sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
382743aa7e983b0c4ec9e17630f2faa47b24c0fbd1e4dc62addb2d86168abe4c | R | 26,038 | 757 | ---
title: "Supp figure 2"
author: "Emma Jones"
date: "2023-10-16"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Comparing DTU, DTE, and DGE continued
The purpose of this script is to compare genes with differential gene expression, differential transcript usage, and ... |
ba4bf5d9f6267eb08c9a5b0363eba5763396820676d1cf3cc51f286a5e4b5b02 | R | 26,276 | 919 | #----Node: functions----
validNode <- function(object) {
#RNA maximum in range
if (!is.na(object@spmax) & (object@spmax < 0 | object@spmax > 1)) {
stop('RNA maximum expression has to be between 0 and 1')
}
#RNA degradation in range
if (!is.na(object@spdeg) & (object@spdeg < 0 | object@spdeg > 1)) {
stop('RNA... |
48b5289f4c3fea045f7b55088997c2638b6bd4b2e1428ae01cb74feb2b88f169 | R | 26,375 | 702 | ---
title: "Download sample-level data"
author: "Nicole Gay"
date: "12/9/2021"
output: html_document
---
```{r setup, include=FALSE}
## WARNING: this code is not self-contained. it requires access to the motrpac-mawg GitHub and gs://mawg-data GCS
library(data.table)
library(MotrpacBicQC)
library(dplyr)
library(testit... |
39f87f36029440058e5a42f93ea7ad6c39b882fec2a8ac2619ee91c04c52854a | R | 26,439 | 737 | ###################################################
# ~~~ FramebyFrame package ~~~
# LME statistics
# Francois Kroll 2022
# francois@kroll.be
###################################################
# function LMEdaynight(...) -----------------------------------------------
#' Title
#'
#' @param pa
#' @param grporder
#... |
36330eba701d8759ad5dfc9ea6ab0a1f0a5c7b1b8f552219249d0410dff2c320 | R | 26,514 | 376 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
9648965cac0f0f332654b9d6939fe8b5e54ae8a1aeb69ccf9f50b48e3c225817 | R | 26,638 | 375 | library(reshape2)
library(tidyverse)
library(ggpubr)
meltextract <- function(res, method, sim_labels){
if(!identical(colnames(res), label_cell_types)){
colnames(res) <- label_cell_types
}
tmp <- reshape2::melt(res)
tmp$method <- method
tmp$true <- reshape2::melt(sim_labels)$value
return(... |
9be089a334e385a1a4520bbd90d1bf94afad7df76449b47afeaaf8d54ebe1387 | R | 26,837 | 472 | ---
title: "Getting Started"
csl: csl/apa-short-authors.csl
editor_options:
chunk_output_type: console
output:
html_document:
fig_height: 3
fig_width: 8
keep_md: yes
toc: yes
pdf_document:
latex_engine: xelatex
number_sections: yes
header-includes: \setlength\parindent{24pt}\setlength{\par... |
3c5c7403dd7c5549f761a5a4045831388b9101831a4a209e0c62a3f608210aa8 | R | 26,876 | 434 | #functions providng various diagnostics for evaluating model assumptions and stability and
#for helping with setting an appropriate random slopes structure for (G)LMMs
#written by Roger Mundry, last modified early 2016
ranef.diagn.plot<-function(model.res, QQ=F, col=grey(0.5, alpha=0.75)){
old.par = par(no.readonly ... |
4562f2d1c029d9fc13f45690e56f9cf12df5eb8ca1c1bbaa1527a0bb7203bc73 | R | 27,030 | 897 | ###################################################
# ~~~ FramebyFrame package ~~~
# various plotting functions
# except any that involves drawing an activity or sleep trace
# Francois Kroll 2022
# francois@kroll.be
###################################################
# function param2Title(...) --------------------... |
e3ad813da4e7ce9f3b2c3ce6ec60fc782943ed75ff0022e29c47a4bb8334ea73 | R | 27,054 | 662 | ---
title: "Supplements for Investigating the impact of vascular risk factors on the progression of white matter hyperintensities"
author:
- Frauke Beyer, PhD [1][2]
- Laurenz Lammer [2]
- Markus Loeffler [4][5]
- Steffi Riedel-Heller [5][6]
- Stéphanie Debette [1]
- Arno Villringer, Prof. [2][7]
- A. Ver... |
ebb9919a0b3ebe2d2048695fcb95674f0ea207968f49f146593078590a7eda71 | R | 27,341 | 743 | ###################################################
# ~~~ FramebyFrame package: ggFingerprint ~~~
# plotting functions for fingerprints
# Francois Kroll 2022
# francois@kroll.be
###################################################
# function ggFingerprint(...) ---------------------------------------------
#' Title
... |
47c9c1025206281fc9bed0290df6b3b7fb6c9a63a308b175f3fd901b646d290a | R | 27,360 | 736 | # Analyze DEG, Fig 2 and Fig 3 C,D
LIB='/cluster/tufts/patralab/rbator01/R_libs/4.0.0/'
.libPaths(c("",LIB))
suppressPackageStartupMessages({
library(org.Hs.eg.db)
library(tidyverse)
library(Seurat)
library(clusterProfiler)
library(org.Hs.eg.db)
library(ComplexHeatmap)
library(ggrepel)
library(openxlsx... |
b7ef7233266aa84a437465a542d3a5bda1ea9300b33ba63861d1577643046393 | R | 27,630 | 621 | #
