used as a prefix for the allele count files. If allele counts are supplied separately, they are expected to have this identifier as prefix.
#' @param no... |
6c6e415b36d9755cfdef0ad56d87c04a6582285bff6361a0d236ff330255b680 | R | 41,749 | 806 | ###### This scripts plots the output from the population genetics model for Brain WGS data from Bae et al. It produces
###### - For each patient the model fit vs data and the posterior probabilities of the parameters
###### - A summary of the 80%HDI estimates across the population
######################################... |
cd3be1e856175e7cdd5542606f170c1a0acf89ffa77bb0ff5d749c9b74f4f0ba | R | 41,923 | 1,266 | # Created by use_targets().
# Follow the comments below to fill in this target script.
# Then follow the manual to check and run the pipeline:
# https://books.ropensci.org/targets/walkthrough.html#inspect-the-pipeline
# Load packages required to define the pipeline:
library(targets)
library(tarchetypes) # e.g. for t... |
54df9236b80594e2d2a3c83363e7378c0e336342165c7ff3fa4785308aa03a22 | R | 42,368 | 1,074 | #*******************************************************************************
# Filename : tmiic.plot.R Creation date: 24 march 2020
#
# Description: Plotting for temporal miic (tmiic)
#
# Author : Franck SIMON
#****************************************************************************... |
d8913a89fa2dd0cca546f892f94956f18a0430c7e077e047bade501799b3f03a | R | 42,774 | 1,025 | # LARYNX ANALYSIS CODE 2.10.2024
library(geomorph)
library(Morpho)
library(rgl)
library(magick)
library(webshot2)
library(gifski)
library(ggplot2)
library(R.utils)
library(ape)
library(geomorph)
library(Morpho)
library(phytools)
library(rgl)
library(jpeg)
library(pls)
library(picante)
library(adephylo)
library(ade4)
l... |
954686f53c6c469bf65fcad93d16171f5971207abfe886b3f58b807b167f5182 | R | 42,776 | 1,111 | ### Analysis of genes or gene-sets of interest from Spatial Transcriptomics (ST) and snRNAseq datasets
library(dplyr)
library(viridis)
library(data.table)
library(ggpubr)
library(rstatix)
library(spacexr)
library(Seurat)
library(lmer)
###############
### Input
###############
# analysis dir
analysis_dir = "/Users/zac... |
68377c4303e7b6c6f5d502f4a72121b95883c083bf1956744570afc020666d9b | R | 43,133 | 1,133 | ---
title: 'Step 2: Multivariate analysis'
author: "Sam Pring, Sarah Lower, Brian Vestal"
date: "`r Sys.Date()`"
output:
html_document:
theme: cerulean
toc: TRUE
toc_float:
collapsed: TRUE
code_folding: hide
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
knitr:... |
be9f03969b2f44c4ba119e8127d0867bdb75abad9c7f85d233036a7ceac845be | R | 43,389 | 853 | ---
title: "Analysis of host cell expression responses to Tha and Tha2P4M mutations"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
#Libraries and Source Files
```{r libraries and functions, message=FALSE}
library(tidyverse)
library(Seurat)
library(Libra)
library(clusterProfiler)
library(enrichplot)
libra... |
20e0566d99fe9818f4b2552b45ecbac075c1f4f8825a733c2859fc42f98373cf | R | 43,449 | 867 | #### load packages ####
targetPackages <- c('tidyverse','arrow','data.table','slider','gtools','sf')
newPackages <- targetPackages[!(targetPackages %in% installed.packages()[,"Package"])]
if(length(newPackages)) install.packages(newPackages, repos = "http://cran.us.r-project.org")
for(package in targetPackages) library... |
07b66df4bc512b3adcf1c50c637e555052a68b1c49372612a5db3e6efdf9b267 | R | 43,878 | 1,024 | #### load packages ####
targetPackages <- c('tidyverse','arrow','normentR')
newPackages <- targetPackages[!(targetPackages %in% installed.packages()[,"Package"])]
if(length(newPackages)) install.packages(newPackages, repos = "http://cran.us.r-project.org")
for(package in targetPackages) library(package, character.only ... |
c1af86079ca1a155601f14315bef11ac863106a5ed74caf85c2ecef36c8dc7d9 | R | 43,986 | 1,046 | # LARYNX ANALYSIS CODE 2.10.2024
