sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
946591e84e2dbeeb63291b7ea2b0f2d1827569c14439d1cfb8c9acb98dbd164a | R | 9,594 | 328 | ---
title: "SF, LR AI DW | 24H WD vs Control 1 groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_optio... |
371ca7436c763ed6cea2576a3c5cf328c8985c671215a245ddffd43ead2fa24c | R | 9,658 | 443 | #!/usr/bin/env Rscript
# ==============================================================================
# 10a. Validate Seurat objects and export count matrices for TF analysis
#
# Description:
# This script validates one or more Seurat objects listed in
# config/sample_manifest.csv and exports the raw count matrix an... |
9d33978034eb748e5511b34bc6f20f2caf67b1166b898411aab464be8b5904f0 | R | 9,672 | 193 | # Preprocessing Experiment 2: SoupX correction, QC, doublet removal, merge, SCTransform, Harmony
# Run this script with working directory set to the project root
library(Seurat)
options(Seurat.object.assay.version = "v5")
library(DoubletFinder)
library(sctransform)
library(dplyr)
library(stringr)
library(patchwork)
li... |
4a3c7b872d095b8d6ae67591a3f22a9ceaee6f4fe4f174213dee03bdba2e36a5 | R | 9,679 | 206 | get_means_sds <- function(cell_type, gene, de_results_list, params_to_test) {
de_results <- de_results_list[[1]]
ct_ind <- which(colnames(de_results$gene_fits$mean_val) == cell_type)
L <- dim(de_results$gene_fits$s_mat)[2] / dim(de_results$gene_fits$mean_val)[2]
ct_ind <- L*(ct_ind - 1) + params_to_test
means... |
e3490386976cacbf2e4a66b0a9fbb820e1c573999a1b0314ccf7edb438598f39 | R | 9,732 | 168 | #Rscript.exe diffExprTestT1way.r "L:/promec/TIMSTOF/LARS/2022/oktober/Ida Beate/sample10_CTR/combined/txt/proteinGroups.txt"
#setup
#install.packages(c("readxl","writexl","svglite","ggplot2","BiocManager"),repos="http://cran.us.r-project.org",lib=.libPaths())
#BiocManager::install(c("limma","pheatmap"),repos="http://cr... |
071fd2df84ac24d00c1e0d613044e26a32942e11bba94adff3f2ab584b64b811 | R | 9,746 | 336 | ---
title: "SF, LR AI DW | 24WD vs Sp groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
ch... |
c542ebff7af6c67e752b373192c515dfb9ed5d2054e61cef803ea1b1f35aa2ff | R | 9,749 | 172 | #follow up from C:\Users\animeshs\scripts>..\R-4.4.0\bin\Rscript.exe diffExprTestT.r L:\promec\TIMSTOF\LARS\2025\250411_HISTONE_SAHA\combined\txt\proteinGroups.txt L:\promec\TIMSTOF\LARS\2025\250411_HISTONE_SAHA\combined\txt\Groups.txt "Bio" "Rem" "LFQ.intensity." "SAHA" "CTR" 0.1 0.5 0.15
#..\R-4.4.0\bin\Rscript.exe ... |
a05a8697b095fa74243ffee1e41ebfdc8ddf8b59cc3b5cd1d34044b6f6e4eecd | R | 9,750 | 327 | ---
title: "SF, LR AI DW | Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_floa... |
23b7aac2d57ae8e0a229baae030310617ce03522af976196cc8ed493e29efa7e | R | 9,850 | 336 | ---
title: "SF, LR AI DW | WD vs Sp vs Control 2/3 groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_... |
ac5d8f18a8b0ce9dfc3fd261bbb8f472901383fb166465c53c19436157abe334 | R | 9,875 | 304 | #!/usr/bin/Rscript --vanilla
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation file... |
78d2fc36e5fb68ea7cd220d140bb1dbd3ff99f1289372965eb8ee2ec31eed07b | R | 9,909 | 178 | ---
title: "Applying CSIDE to Spatial Transcriptomics Data: Multiple regions in Visium with full mode RCTD"
author: "Dylan Cable"
date: "December 20th, 2021"
output:
html_document:
keep_md: yes
pdf_document: default
rmarkdown::html_vignette:
keep_md: yes
vignette: |
%\VignetteIndexEntry{visium-full-regi... |
4f35da4e209f4f642a8b87158eb2fdb1f65315b43b3f7593dcd00a9f6d13852e | R | 9,911 | 335 | ---
title: "SF, LR AI DW | Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_floa... |
738395ff2efb51cdfbb6db49510671cdb47deef932d8f0ce71d824d50e60f2b9 | R | 9,925 | 306 | rm(list = ls())
options(stringsAsFactors = FALSE)
suppressPackageStartupMessages({