# SeuratRun.R
#
#
# Created by Araks Martirosyan on 09/11/18.
#
#
SeuratV3Cluster <- function (FilteredDatabase, PCnumber = 10, res = 0.8, bias = c(), nFeature_RNAmin = 300)
{
obj <- CreateSeuratObject(FilteredDatabase, min.cells = 5, min.features = 1)
obj <- subset(obj, subset = (nFeature_RNA > nFeature... |
f1fa2b9cee96f8c9af881036763763617b9a755fff681305aa904239c234a4a0 | R | 27,651 | 589 | #!/usr/bin/env Rscript
#######################
# load data and results
#######################
e.keep = readRDS('filtered_expression_matrix.rds')
keep.genes = readRDS('keep_genes.rds')
meta = readRDS('cayo_bulkbrain_combined_metadata.rds')
meta = meta[order(match(meta$LID, colnames(e.keep))),]
emma.results = readRDS... |
8eb9b5077bef59ed81773cdbfcc0a1105410ff73cbc83351a8ccfd6b6c3e09a3 | R | 27,944 | 663 | ---
title: 'DADA2 pipeline'
output:
html_notebook
---
```{r knitr, echo=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Copyright (c) 2020 Respiratory Immunology lab, Monash University, Melbourne, Australia.
Converting amplicons nucleotides sequences from FASTQ files to a table of Amplicons Sequences Variants (ASV) us... |
c8342449daff7c879f6ae307344d62d09703d204ef077b1f77161c11d61d117b | R | 27,962 | 742 | #' heatmap3.LW.R
#'
#' This function runs differential gene analysis (linear modeling on normalized counts)
#'
#' @keywords heatmap
#' @export
#' @import gplots
#' @import dynamicTreeCut
#' @import WGCNA
#' @examples
#'
# AUTHOR: Freddie (Edited by Leanne Whitmore)
# DESCRIPTION: This was updated so that... |
0e0ee97493dce27555c000bf427376d65dc45f7d16c04dfe754db059b68acd38 | R | 27,974 | 783 | library(gdata)
library(lme4)
library(ggplot2)
library(reshape2)
library(LMERConvenienceFunctions)
library(parallel)
library(viridis)
library(readr)
library(plyr)
library(readr)
library(gdata)
library(lmerTest)
library(multcomp)
install.packages("readxl")
library(readxl)
#change path to correct path
D<-read_excel("/Use... |
56926f0c02df974cee9b594b27ba7f7026d9e8a8c7eca3af866ab6d6b1d638db | R | 28,276 | 619 | start_time <- Sys.time()
set.seed(123)
#this following code has already been published (Liu et al., 2022) and can be found at the following code
#https://github.com/liuyifang/FlyPhoneDB/blob/master/FlyPhone_parallel_batch.R
#the code has been simply reused to study cell-cell interactions in the control and tau P251L... |
ebac44ce2ce6843808f825ed47764eab1dd27bf4d153e38a6846340f761885ce | R | 28,625 | 635 | ### Frame-by-Frame package ###
### sleep from frames ###
# main function sleepFromFrames(...) detects inactive bouts longer than 1 minute in frame-by-frame deltapx data
# full explanation:
# Rihel lab usually uses middur parameter from xls results file written by Zebralab
# middur is duration by minute (seconds/minu... |
5dbabb1f62dac171a9def1f141dd4e4a2a4d9dc37e716c6b3d3e6e9e91dec7a0 | R | 28,658 | 598 | #'#################################################################################
#'#################################################################################
#' Compare stability of scores
#'#################################################################################
#'###############################... |
3b2163375509ccb5c444e38fb2fd98b27e33f6bda89717a6653b1846611c7c83 | R | 29,220 | 581 | ---
title: "Hierarchical Bayesian Analysis on Hierarchical Gaussian Filter"
csl: csl/apa-short-authors.csl
editor_options:
chunk_output_type: console
output:
html_document:
fig_height: 3
fig_width: 8
keep_md: yes
toc: yes
pdf_document:
latex_engine: xelatex
number_sections: yes
header-incl... |
3609fe40a3261aff7065b444ac0474479df084b24f60408130608e83ee23daed | R | 29,396 | 600 | ---
title: 'GDCRNATools: integrative analysis of protein coding genes, long non-coding genes, and microRNAs in GDC'
author: 'Ruidong Li and Han Qu'
date: "Last update: `r format(Sys.time(), '%d %B, %Y')`"
vignette: >
%\VignetteIndexEntry{'GDCRNATools'}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{... |
412472bd030d77c2f255517c20b828f351ff4058756fa6420720f9c644342765 | R | 29,463 | 637 | #'#################################################################################
#'#################################################################################
#' Run a meta-analysis in PRAD
#'#################################################################################
#'###############################... |
d623cdf19861575b08acb4d9c500938f99cd3c33d46b5d72f6acddf8c8c797e9 | R | 29,627 | 1,296 | ---
output:
word_document: default
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(EnvStats)
require(ggplot2)
require(car)
