sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
0478da579973eddbd9ff5574bfa839c7a5b1f8983c88569017ca9f31849409c1 | R | 4,160 | 124 | #!/usr/bin/env Rscript
# -*-coding: utf-8 -*-
#-----------------------------------------------
# Title: scRNA of the naive human DRG from Renthal lab
# Author: Amanda Zacharias
# Date: 2025-07-22
# Email: 16amz1@queensu.ca
# Notes -----------------------------------------------
# module load StdEnv/2023 r/4.5.0
# Opti... |
b2f9b17c763aa4eafa9ff79039a83c18fa4fecd3d3cd6f5453452a6093a33d21 | R | 4,161 | 135 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
d1a32a4cffadf49864e28da36ca8f753eb7a9822aa6395076fd307de899274b9 | R | 4,165 | 117 | #' banc-dcv-density — Push per-neuron soma DCV count + density to SeaTable.
#'
#' Reads the per-neuron DCV-in-soma parquet from GCS, joins to SeaTable on
#' `nucleus_id`, and pushes `soma_dcv_count` (3D detection count) and
#' `soma_dcv_density` (dcv_voxels / soma_voxels). No `root_id` needed.
#'
#' @section Reads:
#' ... |
2b5ec5c9cecbe824244424b98c77acb3bcd2445ef1fe689beb148734dfa258fa | R | 4,166 | 114 | ########################################################################################
### Metabolomics Heatmap Generation
########################################################################################
# Clean workspace
rm(list=ls())
# Define required packages
required_packages <- c("pheatmap","dendexten... |
c9df7e565a919c9d614641af16c1c9b97c40cc8b7d54b04575a0fab90b969668 | R | 4,169 | 106 | ## Did you miss the previous step? The one about setting up Git and GitHub
rstudioapi::navigateToFile(usethis::proj_path("dev", "02_git_github_setup.R"))
## ***********************************************************
## Setup the core files for your Bioconductor-friendly package
## ************************************... |
292cd8f4353dc0aaae81f26427a068853145bbda73ab00b8ef2a9ee6a69b99ae | R | 4,175 | 144 | tax_glom_fast2 <- function(ps,
rank=NULL, rank_level=NULL,
ignore_lineage=T, ignore_lineage_below_rank=T) {
require(data.table)
ranks <- rank_names(ps)
if (is.null(rank) && is.null(rank_level)) {
stop("Either 'rank' or 'rank_level' must be provided."... |
6ea965f3f46fef08e024e5aef30cc302fc148497d0a54f2e1d77ad103e1aa505 | R | 4,184 | 107 | library(dplyr)
library(R.matlab)
library(ggsegGlasser)
library(ggsegSchaefer)
library(ggseg)
library(ggplot2)
library(ggseg3d)
library(cifti)
library(stringr)
library(factoextra)
library(matrixStats)
library(scales)
library(Hmisc)
library(tidyr)
library(cocor)
library(mgcv)
library(gratia)
library(tidyverse)
library(nu... |
75a4d6a540fdc2d89e18643e50038fc0105077c4f711f260d5b3b321ab436df3 | R | 4,184 | 114 | library(DESeq2)
library(ggplot2)
library(pasilla)
### Choose one matrix to analyze ###
### raw data
dds_data <- adjusted_df_M_KAI_IA_IPSI_A_AC
dds_coldata <- coldata_df_M_KAI_IA_IPSI_A_AC
Target_comparison <- 'M_KAI_IA_IPSI_A_AC'
contrast_vector <- c("Treatment_Lateral","KAI_AMG_IPSI","CTL_SAL_AMG_IPSI")
dds_data <-... |
0a4121f422951fcd21f95884e25abffad7b1f1e5ba3051a16cd6ea44889527eb | R | 4,185 | 131 | #!/usr/bin/env Rscript
#-------------------------------------------------
# Title: Make DRG dataframe cleaner helper
# Author: Christina Meier
# Date: 2025-05-22
# Email: 19cm51@queensu.ca
#-------------------------------------------------
# Notes ------------------------------------------
# module load StdEnv/2023 r/4... |
f6cd39d2c11ab6917f5e0c75f793496430dc2d0f0cb431adb727fcd07180dd93 | R | 4,206 | 187 | ---
title: "Evaluate gene sets by cell type-specific gene expression"
author: "Wei Sun"
date: "`r Sys.Date()`"
output:
html_document:
theme: journal
highlight: tango
toc: true
toc_depth: 3
toc_float:
collapsed: true
smooth_scroll: false
number_sections: false
df_print: paged
par... |
ec6616cace96149bc4e92d33b78e4e1176e4642ac39a6b728b587aed2bdcb93b | R | 4,209 | 136 | ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
# Parameter settings
##### ##### ##### ##### ##### ##### ##### ##### ##### #####
setwd(file.path(getwd(), "R"))
source("00_directorySettings.R") # load baseDir <- "/WORKING_DIR"
outDir <- file.path(baseDir, "results", "GeneLists")
##### ##### ##### ##### ###... |
848b490f15c85e2847d3262168d7d1fa59ef39c0d72d202bd6e9027c19291cd7 | R | 4,210 | 108 | library(Seurat)
library(SeuratData)
library(ggplot2)
library(patchwork)
library(dplyr)
library(data.table)
slide_seq = readRDS("C:/Users/Haoting/Downloads/seurat.rds")
orig_count = slide_seq@assays$RNA@counts
## read location file
locations <- read.csv("C:/Users/Haoting/Downloads/MatchedBeadLocation.csv")
... |
9b24309087b4f8fd9833b908d4d7b02960942747e4bcf21f5dd8f557045ac9c3 | R | 4,214 | 125 | # Figure 1D: PCA Biplot of Fibroblast Lifespan Data