library(geomorph)
library(Morpho)
library(rgl)
library(magick)
library(webshot2)
library(gifski)
library(ggplot2)
library(R.utils)
library(ape)
library(geomorph)
library(Morpho)
library(phytools)
library(rgl)
library(jpeg)
library(pls)
library(picante)
library(adephylo)
library(ade4)
l... |
f31755caa357cd4682817d548c7a3ba3e0d0267753afb53ba5c532aae10ef0e0 | R | 45,658 | 1,421 | #genenames<-rownames(mydata_sub)
#geeout<-H_M_names(genenames=genenames)
#source('/home/clustor2/ma/w/wt215/BTC_project/BTC_R/deseq2_sup.R', echo=FALSE)
#source('D:/Miriam_project/deseq2_sup.R', echo=FALSE)
source('/home/clustor2/ma/w/wt215/RFILES/deseq2_sup.R', echo=FALSE)
# library(One2One)
# # Download and format t... |
5255ad3230e5012535f4d34a48ad1335b39f382498653f9d2e52b1a0b9cf439f | R | 45,872 | 1,303 | # MagellanMapper stats in R
# Author: David Young, 2018, 2021
# library to avoid overlapping text labels
#install.packages("devtools")
#library("devtools")
#install_github("JosephCrispell/basicPlotteR")
# To run stats:
# - Select profiles in runStats
# - Start R in clrstats folder
# - Load source: "devtools::load_all... |
aa5b0a8aec67075c1cd9a5a4bf9b2d9d06a383daef08c5a1965a43afbbe68408 | R | 46,202 | 1,011 | #-----------------------------------------------------
# UMI correlation between SP and ST
umiCorrSpWithSt <- function(obj.sc, obj.sp.lst) {
figs.dir <- file.path(out.figs.dir, "sc_cor_sp")
dir.create(figs.dir, showWarnings = FALSE)
gp.lst <- lapply(names(SC_MAP_SP), function(sn) {
obj.sc.sub <- s... |
74553a0db0076ed07ed92313032627d55d14d756304d4a36a98b4f1e2a58687f | R | 46,295 | 1,177 | ---
title: "Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo - Initial ChIP-seq Analysis"
author: "Jack Kucinski"
data: "04-10-2025"
---
this rmd file contains initial analysis of PAX3::FOXO1, PAX3::FOXO1-minusHD, and H3K27ac ChIP-seq,
which includes running through pipelines and figure... |
5e8797bb878fc7b47e7eed461799b02bf2b7aa8c45c458c766cf284d4ebb8280 | R | 46,337 | 1,357 | #' Construct xgb.DMatrix object
#'
#' Construct an 'xgb.DMatrix' object from a given data source, which can then be passed to functions
#' such as [xgb.train()] or [predict()].
#'
#' Function `xgb.QuantileDMatrix()` will construct a DMatrix with quantization for the histogram
#' method already applied to it, which can ... |
ffadadf8618e2eca1f214354292f08320c850f661e5a9c61bca24e4b5d0947fe | R | 47,242 | 929 | #*******************************************************************************
# Filename : miic.R
#
# Description: main function of the miic the package (user front-end)
#*******************************************************************************
#==============================================================... |
7078f556fd3b2770882c93e2c156404a6f705026e44a237061ff9b32b8b38f63 | R | 47,419 | 839 | ###### This scripts plots the output from the population genetics model for previously published data. It produces
###### - For each patient the model fit vs data and the posterior probabilities of the parameters
###### - A summary of the 80%HDI estimates across the population
##########################################... |
c96ed8479ec1b9ec01504507026b6f42bd4ebc89e6a1c40bd4c02611f972ea2e | R | 48,141 | 1,203 | #*******************************************************************************
# Filename : miic.utils.R
#
# Description: various utilities functions and constants for miic
#*******************************************************************************
#============================================================... |
f691c43e92469d6acf90dd0b2421251c7ab17ddf92ba5f9fcbe7122cd11d5ab5 | R | 48,148 | 713 | ---
title: "CRISPR L1s differential expression analysis of TEs"
output: html_notebook
---
## Here we perform differential expression analysis (DEA) of genes for our CRISPR experiments targeting young L1 elements.