require(ggeffects)
require(emmeans)
require(lme4)
require(MuMIn)
require(coefplot)
require(nortest)
requir... |
e59a309b29429a9fadda9f475f086d790382805e018368d7a7ac9a02dd37c774 | R | 29,901 | 709 | source('~/scripts/single_cell/atac.R')
source('~/scripts/single_cell/wrapper.R')
source('~/scripts/single_cell/markers.R')
source('~/scripts/single_cell/celltype.R')
source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/graphs.R')
source('~/scripts/grn/models.R')
setwd('~/projects/cutntag/')
library(Seu... |
35147958249bb3d794a7a0ce812a9b7c6083e3b737d32b11feb39520fc2ffc90 | R | 29,996 | 889 | ---
title: 'Saldana, Montano, et al. -- 11 ATAC-seq: Annotation and enrichment analysis'
author: 'Florian Halbritter and Luis Montano'
date: '`r format(Sys.time(), "%B %d, %Y %H:%M:%S %Z")`'
output:
html_document:
toc: yes
toc_float: yes
code_folding: show
highlight: pygments
df_print: paged
par... |
fe9412a1f9faefc9f16d139d0fa18f2716474682e059a234f19928aaca220f92 | R | 30,014 | 727 | #!/bin/R
# Author: Nicole Gay
# 6 July 2022
# Set things up -----------------------------------------------------------------
library(MotrpacBicQC)
library(devtools)
library(usethis)
library(data.table)
library(sinew)
load_all()
data_dir = "motrpac/internal_releases/motrpac-data-freeze-pass/v1.1"
# Define tissue co... |
15b09966e0fac2294f70f14bf113a8cf9885daef5e0d267e81ea9c19b6480891 | R | 30,149 | 782 | ---
title: 'Saldana, Montano, et al. -- ATAC-seq: GRNs and target scores'
author: 'Florian Halbritter'
date: '`r format(Sys.time(), "%B %d, %Y %H:%M:%S %Z")`'
output:
html_document:
toc: yes
toc_float: yes
code_folding: show
highlight: pygments
df_print: paged
---
# Intro
In this notebook, we... |
fa044988558d487e43ca607d2f3b09f7e37797d566a4a34e93c05b1a6e0844a8 | R | 31,410 | 726 | ##-------------------------------------------------------
## SEURAT ANALYSIS | MODULES & LIBRARIES
##-------------------------------------------------------
# module purge && module load shared slurm python/3.7.x-anaconda
# module load gcc/8.3.0
# module load hdf5_18/1.8.17
# module load R/4.1.1-gccmkl
##-------------... |
095a7aa78043c053ed7b815ff79ad3b099594b3239319f3dd70822924b8666f4 | R | 31,496 | 741 | ---
title: "Download metabolomics sample-level data"
author: "Pierre M Jean Beltran, Nicole Gay"
date: "7/16/2022"
output: html_document
---
```{r setup, include=FALSE,echo=F}
library(data.table)
library(MotrpacBicQC)
library(MotrpacRatTraining6moData)
library(MotrpacRatTraining6mo)
library(dplyr)
library(testit)
libr... |
848823875feb5d9b401ffffc0d0b4515ab625b54979d8fa95552e2ccc5b09d72 | R | 31,831 | 728 | #!/usr/bin/env Rscript
library(optparse)
options(stringsAsFactors=FALSE)
##################
# OPTION PARSING
##################
option_list <- list(
make_option(opt_str = c("-l","--in_dir"),
type = "character",
default = NULL,
help = "Input directory",
meta... |
8f483311a3775f01f3b5904192f30c4dc179735d25c032c0c907bcf585a24792 | R | 31,972 | 872 | ## ---------------------------
##
## Script name: Transcript level differential expression
##
## Purpose of script: Using salmon transcript counts, perform differential gene and transcript expression
##
## Author: Prakhar Bansal
##
## Date Created: 2021-08-24
##
## Copyright (c) Prakhar Bansal, 2021
## Email... |
bd99d6234baee5172435c8da1b0e3357731c6fb5831bf0328d52a55f9b76672f | R | 32,131 | 698 | #### GEDI biosensor or GEDI-CNN analysis code
###This code will transform voronoi tracking output and
###GEDI biosensor measurements and/or GEDI-CNN output into the following outputs:
###survival analysis, co-variate of death analysis, plate
rm(list=ls())
library(lme4)
library(stringr)
library(splines2)
li... |
b8ce573c644b1eaf95efb0fafb11464ad6af364f6e0eda807399512d2e56f34a | R | 32,613 | 907 | ---
title: "final plots - ee revisions -- realistic"
author: "Sam Ozminkowski"
date: "2023-10-22"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(grid)
library(gridExtra)
library(cowplot)
library(emojifont)
```
# Final plots
- We will base the plots on the existing fu... |
020b60feed003f43d2851b96c024d227ad0c87d85394d3ac705db0315d41a989 | R | 33,184 | 808 | #colocquial.R
#This script performs colocalization between a trait of the user's interest and the GTEx single trait eQLTs or sQTLs from
# the GTEx online GUI. It will perform colocalization for each gene-tissue pair in the GTEx csv file downloaded
# from the online GUI. NOTE it currently assumes you wish to use The GTE... |
3d769270bf0aa0507696562465cbd8d1ecb622bdb0d5f51aa101e92693e1d9d4 | R | 33,530 | 1,208 | #' @noRd
#' @keywords internal