# Shows 339 samples colored by treatment condition
library(here)
library(ggplot2)
library(dplyr)
library(tidyr)
# Source the data processing script to get the datasets
# NOTE: Must source BEFORE defining out_dir because Intro1 cleans up the environment
source(here("... |
caa24ff6369c7a12ba9ce15871a894ac85899401381e1375e6bb810826d0e1cd | R | 4,214 | 134 | library(survival)
library(knitr)
library(kableExtra)
library(tidyverse)
####### LOAD DATA ########
#mydata <- readRDS("/Volumes/TOSHIBA/work_mac/Documents/collab_yr2/Hamed_SNO_0524/july24/matched_data.rds") #1vs4 matching
mydata <- readRDS("/Volumes/TOSHIBA/work_mac/Documents/collab_yr2/Hamed_SNO_0524/nature_comm/clea... |
f13bf36a5d7037241071f08559d7555ea5cf5a87c952acd4ecac0e1c61447582 | R | 4,217 | 122 | #### Section: Boxplot Construction ####
plot_anova_boxplot <- function(data,
info,
layout_values = list(),
line_colors = NULL,
base_size = 14,
share_y_axis = FALSE,... |
d302a3757a4e65964eed8ca3cab8aa22c0cfd6bc3034e169860cabe80ea88dc6 | R | 4,228 | 128 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
9250430726a34fa185c591ac7f79c637b5548c46255796e43418e6fa1c89976e | R | 4,229 | 123 | #!/usr/bin/env Rscript
#-------------------------------------------------
# Title: Write pass 2 scripts for stringtie
# Author: Amanda Zacharias
# Date: 2023-06-30
# Email: 16amz1@queensu.ca
#-------------------------------------------------
# Notes -------------------------------------------
# module load nixpkgs/16.0... |
1fe1759ca6728f2ba82b2437571cb7e84fad7ae7785a3777fbe5d99ae4314d04 | R | 4,239 | 117 | ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
# Parameter settings
##### ##### ##### ##### ##### ##### ##### ##### ##### #####
setwd(file.path(getwd(), "R"))
source("00_directorySettings.R") # load baseDir <- "/WORKING_DIR"
source("00_settings.R")
dataDir <- file.path(baseDir, "data")
nmfDir <- file.path... |
4798e68426d1be1b0b651b74e8ff4cb4cb26347b178e2c998976e23fc919974a | R | 4,243 | 102 | # Purpose: Average CP within frequency bands × time epochs, plot Pre vs Post with error bars.
# Notes: Expects CP matrices shaped [time x frequency].
suppressPackageStartupMessages({
library(ggplot2)
library(dplyr)
library(tidyr)
library(readr)
})
## ---- PATHS (EDIT HERE) ----
freq_path <- "D:/N... |
dd81219b93cd4761b5a30ec0a4e2e0b0e684e806560775f6ee4385cbcb49413a | R | 4,249 | 116 | #' Creates a heatmap visualizing gene expression correlations
#'
#' Generates a heatmap representing Pearson correlation coefficients between
#' query and database expression profiles. Includes optional faceting and annotation.
#'
#' @param ann An object containing correlation data (`ann@results$marker_free$corr`).
#' ... |
2d826874686cb7310bec170ea3f858a1b2de0775e738c0815318b6c2d644a749 | R | 4,251 | 107 | library(ggrepel)
library(ggplot2)
PCA_function <- function(data, groups, useLabels = FALSE, labels = "", pcs = c(1,2), type = 'scores', scale = TRUE, legendName = "Cog task", absolute_loadings = FALSE) {
data[is.na(data)] <- 0
# Vector to calculate colors based on the number of groups
colores <- rainbow(lengt... |
a27d416ab6a6b9bb590c24c028ada2714ae8a558a2d19d5e3d95a4555a4d9144 | R | 4,254 | 114 |
setwd(rstudioapi::getActiveProject())
rm(list = ls())
library(tidyverse)
library(ggpubr)
library(ggrepel)
library(ggbreak)
source("./Scripts/Function_scripts/Pre-processing_functions.R")
load("./Output_Data/Invitro_lpd.mol.pct.Rdata")
load("./Output_Data/GPMV_lpd.mol.pct.Rdata")
load("./Output_Data/Lipids.GPMV.Inv... |
a6725e913e52967768e2d1c42fddcd7d78ca9a63e9014f07341648933b50ea8a | R | 4,255 | 82 | install.packages("easypackages")
library("easypackages")
libraries("readxl", "tidyr", "dplyr", "ggplot2")
Supplementary_Data_S5_feedback <- read_excel("Supplementary Data S5.xlsx",
sheet = "Partial motif count") %>%
filter(grepl("D", Motif))
Supplementary_Data_S5_feedfo... |
6658d1c1e1d371ccfa0c52204e73ab0753d5d311e7e03997c49a09ef79db3ffa | R | 4,260 | 99 | XGBoostHyperparameters <-
R6::R6Class(
"optimize_xgboost_hyperparameters",
list(
plink_location = NULL,
cv_folds = NULL,
XGBmatrix = NULL,
early_stopping_rounds = NULL,
eval_metric = NULL,
booster = NULL,
objective = NULL,
design_steps = NULL,
opt_steps = ... |
a8478578b158d1841de404c8f5394d6572bfba05cfe882016330d1c480995f67 | R | 4,261 | 89 | ## ----setup, include=FALSE----------------------------------------------------------------------------------------
#knitr::opts_chunk$set(echo = TRUE)
# setwd("/Users/warri/OneDrive/Documents/Denver/Research/Data/ashad_n110")
#sessionInfo()
# RDAC R packages location '/home/rcorcoran/R/x86_64-pc-linux-gnu-libr... |
a2f0e94b9399de693af7e5202d184ebb3d2d42a070f42646c72eb53ade786335 | R | 4,263 | 95 | #' banc-hemibrain-mesh-transform — Transform hemibrain meshes into BANC space.