The experimental design is CRISPR inhibition on iPSC where L1s are usually highly expressed, and CRISPR a... |
d442eaf3b6939ea0d2bc2fedd918c6c71bc7d57c748ac484ca9b1141dc250674 | R | 48,393 | 1,332 | # Construct an internal XGBoost Booster and get its current number of rounds.
# internal utility function
# Note: the number of rounds in the C booster gets reset to zero when changing
# key booster parameters like 'process_type=update', but in some cases, when
# replacing previous iterations, it needs to make a check ... |
aadd1e2055e054eeb5dfa80d0df15f6e1b6bb246ded5894fe36af22d1c7a1da3 | R | 49,229 | 1,205 | ---
title: "EEG EPE Analysis (Manuscript)"
author: "Joey Heffner"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: html_document
---
# Setup
To run this analysis script you'll have to have the following packages installed (make sure `tidyverse` is updated):
| Packages1 | Packages2 | Packages3 | Packages... |
e176a46f61e5b8f3225705d8b07ae38a882d90f1fd7429f6cf981d9760dd0e6e | R | 50,323 | 770 | ---
title: "L1-CRISPRi organoids: Cell cycle and commonly dysregulated genes"
output: html_notebook
---
This markdown relates to the visualization of day 15 cerebral organoids.
Main questions:
1. Cell cycle
2. Biomarkers
3. Characterize the present clusters
4. Commonly down / up regulated genes overrepresentation te... |
e3c6849dbfd3834e4f9965009f8b4852d8d7225c222d887bebcccb31328de69e | R | 50,341 | 1,007 | #' Function to conduct set enrichment analysis
#'
#' \code{oSEA} is supposed to conduct set enrichment analysis (SEA) given the input data, annotation and/or ontology. The annotation is provided as an object of class "SET", while the ontology as an object of class "igraph", usually direct acyclic graph (DAG). It return... |
c3c543aeeed4148fcb4dd0f3903aeac7a8d1b3ba9087da564d72df4ca4278c12 | R | 51,192 | 1,091 | ---
title: "scRNA-seq analysis of Tha gene expression across cell types and experimental conditions"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
#Libraries and Source Files
```{r libraries and functions, message=FALSE}
library(tidyverse)
source("~/OHSU Dropbox/Saunders Lab's shared workspace/arpy/man... |
1393ea233f662a18aed699633efc9fa4c0ff77ffb18fea9bc5c966e11b6905f0 | R | 52,649 | 1,007 | #' Chromosome notation standardisation (removing 'chr' string from chromosome names - mainly an issue in hg38 BAMs)
#'
#' @param GERMLINENAME The germline identifier, this is used as a prefix for the allele count files. If allele counts are supplied separately, they are expected to have this identifier as prefix.
#' @a... |
068a1e1a93febe9b78bfeb987f838c4acfb15b339d7fd1f45872dfca17ee0746 | R | 53,304 | 860 | #' @title Fit XGBoost Model
#' @description Fits an XGBoost model to given data in DMatrix format (e.g. as produced by [xgb.DMatrix()]).
#' See the tutorial [Introduction to Boosted Trees](https://xgboost.readthedocs.io/en/stable/tutorials/model.html)
#' for a longer explanation of what XGBoost does, and the rest of th... |
f88d38439d6e9a1178b6c1b049f31637f5815d84bf1ae3d50a1a262bf0b3224e | R | 53,457 | 1,272 | #*******************************************************************************
# Filename : tmiic.utils.R Creation date: 10 may 2023
#
# Description: Utility functions for temporal MIIC
#
# Author : Franck SIMON
#***************************************************************************... |
8858368318ac909961fdcdd0fe4bd471f699942f50f9b87b3bc76e5398978a6e | R | 54,178 | 1,379 | #code to generate the mushroom body video for the Platynereis 3d connectome paper
#Gaspar Jekely 2022-2023
#clear memory, load natverse and other packages, some custom natverse functions and catmaid connectivity info
source("code/Natverse_functions_and_conn.R")
#create temp dir to store video frames
mainDir = getwd()... |
ec8f06de040acf3aaea20a9054b4157dfe53cd3a48c63f7c1b71f4264eabc578 | R | 54,813 | 1,564 | #!/usr/bin/env Rscript
# -----------------------------------------------------------------------------
# PCL I/O
library(plyr)
library(dplyr)
pcl.read <- function(datafile, metadata.rows = NA, rowfeatures=T, sep="\t") {
# Read a pcl structure from a file
# if metadata.rows is NA, it tries to guess... |
ec22a15c45bc8e3cbd8e9ffdeb49b6fe218e0fa9df7ed55bf3e50eae119b179d | R | 56,777 | 785 | ---
title: "CRISPR L1s differential expression analysis of TEs"
output: html_notebook
---
Here we perform differential expression analysis (DEA) of all TEs using a unique mapping approach for our CRISPR experiments targeting young L1 elements.