alt_preprocess_func <- function(raw_data, general_info) {
# Currently class(raw_data) == "data.table"
# Use general_info of raw_data
subjs <- general_info$subjs
n_subj <- general_info$n_subj
t_subjs <- general_info$t_subjs
t_max <- general_info$t_max
# Initialize (mo... |
44d73d1b4e52c6a5cc982000c3e74e6c5391d24e5a59d6692747169c817f8de0 | R | 34,376 | 814 | #!/usr/bin/env Rscript
library(MOFA2)
library(tidyverse)
library(DESeq2)
library(org.Mm.eg.db)
library(org.Hs.eg.db)
library(argparse)
#pathway enrichment
library(data.table)
library(purrr)
library(ggplot2)
library(cowplot)
#library(MOFAdata)
#library(msigdb)
library(msigdbr)
library(reshape2)
library(pheatmap)
varia... |
05f76aa65706038ea9a5cb47b0e10535cf41bce2adb33d72e9a0ef333201ab6c | R | 34,379 | 968 | ---
title: "final plots - ee revisions"
author: "Sam Ozminkowski"
date: "2023-10-22"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(cowplot)
library(emojifont)
library(grid)
library(gridExtra)
```
# Final plots - Realistic Simulations
- We will base the plots on the ... |
365f9f7f1625799f41e1d472ed3440a2159e03a55422ac7c483bf6f56936ec53 | R | 34,635 | 664 | ---
title: "*Drosophila* Time Series - Single Fly Quality Control Report Sheet"
output:
html_document:
number_sections: true
toc: true
toc_float: true
---
<style type="text/css">
body .main-container {
max-width: 1800px !important;
}
h1.title {
font-size: 38px;
color: DarkRed;
text-align:... |
9b8bee6e4c61c2ace1130ff78279cc769b58e2ce8904cf39668d67c1981825f9 | R | 34,684 | 764 | #colocquial.R
#This script performs colocalization between a trait of the user's interest and the GTEx single trait eQLTs or sQTLs from
# the GTEx online GUI. It will perform colocalization for each gene-tissue pair in the GTEx csv file downloaded
# from the online GUI. NOTE it currently assumes you wish to use The GTE... |
3185c826b823c0f1b169c432522bd5fe0d37286b447e54b111d4ed5fc86f4214 | R | 34,810 | 825 | ---
title: "figures nasa rr3"
author: "Yuvarani Masarapu"
date: '2022-07-12'
output: html_document
---
# Libraries
```{r lib-load, message=FALSE, warning=FALSE, echo=FALSE}
library(Seurat)
library(SeuratObject)
library(STutility)
library(ggplot2)
library(patchwork)
library(dplyr)
library(data.table)
library(Signac)
li... |
2b99ccac04848654461ce90681ac5d2f3547a2e3755f4b06c3b4223459487ee3 | R | 35,212 | 1,005 | library(tidyverse)
source('~/scripts/single_cell/wrapper.R')
source('~/scripts/single_cell/de.R')
library(Signac)
library(Seurat)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)
select <- dplyr::select
Matrix <- Matrix::Matrix
setwd('~/projects/cutntag/')
rank_cols <- function(x){
xr <- presto:... |
9747df093d1ccca5601a0c4b42d26bca512b66dfb1c309abf24a955a6bd0fc59 | R | 35,240 | 864 | ###################################################
# ~~~ FramebyFrame package ~~~
### ggParameter ###
# functions to plot parameters
# Francois Kroll 2022
# francois@kroll.be
###################################################
# function ggParameter(...) -----------------------------------------------
# expects ... |
57442328e5038e585b9d7d2befc678d2001a33fe792df19edcd40e886be80d98 | R | 35,367 | 752 | #' Ancestry-Informed STAAR-SPA procedure using omnibus test
#'
#' The \code{AI-STAAR_Binary_SPA} function takes in genotype, the object from fitting the null
#' model, and functional annotation data to analyze the association between a
#' imbalanced case-control phenotype and a variant-set by using an ancestry-informed... |
ade875b7f8121f0d10291171687377d8f26a3f2521ad3f9dc9882b2d23f3264d | R | 35,493 | 1,121 | ---
title:"BrainAge_VidalPineiro_ModelGeneration(XGB; Lifebrain replication)"
author: "DVP"
date: "12/27/2020"
output: html_document
---
# Setup
```{r setup, include=T}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(magrittr)
library(janitor)
library(ggridges)
library(xgboost)
library(mgcv)
library(GGal... |
992cf431f557be3cfe91bfe5ee542c56a865dcd745d6fcc412e8d78b1e2e4e87 | R | 35,556 | 901 | ---
title: "Saldana, Montano, et al. -- scRNA-seq: 03_WT_marker_analysis"
author: "Luis Montano"
date: '2023-08-07'
output: html_document
params:
inputdata: '~/path/to/input_data/'
plotpath: '~/path/to/plots/'
cachedir: '~/path/to/cachedir/'
outpath: '~/mnt_out/figures/'
resourcepath: "~/mnt_resources/"
fig... |
2fe042f8a52565c4e8e5d52793c6746c72274318e69b87ab9f271ea474eb2ec1 | R | 35,787 | 770 | ---
title: 'DADA2 pipeline'
output:
html_notebook
---
```{r knitr, echo=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
Copyright (c) 2022 Respiratory Immunology lab, Monash University, Melbourne, Australia.