#'
#' For each hemibrain bodyid, fetches the OBJ mesh and applies the
#' JRCFIB2018F → JRC2018F → BANC registration chain. Saves the
#' transformed OBJ.
#'
#' @section Reads:
#' - `<banc.meta.save.path>/hemibrain_meta.csv`
#' - hemibrain... |
b4e044a28d8bd9f186e174f31ed30baa47435eccede68a882655d7298934a1f2 | R | 4,266 | 106 | # conda activate R411
# Activate the environment
# conda activate R411
# Load necessary libraries
pacman::p_load(data.table, stringr, dplyr, readxl, feather, biomaRt, tidyverse, openxlsx, ggplot2, VennDiagram, janitor, gridExtra)
library(GenomicRanges)
library(Biostrings)
library(BSgenome)
library(BSgenome.... |
f7260eb72e52341db3a1b03be18fa8dbdd16d33774ebebd9255ac52d767246a4 | R | 4,270 | 91 | #' Turn PANDA network into a CONDOR object
#'
#' \strong{CONDOR} (COmplex Network Description Of Regulators) implements methods for clustering biapartite networks
#' and estimatiing the contribution of each node to its community's modularity,
#' (Platig et al. (2016), \doi{10.1371/journal.pcbi.1005033})
#' This functi... |
28365e0c1008b3dee7dd3043d6f908d2db2d2aaac1bc1d5012692cf15919b8f0 | R | 4,274 | 124 |
library(VariantAnnotation)
#setwd("/fastscratch/verhaak-lab/GLASS-WG")
## Parse snakemake
f1f = snakemake@input[["freebayes1"]] # "results/mutect2/freebayes/batch1/GLSS-MD-LP10-R1-01D-WGS-CYN7CI.normalized.sorted.vcf.gz" #
f2f = snakemake@input[["freebayes2"]] # "results/mutect2/freebayes/batch2/GLSS-MD-LP10-R1-01D-W... |
66e79237f5b5bb0772f2d6da9818c9e806a86fd350c77c297e9798ded119e257 | R | 4,277 | 107 | ##################################
# Report quality metrics for snRNA that ended up in the final analyses
# Author: Kevin Johnson
##################################
library(tidyverse)
library(EnvStats)
library(cowplot)
library(ggpubr)
proj_dir <- "/vast/palmer/pi/verhaak/kcj28/care_idh_mut/"
fig_dir <- file.pa... |
9d8643ac107fdb28c2a3885707060ade3d7008f882d9607ae6daeb5d71d4a7d7 | R | 4,278 | 114 | # ============================================================================
# Figure 1G: Hedges' g Effect Sizes — Each Condition vs Control_No_Tx
# ============================================================================
# Computes Hedges' g (bias-corrected Cohen's d) for each experimental
# condition compared t... |
91b41e25c026f782a9ac547444a7785ca6ab251a01ad097a69f705c8b29d01f9 | R | 4,291 | 124 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
f5bf0796ad1f3372de5bc311db8edb8eaa440479a8d46e4a9f3b5250f94bfab6 | R | 4,294 | 126 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
369246a4ee2864582b8d19347b2968f2d698a55c46da0fd05dce60a43ad5527e | R | 4,296 | 102 | #' This function finds the most upstream overlapping feature (usually CDS) from a genome annotation (feature.df) for
#' each exon and subsequently each transcript. The default is fully overlapping features, but
#' the 'type', 'maxgap' and 'minoverlap' arguments can be used to change that.