The experimental design is CRISPR inhibition on iPSC where L1s are usually... |
c38cda4b1ee701624b769dcece3b327da1a1a72455ec7fd829eb91cc582f969f | R | 59,471 | 1,492 | # Safe font family: fall back to system default if Helvetica is not available
.fbt_family <- function() {
if (nzchar(system.file(package = "systemfonts"))) {
avail <- systemfonts::system_fonts()$family
if ("Helvetica" %in% avail) return("Helvetica")
}
"" # ggplot2 default sans-serif
}
fbt_theme <- funct... |
1902aeed338d54cf7f59c4160611d6d0a9cdf8b6574c8f5bea4bf5d91b36b278 | R | 60,563 | 1,609 | prescreen.objective <- function(objective) {
if (!is.null(objective)) {
if (!is.character(objective) || length(objective) != 1L || is.na(objective)) {
stop("'objective' must be a single character/string variable.")
}
if (objective %in% .OBJECTIVES_NON_DEFAULT_MODE()) {
stop(
"Objectiv... |
49d81d9082c35cb7e8f5cca898b2179e906e697e93e416679bde8bc963147977 | R | 61,867 | 1,812 |
################################################################
#
#
# Supplementary analysis (comparing SMD for 1:1 vs 2:1 matching) of psychiatric symptoms,
# diagnoses and service use using MatchIt for propensity score matching in the study:
#
# Only Anxiety Remains Reliably Associated with Paediatric
# ... |
008aaa222731b0ed00e6d3376dda4b9ec0b23eaded862d8c91f35e45083ca2dd | R | 62,788 | 1,610 | ################################################################
#
# MANY-TO-ONE PSM ANALYSIS
# Analysis of psychiatric symptoms, diagnoses and service use using MatchIt
# for propensity score matching in the study:
#
# Only Anxiety Remains Reliably Associated with Paediatric
# Mild TBI at Two Years Follow-up ... |
58d4a29d54bc9e8c7c6e8b1e7961d20fe299a1f6a71de52d01d96e2bce48303e | R | 69,015 | 1,721 |
####################################################################################################
#' A helper function to split the genome into parts
#' @param SNPpos A data.frame with a row for each SNP. First column is chromosome, second column position
#' @noRd
split_genome = function(SNPpos) {
# look for gap... |
b1c07d76095dca074b966bb3f9c407ef36c221557b1a512f35b02c585df19105 | R | 69,846 | 1,176 | ---
title: "Cell-autonomous functional inference of Cluster 1 and Cluster 2 Astrocyte Gene Signatures"
author: "Arpy"
date: '2024-09-24'
output: html_document
---
```{r libraries and functions, message=FALSE}
library(Seurat)
library(tidyverse)
library(readxl)
library(dplyr)
library(clusterProfiler)
library(ReactomePA... |
d1fa137b03c2ad5f20873577a332a26a1d10f1fcd5677b8d69c3be0f6b3c9874 | R | 70,562 | 2,270 | ---
title: "marcos_wgcna"
output: html_notebook
---
# Details
Aunoy Poddar
May 12th, 2024
This is a notebook to pre-process cellranger data. The chunks iteratively
will display quality control metrics and ask the user to input the thresholds
that should be used to generate a final dataset.