Converting amplicons nucleotides sequences from FASTQ files to a table of Amplicons Sequences Variants (ASV) us... |
c82d73601672beccd783fe3d4109dd7a500a76b747a13a0c065b004fd00fcbee | R | 35,826 | 1,072 | ###################################################
# ~~~ FramebyFrame package ~~~
# ggTrace
# every plotting function that involves drawing an activity or sleep trace
# Francois Kroll 2022
# francois@kroll.be
###################################################
# function ggActivityTraceGrid(...) ---------------... |
681b051bca6aa3c4f0ec2132b1a4668a3443ac9a40ff1d2018c84279c4a80413 | R | 36,431 | 1,093 | #' @importFrom ggplot2 ggplot_add geom_segment
#' @export
ggplot_add.geom_panel_grid <- function(object, plot, object_name) {
obj <- geom_segment(aes_string(x = "x", y = "y", xend = "xend", yend = "yend"),
data = get_grid_data(plot$data, drop = drop),
colour = object$colour... |
89755d2e3adfcd770da1486268a0015f3a09e3b75e5cd0af2e957b621b42bbe5 | R | 36,559 | 937 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
source('~/scripts/perturbator/enrichment.R')
library(Pando)
library(SeuratWrappers)
library(harmony)
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
Matrix <- Matrix::Matrix
setwd('~/p... |
5ce85091e9d0ac409b7215c28bb64972a28a238cc9b9c0713392a14ab3abc1f3 | R | 37,127 | 877 |
################################################################################
# Transform dat0 methylation data and filter #
# #
############################################################################... |
cd166852b6df612e3610d0a2d5d19fcbc5f8512d39fd3abe97114557eb5d4da9 | R | 37,757 | 885 | # run_spp.R
# =============
# Author: Anshul Kundaje, Computer Science Dept., Stanford University
# Email: akundaje@stanford.edu
# Last updated: Oct 8, 2010
# =============
# MANDATORY ARGUMENTS
# -c=<ChIP_tagAlign/BAMFile>, full path and name of tagAlign/BAM file (can be gzipped) (FILE EXTENSION MUST BE tagAlign.gz, t... |
6960a2872fcbc7ec3eda2d1f4395ec3495e2af2216b8248f9d18edfa8901ec95 | R | 38,106 | 1,037 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
library(doParallel)
setwd('~/projects/cutntag/')
select <- dplyr::select
filter <- dplyr::filter
#### Read data ####
marks <- read_rds('data/all_marks_list_v3.4lines.rds')
rna <- read_rds(... |
58c3e61f37045658e0e6441c329dea2368b8dbbaf0fe5a943f57655425260c21 | R | 38,118 | 1,004 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
library(destiny)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
Matrix <- Matrix::Matrix
setwd('~/projects/cutntag/')
rank_cols <- function(x)... |
c6c550ab4490404cad4804c20543165003f5450f514df0cae2b4879abd4f97cd | R | 38,401 | 915 | ############################################################################################
# Copyright (c) 2024 - Mucosal Immunology Lab, Monash University, Melbourne, Australia #
# Author: Matthew Macowan #
# This script is provided under the MIT l... |
6a14514f099b1dccd98c35f28c386b63bafaa7784334ff9ba4c973e086450239 | R | 38,474 | 804 | # bulkRNAseq------------------------------------------------------------
## setup----
# load library
easypackages::libraries(c('recount3','edgeR','tidyverse','org.Hs.eg.db','patchwork','fgsea','msigdbr'))
# load objects
save.path <- 'object folder path'
d <- readRDS(paste0(save.path,'edgeRobj.rds'))
lcpm <- edgeR::cpm(... |
e24a76c1728421056c6eaed1e42b839105b15f2fc89676f92ab2b6d3df594d65 | R | 38,708 | 593 | # Plotting functions for each model
plot_gng_m1 <- function(obj, font_size = 10, ncols = 3, bin_size = 30) {
pars = obj$par_vals
h1 = plot_dist(sample = pars$mu_xi, font_size = font_size, bin_size = bin_size, x_lim = c(0, 1), x_lab = expression(paste(xi, " (Noise)")))
h2 = plot_dist(sample = pars$mu_ep, font_siz... |
a5d7ccecf29bce14b202537bc37d691a9df5972f62209e41f98ee62b5dbbf57a | R | 38,742 | 932 | ---
title: "Ventral analysis N+"
output:
word_document: default
html_document: default
pdf_document: default
date: "2023-01-17"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(pacman)
p_load(tidyverse, ggsignif,multcomp, broom, emmeans, DescTools)
setwd("~/Documents/ESYT1_s... |
a9656fb6e47c77124933dfa474ec56fa2be9278d9d20fdb50ef9c5a266f847f3 | R | 39,478 | 776 |
###############################################################################################################################################
# DEFINING COLORS
###########################################################################################################################... |
b7e1b20cb523af32cda4ed18cbc4a51dc68a07e483dfea26dafc816e9925e766 | R | 39,947 | 559 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
f105b642a6df549abfca4e6126f4412f64ee47e13a01ddb4dd7b976f4e8681dc | R | 40,138 | 1,033 | ---
title: "Saldana, Montano, et al. -- scRNA-seq: Import and quality control and initial integration of all ncnb datasets "
author: '`r Sys.info()["user"]`'
date: '`r format(Sys.time(), "%B %d, %Y %H:%M:%S %Z")`'
output:
html_document:
toc: yes
toc_float: yes
code_folding: show
highlight: pygments
... |
6538f94c33b5fbe4638dac772017d21efb6b1ca93809203e843d209719a7da51 | R | 40,939 | 1,001 | ---
title: "Saldana, Montano, et al. -- 09 patients_bulkrnaseq developmental signatures"
author: "Luis Montano"
date: '2023-11-14'
output: html_document
params:
inputdata: '~/path/to/input_data/'
plotpath: '~/path/to/plots/'
cachedir: '~/path/to/cachedir/'
outpath: '~/mnt_out/figures/'
resourcepath: "~/mnt_re... |
98ca0fe6c91bdbfbe5b481be329b45237425a7adbc11001b89cb1b7648a72c00 | R | 40,951 | 704 | #####load Libraries ####################
library(readxl)
library(dplyr)
library(tidyr)
library(matrixStats)
library(ggplot2)
library(gridExtra)
library(reshape2)
library(lubridate)
library(readr)
rm(list = ls())
Sys.setenv(TZ = "Etc/GMT-1")
dt_all <- c()
##########
# LLT Data
##########
###########################... |
b1bcf5921ced356bfcb4b14a42b71d1082ce85920f5a14d901bf9d8d7e5b4d4b | R | 41,522 | 919 | #library(kit)
library(readxl) #read xlsx, ods etc.