#'
#' @export
#'
#'
require... |
df20973ca9b640c71335596208c569eb1dc92338cb234d89aee74003519261c4 | R | 4,300 | 118 | library("tximport")
library("AnnotationHub")
library("ensembldb")
library( "biomaRt" )
library("dplyr")
dir <- "/input_path"
outdir <- "/output_path"
#example change sample name as needed
fam1_111 <- list.files(path = dir,
pattern= "fam1iPSC_111",
full.names = FALSE)
fam1_156 ... |
9ebfe33a5e2a623c94f0f8297283279f848599a93c6a429b1064f1aa5c07da79 | R | 4,302 | 97 | #' @docType methods
#' @rdname mr_lasso
#'
setMethod(mr_lasso,
"MRInput",
function(object,
distribution = "normal",
alpha = 0.05,
lambda = numeric(0)){
Bx = abs(object@betaX)
By = object@betaY*sign(object@betaX)
... |
709ae601d718ceea679f5303025ea43677c4a51882ea35b972a6c454cee3b07b | R | 4,305 | 138 | library(dplyr)
library(tibble)
# Function to perform hypergeometric test
perform_hypergeometric_test <- function(male_deg_list, female_deg_list,
male_combined, female_combined,
cluster_name) {
# Get the total number of genes tested f... |
76fdb89ec12e6045a9ed6d48acbb98a1ae318c0d5b26396274cbac73c28c7504 | R | 4,306 | 115 | # Phase 1: 使用TCMNP包批量获取8味活血止血双效药材的活性成分和靶点
# herb_target() 接受中文名，筛选OB>=30, DL>=0.18
library(TCMNP)
data_dir <- "c:/Users/huizh/Desktop/拟发表论文/活血止血/data"
results_dir <- "c:/Users/huizh/Desktop/拟发表论文/活血止血/results"
# 8味药材
herbs_cn <- c("三七", "蒲黄", "茜草", "五灵脂", "花蕊石", "降香", "血竭", "儿茶")
cat("==============================... |
125bb23b1396dbd7e08756e3e31f8c5e981b4e2461405ed3c1d8dc9d6023436b | R | 4,315 | 114 | #' Query FANC tables in the CAVE annotation system
#'
#' @param ... Additional arguments passed to
#' \code{\link[fafbseg]{flywire_cave_query}}
#' @inheritParams fanc_partner_summary
#' @inheritParams fafbseg::flywire_cave_query
#'
#' @return A data.frame
#'
#' @family fanc-cave
#' @export
#' @seealso \code{\link[faf... |
b84307e402fabff8ec018030968836abab7737f9ebde89cf770464c2b1e015a2 | R | 4,315 | 90 | here::i_am("scripts/2.validations/2.1.regulator_interactions_and_module_overlaps/2.1.3.test_association.R")
library(tidyverse)
library(here)
library(igraph)
library(ggraph)
wd <- here("data/validations/regulator_interactions_and_module_overlaps/")
dir.create(paste0(wd, "figures/"))
## Module overlaps for interactin... |
1c96b1d5519771608f8a5a95cc31ba448a1a75ce0988eaf4e7fea61bff846c55 | R | 4,319 | 131 | #!/usr/bin/env Rscript
#-------------------------------------------------
# Title: Make heatmap gene counts across samples
# Author: Amanda Zacharias
# Date: 2023-07-13
# Email: 16amz1@queensu.ca
#-------------------------------------------------
# Notes -------------------------------------------
# module load nixpkgs... |
a32519f64d4db161499d55f5bf4f07e89ffa36176b912c017408c8fb5d3d5cfe | R | 4,320 | 134 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
e57a25997564279e6a9f3394c84cc273a9d4d8e6db3b398a0b46d7420603bc41 | R | 4,322 | 108 | library(ggplot2)
rm(list=ls())
options(digits = 10) # by default, print results to ten decimal digits
set.seed(1823) #for replication - the year Trinity College was founded!
#replace the empty quotes with the file path to the location where you downloaded the files from Zenodo below
path = ""
chance = rep((1/6), ti... |
a31aac9f99b612d91e4a599e3a09fbbd56be122e4c1ae6adc42b1f53bee158a8 | R | 4,326 | 115 | #' Spatial registration: compute ANOVA statistics
#'
#' This function computes the gene ANOVA F-statistics (at least one group is
#' different from the rest). These F-statistics can be used for spatial
#' registration with `layer_stat_cor()` and related functions. Although, they
#' are more typically used for identifyi... |
09b275b016728bc0d11061ac07433a9fcf7ef03e4aacdb3d6024f2dba97d1e25 | R | 4,330 | 108 | #--Permutation test for "whether A disease peak set overrepresent/downrepresent methylated peaks (over - LOH; down - GOH)"
args <- commandArgs()
group <- args[6]
print(group)
library(dplyr)
library(ArchR)
library("stringr")
library(ggplot2)
library(ggpubr)
library(reshape2)
library(ggsignif)
outp <- "sn_mC"
peakMC <... |
1e34ba1aa38d6b6f8136b0fe081cacdc96f358e948ead46067cd78767289304e | R | 4,330 | 118 |
setwd(rstudioapi::getActiveProject())
rm(list = ls())
library(tidyverse)
library(stringi)
library(ggpubr)
library(patchwork)
source("./Scripts/Function_scripts/Effect_size_functions.R")
source("./Scripts/Function_scripts/Pre-processing_functions.R")
## ====In vitro====
load("./Output_data/Invitro_conc.lipid.qNSC.Rda... |
484231df1105e16f399428bd73b1c97e51f1e73686568289cb6bfb31fb59af84 | R | 4,331 | 109 | # --- 1. Check and Install Required Packages ---
# This block ensures that all necessary packages are installed before running the script.
cat("Checking for required packages...\n")
required_packages <- c("vroom", "readxl", "tidyr", "openxlsx","edgeR")
new_packages <- required_packages[!required_packages %in% installed... |
9b2b2611a11e8cc7db48ef4c30df16d1cc89a97735b4793d61dced96cc9f8f19 | R | 4,331 | 114 | # -------------- Function for parsing xml HMDB object --------------