Currently, these metrics wi... |
923480329b5b0b6dd2a4c1db6f6d2ceed6931ea8011b964b2fa0348acbb0996a | R | 71,793 | 1,311 | source("./Settings.R")
####################################################################################################################################################
## In the paper, we show parameter estimates obtained with both the one-clone model and the 2-clone model.
## We first source the file "Assess_fits... |
e5247d9f5cafbb9e3781d3a6475d9d973ad62fadf5aba81269a2ed2bc375961f | R | 72,330 | 251 | # R script to download selected samples
# Copy code and run on a local machine to initiate download
# Check for dependencies and install if missing
packages <- c("rhdf5")
if (length(setdiff(packages, rownames(installed.packages()))) > 0) {
print("Install required packages")
source("https://bioconductor.org/bio... |
9a815bb448251d7b6f10010e7f972ccd70188cfa0c4f118eb1ac8f60ddeb0f86 | R | 72,876 | 1,892 | #R/natverse code to generate Figure MB anatomy overview for the Platynereis 3d connectome paper
#Gaspar Jekely 2022
# load natverse and other packages, custom natverse functions and --------
source("code/Natverse_functions_and_conn.R")
# read MB neuron types ----------------------------------------------------
{
... |
7ee435945f8454aa253056153d06266c3fd6e94428d59def0053acb054f0eb20 | R | 75,156 | 1,407 | #' Fit copy number
#'
#' Function that will fit a clonal copy number profile to segmented data. It first
#' matches the raw LogR with the segmented BAF to create segmented LogR. Then ASCAT
#' is run to obtain a clonal copy number profile. Beyond logRsegmented it produces
#' the rho_and_psi file and the cellularity_ploi... |
61063d2fc3a1edc555d8cfa597ccf9f01aa3c233b9b9a7a014c662c1cff6a45b | R | 75,228 | 2,402 |
library(ggplotify)
library(directlabels)
library(circlize)
library(GenomicRanges)
library(EnrichedHeatmap)
#frequent used colors##########
# message(
# cyan$bold(
# '
# Run plot_grid(qq2) to plot \n
# DIY color: \n
# Discrete: scale_color_manual(values=SpatialColors(7)) \n
# or: colorRampPa... |
149baddb8892e08cb8a9913e05fb429591784e5253f8df24b5a0c0e787be33d0 | R | 75,447 | 1,378 | ### example Seurat code for initial single cell RNA seq analysis ###
### written by Lay Kodama, Bang Liu, and Li Fan ###
### please reference https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html for details on the Seurat package parameters ###
#set working directory ====
setwd("/athena/ganlab/scratch/lif4001/Human_P... |
105b723bcaab207f1fefb689dce33ca108ef8e9d5732ddb31e061afcfbffc9a1 | R | 80,017 | 1,966 | ---
title: "Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo - Integration of P3F ChIP-seq, ATAC-seq, H3K27ac ChIP-seq, and RNA-seq"
author: "Jack Kucinski"
data: "04-10-2025"
---
## make directories
```{bash}
WORKDIR="path/to/working/directory"
mkdir chip/p3f/2mil_pcChIP/outputs/bigwig... |
1791eca59705d0abb4a5d241847be375cdb7aab3d511acf9beedfb27940315ca | R | 81,225 | 1,906 | #Platynereis 3d larva connectome paper Figure on segment 0 and segment 1
#Gaspar Jekely
source("code/Natverse_functions_and_conn.R")
# load all cell clusters by segment ---------------------------------------
{
head = nlapply(read.neurons.catmaid("^episphere$", pid=11),
function(x) smooth_neuron(x... |
58920d2aaccdb1176987fd84392c6e29fab73d83900152ef66363d28b26b09ec | R | 81,637 | 2,303 | # Code to generate Figure6 and 7 of the Platynereis 3d connectome paper
# Gaspar Jekely
# load natverse and other packages, some custom natverse functions and catmaid connectivity info
source("code/Natverse_functions_and_conn.R")
# read sensory cell clusters
Dorsal_SO <- nlapply(
read.neurons.catmaid("^Dorsal_senso... |
72de7d4e437e8e45fe5b596871a0db7f80ed208674b7386f90ddbc2801829926 | R | 83,032 | 1,659 | #########################################################################################################################################
####### Non-critical b-d-process
#########################################################################################################################################
#' Non-cr... |
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