library(tidyverse) #includes ggplot2, dplyr, tidyr, readr, tibble, stringr ...
library(lubridate) #package to work with data and time
#library(eeptools)
#library(data.table)
library(naniar) # helps to deal with NA
#library(lme4)
#library(stringr)
library(mice)
#Prepar... |
08554eb0b9ae77dcc4a049cb10ea1d0fc553b3ccd0c7c3310f4bf1f8de2013c5 | R | 41,936 | 925 | #library(kit)
library(readxl) #read xlsx, ods etc.
library(tidyverse) #includes ggplot2, dplyr, tidyr, readr, tibble, stringr ...
library(lubridate) #package to work with data and time
#library(eeptools)
#library(data.table)
library(naniar) # helps to deal with NA
#library(lme4)
#library(stringr)
library(mice)
#Prepar... |
f54ca8e08505221b5069ed17ef6495c781705c3ddac2c82a88a9458e6eb2e54c | R | 43,310 | 1,111 | ### Frame-by-Frame package ###
### behaviour parameter ###
# main function is behaviourParameter(...)
# function splitFramesbyDayNight(...) -------------------------------------
# path = path to any file in the experiment folder that is YYMMDD_...
# ! assumes vpSorter(...) was run and wrote YYMMDD_BX_lights.csv wit... |
354bc64b79220c18ecde0d1a96fe89985c241af6e0551e2f17e3c4c19fc8b1bf | R | 43,694 | 1,085 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
library(destiny)
library(dtw)
filter <- dplyr::filter
select <- dplyr::select
setwd('~/projects/cutntag/')
rank_cols <- function(x){
xr <- presto::rank_matrix(t(x))$X_ranked
colnam... |
3d013986c040620bd52076f6a3ffaa339199f9b075c97ffcb88de30b9129b1e0 | R | 44,421 | 1,179 | ---
title: 'Saldana, Montano, et al. -- ATAC-seq: Comparisons to public data'
author: 'Sara Wernig-Zorc & Florian Halbritter'
date: '`r format(Sys.time(), "%B %d, %Y %H:%M:%S %Z")`'
output:
html_document:
toc: yes
toc_float: yes
code_folding: show
highlight: pygments
df_print: paged
---
# Intr... |
40971058661191f1b02657a1aa6c7577615c60332a8053b01d8abad920856bef | R | 44,790 | 1,362 | ---
title: "BrainAge_VidalPineiro_ModelGeneration(XGB & LASSO)"
author: "dvp"
date: "11/2/2020"
output:
html_document: default
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(kableExtra)
library(cowplot)
library(psych)
library(boot)
library(tidyverse)... |
240e29ff4e73faaee6c51b0c53925bb2de21ac353810c75279d2ab6bcccd648f | R | 45,848 | 1,262 | ---
title"BrainAge_VidalPineiro_Tests(early life v. aging) (XGB & LASSO)"
author: "dvp"
date: "11/2/2020"
output:
html_document: default
pdf_document: default
---
# Setup
```{r setup, include=FALSE}
#install.packages("~/R/imported_packages/3.6.0/itsadug_2.3.tar.gz", repos = NULL, type = "source")
knitr::opts_chunk... |
afc646aa133492e2cc711af8e934d9dbc1c81e75cc15b266b03b26e96f4a858b | R | 46,628 | 1,403 | ---
title: "RNA-seq + ATAC-seq, all brain data"
author: "Jakub Orzechowski Westholm"
output:
html_document:
code_folding: hide
toc: true
toc_float: true
toc_depth: 5
collapsed: false
number_sections: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning=FALSE, messag... |
83ef97138e3b760516d04ff4862834281639cd7d9df01c5e6a3a59f2458e7a30 | R | 46,684 | 789 | #------------------------------------------------------------------------#
#############PROJECT: infection & child brain development#################
#------------------------------------------------------------------------#
# Author: Anna Suleri
### Parts in this script:
#' Part 1: Loading, cleaning, renaming data a... |
9ea6779cd07d8b361143d8c5df00d07e41195e4a4c3f7246ae978455c1d4e1ca | R | 46,706 | 1,123 | ##############-- Libraries--##############
options(mc.cores = 8)
library(SetRank)
library(GeneSets.Homo.sapiens)
library(stringr)
library(factoextra)
library(umap)
library(amap)
library(ggplot2)
library(mclust)
library(dendextend)
library(limma)
library(edgeR)
library(Rtsne)
library(corrplot)
library(fossil)
library(sv... |
7b5c99ddbb24570927a80aa3291f295df9ccee2a29d4ac09fc47976f565d348b | R | 46,828 | 1,134 | ### Functions for CCC in AD project