# The "store" slot within any hmdb object is not very convenient,
# it's an xml converted to a list. Here I turn it into a readable
# string, which can be later explored with simple regular expressions.
hmdb.store.to.string <- function(root) {
if... |
ea064dddde381a61ca198d020324998b099898c26ec8ac10ea4e5667f5b404bc | R | 4,332 | 127 |
```{r}
library(dplyr)
library(tidyr)
library(purrr)
library(lme4)
library(broom.mixed)
# Baseline group comparisons (2×2 repeated-measures ANOVA analog via LMM)
# Outcome: SCFA concentration (per acid)
# Fixed effects: group (HC vs SAD), time (BL1 vs BL2), and their interaction
# Random effects: random intercept for ... |
d32e08dc7bc4ae6bffcf01661b08504e7a2e72783eb56b8243a6a707e7d0f88c | R | 4,334 | 126 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
d5a26d45897163712b03a4e16df88e2b820a9cb5dbd21e5332a2c8856d809daf | R | 4,334 | 95 | ## Side chain analysis across 2 in vitro studies
## Remove LPC-O and LPE-O with 1 or 2 double bonds, as well as LPC-P and LPE-P with 0 or 1 double bond due to annotation ambiguity.
setwd(rstudioapi::getActiveProject())
rm(list = ls())
library(tidyverse)
library(ggpubr)
source("./Scripts/Function_scripts/Effect_size_f... |
e42a94f46041bbe1db1fc5c1f35161222f785559d96cb1fa7842d40b35b9c193 | R | 4,335 | 128 | ### -----------------------------------------------------------------
### Legacy exploratory analysis by a member of the Wilson Lab.
### Historical record only — not part of the bancpipeline release.
### -----------------------------------------------------------------
# Find neurons connected to DNg27 - to find coraz... |
5c382312816d32521f1eef122bcbae1b02baa17cd9fb88bec3ed3f34e38a632d | R | 4,338 | 114 | ---
title: "Seurat_neural_clusters"
output: html_document
date: "2025-07-09"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(ggplot2)
library(dplyr)
library(Seurat)
library(scCustomize)
```
Load dataset
```{r}
neural <- LoadSeuratRds(file = "neural_final.rds")
```
Looking at ba... |
44a0194ddfa118004c89242ef1e74e3a78917f5ed666edaff59bfeacd155958d | R | 4,340 | 135 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
18024f7f0b2e489fe97a80c84dd4c2aa563ccf614f6b109710bb1fd02eef5557 | R | 4,344 | 127 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
ee1d36157778cd22cd66ca188d934607adb185335d1bf2fdcf529f9110b741ee | R | 4,349 | 87 | #!/usr/bin/env Rscript
# Copyright 2023-2023 Chun-Hui Gao <gaospecial@gmail.com>
#
# This file is free software: you may copy, redistribute and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 2 of the License, or (at your
# option) any ... |
01b695fba2ccffcd63fc70ea76f76d049cff245194f89955e5d13d8505b55ad1 | R | 4,351 | 131 | #!/usr/bin/env Rscript
#-------------------------------------------------
# Title: Write individual bash scripts
# Author: Amanda Zacharias & Christina Meier
# Date: 2023-08-11 & 2025-08-11
# Email: 19cm51@queensu.ca
#-------------------------------------------------
# Notes ------------------------------------------
#... |
48d495bf81a50811a564f975e1228c18a7e427448916b784edf7ff4f3f45ba90 | R | 4,353 | 124 | ---
title: "Fig_S4E_tumor_cell_type_composition"
output: html_document
date: "2026-02-17"
---
```{r}
library(Seurat)
library(tidyr)
library(ggplot2)
library(ggpubr)
library(dplyr)
library(harmony)
library(purrr)
library(cowplot)
library(rstatix)
library(ggbeeswarm)
library(ggbreak)
```
# Set up and adjust metadata
... |
c0ec0b000a581bc3d1152cd25d1542f110adcef13dafb99b0d8683618e0551e3 | R | 4,356 | 106 | ### Validation on young PM lipid supplementation by lipidomics
setwd(rstudioapi::getActiveProject())
rm(list = ls())
library(tidyverse)
library(ggthemes)
library(ggpubr)
source("./Scripts/Function_scripts/Effect_size_functions.R")
source("./Scripts/Function_scripts/Pre-processing_functions.R")
##==== Effect size betw... |
fa283e5557232a3e126e91fb8ca438c6010d18efc73ecdda358d22b95ad6f321 | R | 4,356 | 154 | # set up
library(reshape2)
library(dplyr)
library(ggplot2)
library(pheatmap)
library(tibble)
library(gridExtra)
#### Helper functions - dataframe handling ####
# Normalization function used in ChromHMM
normalize_column <- function(y) {
(y - min(y)) / (max(y) - min(y))
}
# Filter and sort a df by columns
filter_sor... |
01df02a435e4b3fbd9e4f08631399784936a3bb6b5329ff8b89e3e5d23f3cc84 | R | 4,367 | 131 | #' Compute Spatial Enrichment Index (SEI) for Each Gene
#'
#' Calculates the spatial enrichment index (SEI) for each gene based on
#' a user-supplied set of spatial weights. The SEI reflects the extent to
#' which gene expression is enriched in spatially weighted regions of
#' the tissue (e.g., near boundaries or centr... |
541322ba09af011de0eac9af019cbb8f0b58e111ff3f186f1218ecfd3f4fad67 | R | 4,372 | 90 | #######################################################