# Tabea M. Soelter
## remove_ambientRNA
# A function which removes ambient RNA from h5 files outputted from Cell Ranger for single cell data.
remove_ambientRNA <- function(inputs, outputs, plots) {
print("Making list of objects")
counts_list <- list.dirs(inputs,
... |
ae13c37591b1b4fc71393cfe69e50c353262d6fb25af4d67b302e35224e00d9f | R | 46,885 | 990 | ######################################################################################################################################################################
#
# LEMON behav analysis script
# Run regression models and Bayes Factor analysis for
# Time-reso... |
d8a454251992db770a77fa3ec5628e38f955faaf435d7e9ccc2108a50a04edd9 | R | 47,149 | 929 | # EpiTrace: package for computing cell age and phylogeny from ATAC-seq data
# Zhang Yi, <synapse@pku.edu.cn>
#' Negated Value Matching
#'
#' This function is the reciprocal of %in%. See the match funciton in base R.
#'
#' @param x The value to search for in `table`.
#' @param table The set of values to serve as the b... |
ff9a2f4321102430b2af192f2eee9f63180b1959b5d89204785a3dcbe0df8f5b | R | 47,324 | 692 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
f705e975c964c0eeea25aaedeee0243009b0f45f04364a836b124d2960e7b9de | R | 47,875 | 415 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
38b06283aa21ec195beb7c1b9967265203bfc24a5063a9de2b7cda94d95c38ee | R | 47,910 | 416 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
ff6e9282c1c6b2a6f431cd5cc110de6df37862aa94dab40971f038b8c611a136 | R | 49,091 | 1,215 | library(tidyverse)
source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/wrapper.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
Matrix <- Matrix::Matrix
setwd('~/pr... |
96855d0a8904b8e58af69304e5fbdfcbe0bb4df9263954cf262693e6219bd03b | R | 49,553 | 1,076 | #!/usr/bin/env Rscript
### Work up vast-tools output, save tables and do a few analysis of changing events
###
### U. Braunschweig 2019-2020
###
### Changes: Option 'depth' has been replaced with 'filter', with the default settings now allowing
### a quality score of OK/LOW/VLOW for CE/MIC depth and OK/B1/B2... |
d628e2531e11195e3b1aa7e90f2f0870029df9e2d527c971aa4916087f04dad5 | R | 49,753 | 1,735 | require(RColorBrewer)
require(gplots)
require(pheatmap)
require(glmnet)
require(rsvd)
require(qvalue)
#' @keywords internal
#' find the common rows of two data matrices
#' @param data1 first data matrix
#' @param data2 second data matrix
commonRows=function(data1, data2){
intersect(rownames(data1), rownames(data2))... |
4b01d8aec28b679dc2ba1f777dd4ffa85537863410f776c5b3aebb266e2bf110 | R | 49,813 | 999 | library(tidyverse)
library(ggpmisc)
library(interactions)
library(ggtext)
library(modelsummary)
######################### data preparation #####################################
#define remove_outliers function
remove_outliers <- function(x, na.rm = TRUE)
{
## Find 25% and 75% Quantiles using inbuild function
quan... |
96a195af26490cd46f33cfca244fbe8d79aac6cac925b56d755e7f286bee24a7 | R | 50,198 | 1,091 | #!/usr/bin/env Rscript
### Work up vast-tools output, save tables and do a few analysis of changing events
###
### U. Braunschweig 2019-2024
###
### Changes: New option --vastMain
cArgs <- commandArgs(TRUE)
## Check dependencies
libMissing <- !require("optparse", quietly=T) && stop("Failed to load R package 'optpars... |
ca465daccd9aae4c8a262e6048c68061e6cce7675f5227a4cf5656000c652ebe | R | 50,217 | 1,247 | library(tidyverse)
source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
library(ChIPseeker)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)
library(rGREAT)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::sele... |
dca0c085c8cb86a22f8f6fd394f3ecb3c3a92ff83dd0d4e913448595ba8aa349 | R | 51,660 | 731 | #------------------------------------------------------------------------#
#############PROJECT: infection & child brain development#################
#------------------------------------------------------------------------#
# Author: Anna Suleri
### Goal of this script: make a flowchart and baseline table & figures ... |
60caafe69d44d6a85f15429a082eeccfafcb27dbb9f2710a2c0f7fc70af0bc0b | R | 52,270 | 1,327 | ---
title: "Saldana, Montano, et al. -- scRNA-seq: 04 full dataset analysis, cell type identity analysis, mutation score."