# Determination of samples that were mismatch per GATK fingerprinting tool
# Date: 2018.12.05
# Author: Kevin J.
#######################################################
# Current location of files:
workingdir = 'Volumes/verhaak-lab/GLASS-analysis/results/fingerpr... |
016dd9cd298f8910daaafe73f30fe0160a98cdc207cb0cd4878eb2bc41b02c4d | R | 4,374 | 91 | # Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
RjnmfC <- function(Xs, Xu, k, alpha, lambda, epsilon, maxiter, verbose) {
.Call('_conos_RjnmfC', PACKAGE = 'conos', Xs, Xu, k, alpha, lambda, epsilon, maxiter, verbose)
}
adjustedRandcpp <... |
e81659d16cceccb3ae80af388acc0af04bce03f0bcc72126e24576bbc762e0ea | R | 4,380 | 152 | library(Seurat)
library(ggplot2)
library(scCustomize)
library(patchwork)
library(RColorBrewer)
library(viridis)
library(dplyr)
library(stringr)
#load spatial seurat object
data <- readRDS("nodose_st_RCTD_251025_metadata_updated.RDS")
DefaultAssay(data) <- "RNA"
View(data@meta.data)
##Reorder levels by cell types
cell... |
f342379ddb42f864fc529d6fc92e37149e58d29993f1f12128e1301763a0043e | R | 4,380 | 128 | #' Runs the neighbor voting algorithm.
#'
#' The function performs cell type identity prediction based on 'guilt by
#' association' using cross validation. Performance is evaluated by calculating
#' the AUROC for each cell type.
#'
#' @param exp_labels A vector that indicates the dataset source of
#' each sample... |
f486d9ce6fb0ce5d3a8fdeeb52403b59e0f3f839f162524ba489f78157f60e31 | R | 4,380 | 132 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
2a84d1b33fe552ef451aef66556a31eca134e12e2550cd5294d3f7c09f02ae87 | R | 4,384 | 102 | ---
title: "Motor_Neurons"
output: html_document
date: "2025-08-21"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(ggplot2)
library(dplyr)
library(Seurat)
library(scCustomize)
neural <- LoadSeuratRds(file = "neural_final.rds")
```
# Load dataset and level Samples
```{r}
DimPlot... |
146a2f4591c35ad559800b5e5db4f6c423eed7b595c050da654ca12d8903d636 | R | 4,386 | 126 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
36da980fd78f526c7f6ac2f36ba16343e8df23731ae2f577d6db84563a3eee48 | R | 4,388 | 143 | here::i_am("scripts/2.validations/2.8.POU5F1_CRISPRi/2.8.9.DE_analysis.R")
library(tidyverse)
library(SingleCellExperiment)
library(foreach)
library(doParallel)
library(limma)
library(scran)
library(scater)
library(variancePartition)
library(ggrepel)
library(ggsignif)
library(patchwork)
library(Seurat)
library(here)
l... |
d697a1f622c542f7fd9b15eb499f3a8a336b8a5d7a1f0a3beab8fd954572d356 | R | 4,392 | 165 | #!/usr/bin/env Rscript
suppressPackageStartupMessages(library("argparse"))
# create parser object
parser <- ArgumentParser()
# specify our desired options
# by default ArgumentParser will add an help option
parser$add_argument("-i", "--input", required=TRUE, help="load preprocessed RData")
parser$add_argument("--pc_... |
45af239be1ad629b0d80afe8ed2abdbde87adbad05e7a4d0119c502f63c894e9 | R | 4,394 | 188 | library(readr)
events_gen <- function(sub,ses){
sub <- as.character(sub)
ses2 <- sprintf("%02d", ses)
ses <- as.character(ses)
ses2 <- as.character(ses2)
for (r in 1:2){
#Reset dataframes
mid.events <- sr.events <- as.data.frame(matrix(NA,0,4))
#Generate folders,... |
2e48e756aec7bde04403639284ac0528a4a3a69ee9e48911285ff1c86f418284 | R | 4,399 | 144 | # Load Arguments
args.split <- function(x) {
x <- stringr::str_replace_all(string = x, pattern = " +", replacement="")
x <- unique(stringr::str_split(string = x, pattern = ",", simplify = TRUE)[1,])
return(x)
}
dft.args <- list()
dft.args[["iter"]] <- FALSE
dft.args[["input"]] <- "/home/whe/project/multiom... |
99c3b361932b2c6b1fb94ddf5287034c2ee385abc42023e7a01a29d898d30c94 | R | 4,400 | 101 | ##
##Load regNet package
##
#- See https://github.com/seifemi/regNet for details how to install regNet.
library( regNet )
##
##Set the following paths according to your system
##
#- Must be modified to fit to your own system
#- Central project path prefix for regNet to store outputs of regNet
centralProjectPathPrefix... |
863a44a7812af48238c7952011d311410095128cd244e733f86f2cc0750d22a5 | R | 4,404 | 90 | #!/usr/bin/env Rscript
args <- commandArgs(trailingOnly = TRUE)
# args order: depth file, variants file, Name, GeneLocs file
GeneLocs <- TRUE
if(length(args) < 4 || args[4] == "" || is.na(args[4]))
GeneLocs <- FALSE
library(tidyr)
library(dplyr)
library(tibble)
library(ggplot2)
library(stringr)
library(ggrepel... |
6d432fac3bd42ee8a561880b3866a917cd4df3e434318662efa8947ada4aa135 | R | 4,411 | 118 | #Create a new ArchRproject with samples (14 individual-QC-filter samples + 72 remainning)
library(ArchR)
library(parallel)
addArchRThreads(threads = 10)
addArchRGenome("hg38")
outp <- "path_to_outdir"
setwd(outp)
# create new arrow files for some samples
mysample <- read.csv("/home/xhan/atac/archrproject0318/list.qc... |
1224f8d053144c276ac4efe02d6f20a70dd10259937e54c13b6d06949a4e4eb0 | R | 4,414 | 120 | ---
title: "Fig_3B_C_tumorcell_umap"
output: html_document
date: "2026-01-23"
---
# Set up and adjust metadata
```{r}
srt_merge <- readRDS("~/path/to/tumor/seurat/object")
#srt_merge <- readRDS("~/processed_data/tumors_normalized_scaled_dimreduction_annotated_refined_miller_with_malig_states_srt_revision.rds")
srt_mer... |
b2571b562559cfc8950c29572a638d6980d1e9e6a2025b1c61399cd0450cfe16 | R | 4,415 | 106 | library(Seurat)
library(ggplot2)
data_dir<-'/cephfs/scratch/bruening_scratch/gdowsett/data/nodomap/'
source(paste0(data_dir, "utility_functions.R"))
source(paste0(data_dir, "plotting_functions.R"))
load_plot_params()
load_colors()
getLongPalette = colorRampPalette(long_palette_strong)
getOkabeItoPalette = colorRampPal... |
cb0d435581d31a355457611ed292712e26b061b8ea916d2086d69bfac5cd124c | R | 4,415 | 167 | ### -----------------------------------------------------------------
### Legacy exploratory analysis by a member of the Wilson Lab.
### Historical record only — not part of the bancpipeline release.
### -----------------------------------------------------------------
# Double check that all DNs have assigned type
#... |
4d0a2da6bf7ad511b7455fe86ff89ec6fcd9ef7d894ec61d16f32850f5677fd5 | R | 4,417 | 108 | ##### Combining Tany-seq and Hypomap Data #####
#To observe the sources of the original data in both dataset
table(tanyseq$Origin)
table(tany_hypomap$Dataset)
#In hypomap we have already have Campbell and Chen databases. These are removed from Tany-seq.
tanyseq <- subset(x=tanyseq, subset = Origin %in% c("Blac... |
b0cbd2dd1accb4fe36d56f886aeb9da8996bc7069f70716ad25b770b0e67c4e8 | R | 4,418 | 135 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
79bfa2da67e52e42068d49d3d7d42c6041f56b5b2b8ee6344bdea15a765db96c | R | 4,419 | 119 | #!/usr/bin/env Rscript
#' Author: Sumaiya Nazeen (sumaiya_nazeen@hms.harvard.edu)
#' This program runs NERINE for a given network and observed mutation counts
#' in a specific variant category for a case-control cohort
#'
#' @param case_count_file file containing case frequency table
#' @param control_count_file file ... |
e54a3be7e6978f7f9bfcb4b248e0971c69bceeb613b79253b9d8e338aec0af02 | R | 4,420 | 97 | #De-convolute spot-level spatial data with scRNA-seq reference
library(spacexr)
library(Seurat)
library(ggplot2)
#Set up reference
ref <- readRDS("/cephfs/scratch/bruening_scratch/gdowsett/data/nodomap/nodomap_cleaned_20251025.RDS")
DefaultAssay(ref) <- "originalexp"
Idents(ref) <- "cluster_number"
#Extract counts/clu... |
e31a854a18c9a9059c486901d9ce53ed69dd11f68e679aa641b8a05bd5dafc82 | R | 4,421 | 107 | # Purpose: Plot CP heatmaps (Pre vs Post) with fixed contour levels and a 0.51 outline.
# Notes: Expects CP matrices shaped [time x frequency] with 36 time bins and 149 freq bins (cols 4:152).
suppressPackageStartupMessages({
library(ggplot2)
library(dplyr)
library(tidyr)
library(readr)
})
## ---- P... |
39a94af52280459a73bc3f357268bd70c074bf45702f7ed1dfd8b150aa3b69ea | R | 4,423 | 120 | # ==============================================================================
# Script 16: Figure 3B - Chromosomal Topography of Translocation Breakpoints
# ==============================================================================
# Description: Generates translocation breakpoint heatmap showing chromosomal
# ... |
8b4eafc26a6615114fc8c43f57c561b4dfed5844372a056a29cb13f1c78cd349 | R | 4,423 | 93 | #######################################################