author: "Luis Montano"
date: '2023-08-07'
output: html_document
params:
inputdata: '~/path/to/input_data/'
plotpath: '~/path/to/plots/'
cachedir: '~/path/to/cachedir/'
outpath: '~/mnt_out/f... |
1c3ab7354defb815714e2b7b2dd8d22b31d46790a2d08b785837b0da907ea7a0 | R | 52,522 | 1,084 | #R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
#RStudio 2023.03.0+386 "Cherry Blossom"
rm(list = ls())
# environment ####---------------------------------------------------------------
# install.packages("renv")
# Step 1: initialize a project level R library
# renv::init()
# Step 2: save the current status ... |
7f08b8a532f6ddfc96de4ae947d844c66bbeaf221afc8a051d36966e122dc77d | R | 52,895 | 1,349 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
setwd('~/projects/cutntag/')
#### Read data ####
marks <- read_rds('data/CT/all_marks_list_v3.3... |
41496e9f29ae88af002ca3201cb9c2e00cb57d5022ef8260aece22206c73818a | R | 57,520 | 1,716 | ######
# Parameters
#
path_home <- './'
# Working directory with temperature data
setwd(path_home)
# Libraries to use
library(readr)
library(tidyr)
library(purrr)
library(ggplot2)
library(lubridate)
library(jsonlite)
library(dplyr)
library(stats4)
library(gridExtra)
library(grid)
library(stats4)
library(bezier)
libra... |
9d9721b01c9db516ce2fce48bbbf88e1b2454bbd848a2e54e3dd5059cc34d86c | R | 58,224 | 1,161 | ######
# Parameters
#
path_home <- './R'
# Working directory with temperature data
setwd(path_home)
# Libraries to use
library(readr)
library(tidyr)
library(purrr)
library(ggplot2)
library(lubridate)
library(jsonlite)
library(dplyr)
library(stats4)
library(gridExtra)
library(grid)
library(stats4)
library(bezier)
libr... |
1577cd9506b99414e8eada2469a501ef1131353c4844faacfbb032623b22fd16 | R | 58,347 | 1,498 | ---
title: "Saldana, Montano, et al. -- scRNA-seq: 04_WT_projecting_other_cell_lines_onto_wildtype"
author: "Luis Montano"
date: '2023-08-07'
output: html_document
params:
inputdata: '~/path/to/input_data/'
plotpath: '~/path/to/plots/'
cachedir: '~/path/to/cachedir/'
outpath: '~/mnt_out/figures/'
resourcepath... |
c5f066ffd11e0d5836fe7da9d478f7688ec91bc9933e506f5b098f631d3d9114 | R | 59,993 | 1,302 | #' Ancestry-Informed STAAR procedure using omnibus test
#'
#' The \code{AI-STAAR} function takes in genotype, the object from fitting the null
#' model, and functional annotation data to analyze the association between a
#' quantitative/dichotomous phenotype and a variant-set by using an ancestry-informed STAAR procedu... |
ee2fd490b9b83ff0ba5dc4202334612d42126f5ab7453c8a73773748d80355a8 | R | 60,992 | 1,642 | title: "Saldana, Montano, et al. -- scRNA-seq: 06_WT_projecting_patients' cells_onto_wildtype"
author: "Luis Montano"
date: '2023-08-07'
output: html_document
params:
inputdata: '~/path/to/input_data/'
plotpath: '~/path/to/plots/'
cachedir: '~/path/to/cachedir/'
outpath: '~/mnt_out/figures/'
resourcepath: "~/... |
1cc45f5e31cb6579c2ba0b845dc8584a78481ab6a9265cc562f330e246540058 | R | 61,106 | 1,375 | ###################################################
# ~~~ FramebyFrame package ~~~
# VpSorter
# function VpSorter to sort raw xls files
# Francois Kroll 2022
# francois@kroll.be
###################################################
# VpSorter was previously a script, which went up to v15
# so the present function co... |
3131588e54c0111bab37ecaefac789d7204004a2553a6a4e58ec8b1b7dffdd35 | R | 61,253 | 1,492 | # Mate choice in the brain WGCNA
# housekeeping: clear all existing data
rm(list = ls())
library(WGCNA)
library(car)
library(genefilter)
library(reshape2)
library(ggplot2)
library(circlize)
library(ComplexHeatmap)
# The following setting is important, do not omit.
options(stringsAsFactors = FALSE)
##############... |
4965bb2cd6116bf863dfca218a7320eb2d8754b57c461ddc6c5e69912a68b83c | R | 64,385 | 1,781 | ######
# Parameters
#
path_home <- './'
# Working directory with temperature data
setwd(path_home)
# Libraries to use
library(readr)
library(tidyr)
library(purrr)
library(ggplot2)
library(lubridate)
library(jsonlite)
library(dplyr)
library(stats4)
library(gridExtra)
library(grid)
library(stats4)
library(bezier)
libra... |
a3f89cc97ec73e01accbd7a74d6cf54078465f33cebc4a0dbf3954a54d5fe085 | R | 65,288 | 2,759 | # Final plots
- We will base the plots on the existing functions in [plot_result.R](https://github.com/samozm/bayesian_network_regression_imp/blob/main/additional_materials/plot_results.R).
- The result files are in the [Google Drive](https://drive.google.com/drive/u/2/folders/1obkVu6qJfC6tdNAnLFHhsSSn9SUwTxE2) which ... |
c3228a8bc483bc70bb3e9d790f73e91d4e99286c3ebdd39c257dee7d5387281d | R | 65,334 | 1,450 | ###Read Data
PriCog<-read.csv("~/PriCogSubmit.csv")
rownames(PriCog)<-PriCog$species_scientific
###Read tree
PriCogtre1<-read.tre("~/PriCogtre1.tre")
library(car)
library(lme4)
library(ape)
library(phylolm)
library(mulTree)
`%ni%` = Negate(`%in%`)
##Function
extract_pMCMC<-function(model_name) {
Files<-NA
Files<-... |
f3d9381fb9198a77bd5f6398ee1e77bf0bd45a079761d25e5fa4876c29d47c69 | R | 65,725 | 2,089 | #### Code for plotting survival curve in Lam, Ndayisaba et al 2024 Neuron FIGURE 8G LEFT
#### HCNT114 shRNA MOI20
# 6/16/23: HCNT114 (3K-sfGFP/sfGFP + shRNA-RHOA/control at MOI5,10,20) run with Nikon BioStation Survival v2 software
##################################################################################... |
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