# Determination of samples that were mismatch per DNA fingerprinting tool
# Date: 2022.05.28
# Author: Kevin J.
#######################################################
# Current location of files:
workingdir = '/projects/verhaak-lab/USERS/johnsk/glass4/results/fi... |
a59a9675fa1bf0864650afc0afe3d417ddef62ab09f638a2deb89c0e48c4f152 | R | 4,423 | 135 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
d70c11c85a86ee66e58ac17dba9882bb237bf3530744aafc984e74ef3bce48e7 | R | 4,423 | 129 | #!/usr/bin/env Rscript
# ============================================================================
# TsImpute Benchmark on scMixology 3cl Dataset
# ============================================================================
setwd("/projects/radlab/Wan//NSF/CoMemEmpirical/")
options(Seurat.object.assay.version =... |
52c14d6edb5b94253d1ffbc84117198068d4fb7ac47da83799aa711e939b0241 | R | 4,426 | 102 | ---
title: "Using CONDOR for community detection in bipartite graphs"
author: "John Platig"
date: '2015-09-28'
output:
html_document:
df_print: paged
rmarkdown::html_vignette: default
pdf_document: default
vignette: |
%\VignetteIndexEntry{CONDOR}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{U... |
1b367618cce110bf562b9604f6a46241c2a19643e3cfe408e15f8ca76d491ea3 | R | 4,429 | 122 | # ==============================================================================
# Load Copy Number Variation (CNV) Data
# ==============================================================================
# This script loads and prepares CNV data from CytoSNP arrays
#
# Author: Osama Shiraz Shah
# ========================... |
c0a48d224ab411373992ef3f89a490aa544b7659e83d859da84c11a8e56f94f4 | R | 4,433 | 102 | ##############################################################
# Script: 02_load_normalize_batchcorrect.R
# Purpose: Load, clean, normalize, impute, and batch-correct
# proteomics data for IMP-1088 analysis
##############################################################
####################################... |
63383a5bd39067fa405b957fa9caeefe58403074a26f8ceda9dfe8df38ed9ab0 | R | 4,435 | 93 | #######################################################
# Determination of samples that were mismatch per DNA fingerprinting tool
# Date: 2022.05.28
# Author: Kevin J.
#######################################################
# Current location of files:
workingdir = '/projects/verhaak-lab/USERS/johnsk/glass4/results/fi... |
e83da276c1187f677bd3f190e7bd3845852ff181d5fac86617a69566337edd60 | R | 4,435 | 128 | ---
title: "YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization"
author: "Joseph N. Paulson & John Quackenbush"
date: "`r Sys.Date()`"
output: rmarkdown::pdf_document
vignette: >
%\VignetteIndexEntry{YARN: Robust Multi-Tissue RNA-Seq Preprocessing and Normalization}
%\VignetteEngine{knitr::rmarkdown}
... |
d29e8f79bd76d8877286d24132bc299160a9b2f8773aa5d6ce91e7d9fbd7e3ab | R | 4,436 | 191 | ---
title: "Find association between significant, Aging-associated CpGs or DMRs and epigenetic clocks"
subtitle: "Read and pre-filter ROSMAP data"
author:
- David Lukacsovich^[University of Miami]
- Lily Wang^[University of Miami]
date: "`r format(Sys.time(), '%d %B %Y')`"
output:
rmarkdown::html_document:
hi... |
28d253ed6d714eb9c53624a6a8683f8a73fef096f1b0aa272dada2c83d61eba0 | R | 4,441 | 206 | ---
title: "Evaluate gene sets identified by SDAN"
author: "Wei Sun"
date: "`r Sys.Date()`"
output:
html_document:
theme: journal
highlight: tango
toc: true
toc_depth: 3
toc_float:
collapsed: true
smooth_scroll: false
number_sections: false
df_print: paged
---
```{r setup, incl... |
dd0ae559af7516048b724159ee203c0639d0c4ebca027a470c47cc498aa9aadd | R | 4,442 | 93 | #######################################################
# Determination of samples that were mismatch per DNA fingerprinting tool
# Date: 2022.03.20
# Author: Kevin J.
#######################################################
# Current location of files:
workingdir = '/projects/verhaak-lab/USERS/johnsk/glass4/results/fi... |
0c0e00e1587c2a995933ba3a57912fa8c1dd182a68cd6b9d79f0cf282fc2d733 | R | 4,443 | 95 | context("test LIONESS result")
test_that("lionessPy() function works", {
# test 1: check test error message when empty inputs
expect_error(lionessPy())
unlink("lioness_output", recursive=TRUE)
# input file path
system("curl -O https://netzoo.s3.us-east-2.amazonaws.com/netZooR/example_datasets/expr4... |
e5af3c0b5248f7707d795286f219b9c2946f4799b5963a87169a30e31e755fff | R | 4,448 | 107 | ### Example Analysis Code - Mitric, Beerens et al., 2026.
### Threat intensity shapes cortical engram architecture supporting remote memory retrieval. Nature Communications
## FIG 6 - structural analysis
#### set up R
# clear existing workspace objects
rm(list = ls())
graphics.off()
# set working directory to whe... |
bb0212e0125479b3e03537b7619f748c0382028e7b5a0e1f9a3118aafa6bd0d6 | R | 4,453 | 128 | #------------------------------------------------------SETUP-----------------------------------------------------#
# Load libraries
library(tidyverse)
library(data.table)
library(BuenColors)
library(Seurat)
library(irlba)
library(Matrix)
library(future)
library(reticulate)
library(ggrastr)
library(tidytext)
library(ma... |
34f79aa6d264ddec273c45eba4595462b38b60a181376644221e743fe0717f0e | R | 4,458 | 99 | #' Add Harmony Batch Corrected Reduced Dims to an ArchRProject
#'
#' This function will add the Harmony batch-corrected reduced dimensions to an ArchRProject.
#'
#' @param ArchRProj An `ArchRProject` object containing the dimensionality reduction matrix passed by `reducedDims`.
#' @param reducedDims The name of the `... |
ed11f05903242699f9044d7ec7e7592d058d7d19eb0bbed4ba2559cf5541f378 | R | 4,458 | 54 | #!/usr/bin/env Rscript
library(Matrix)
library(Seurat)
library(tidyverse)
library(readxl)
library(Augur)
source("scRNAseq_funs.R")
#####################################################################################################################################################################################
## ... |
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