library(rstan)
library(matrixStats)
library(dplyr)
})
# =========================================================
# 0) Path settings: modify these paths as needed
# =========================================================
# ---... |
5e2b26b566b13fee1dcff1330d9c5067836900d1bf99bc94d715b4b567e67f4c | R | 9,952 | 52 | library(clusterProfiler)
library(org.Hs.eg.db)
# Define the list of genes
# ECCITE
gene_list <- c('TERT', 'KLRD1', 'FABP6', 'SCGB1B2P', 'KLHL31', 'NXPH3', 'AC098973.2', 'NUTM2B', 'CD207', 'SDK2', 'LRCOL1', 'RP11-55K13.1', 'PLA2G4B', 'BTNL2', 'ZNF503-AS1', 'PDE6A', 'RP5-827C21.6', 'RP11-981G7.2', 'TAL1', 'KRTAP5-9', 'A... |
b16f6511233f47d6a51c4e4aae714a15b8559e6f5d5a2f2e4c007bb27d56e0ad | R | 10,003 | 180 | ---
output:
html_document:
keep_md: true
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, cache.lazy = FALSE, results = 'hide')
```
# CSIDE on the Slide-seq cerebellum
### Visualize cerebellum regions
```{r fig-1, fig.height = 6, fi... |
89128710b7a4ea0261f3b8d829061e0478c2ed44d987402a610cc489a675525b | R | 10,022 | 234 | # Preprocessing Experiment 1: QC, doublet removal, merge, SCTransform, Harmony integration
# Run this script with working directory set to the project root
library(Seurat)
options(Seurat.object.assay.version = "v5")
library(DoubletFinder)
library(sctransform)
library(dplyr)
library(stringr)
library(patchwork)
library(... |
da2339b72e7d17e2c5ef631acbb1af5644b40795ca83a75dc3e0708088585891 | R | 10,047 | 193 | #C:\Users\animeshs\R-4.2.3\bin\Rscript.exe diffExprTestRank.r L:\promec\TIMSTOF\LARS\2023\230217_Caroline\combined\txt\ Bio
#https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cmdscale
x <- loc[, 1]
y <- -loc[, 2] # reflect so North is at the top
## note asp = 1, to ensure Euclidean distances are repre... |
751ee0efda90dab0f121b31a3d0eda611cc56fa52ac687cc43f59dfb3621d5b4 | R | 10,063 | 220 | ---
title: "Microglia Gene Expression Analysis: batch and sex covariates"
author: "Raquel Garza"
output:
html_document:
df_print: paged
---
## Overview
This notebook is a repetition of gene_DEA_GSEA.Rmd to verify that the results hold when adjusting for batch and sex effects in the design formula of the differen... |
8b1d173afaaaa4e47c629ec0c82b432abb9758f60239527402aa8e2746f240be | R | 10,130 | 192 | ---
output:
html_document:
keep_md: true
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# Comparison of Ordinary Least Squares and RCTD
```{r libraries}
library(spacexr)
library(Matrix)
library(ggplot2)
librar... |
c3b2d703f75be253a9f77af21743cccadd18145d7982af4c4fec1b305760088c | R | 10,158 | 251 | ---
title: "Statistical analysis (secondary dependent variable)"
output:
word_document:
reference_docx: template.docx
html_document:
df_print: paged
---
<font size="4"> Brent J. Raiteri (assisted by Alain C. Vandal) <br>
2025-12-12 </font>
## Coefficient of variation in motor unit discharge rat... |
37ac86520a61cd07262776676e9279a6e048c6d8136e58dff7c4d6a39e5f8e45 | R | 10,206 | 359 | # run_gam_cluster_trajectory_single_solution.R
#
# Purpose:
# Fit generalized additive models (GAMs) to test age-related trajectories of
# cluster-level structure-function coupling (SFC) values for one selected
# 3-cluster NMF solution.
#
# Overview:
# 1. Load subject/session metadata, parcel-wise SFC matrix, a... |
cb95728c988431012d774ebbf58d18c2fb16a8f3c4ba9bc419d0211e6e6a4cbf | R | 10,238 | 212 | ---
output:
pdf_document: default
html_document:
keep_md: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
library(spacexr)
library(Matrix)
library(devtools)
library(ggplot2)
library(ggpubr)
library(reshape2)
library(dplyr)
library(gg... |
b61a52add608e092219003912fc7cb96385e2503e9da23551c95b7e9794c9f5a | R | 10,282 | 299 | S <- matrix(c(1, -1, -1, 1), ncol = 2, dimnames = list(NULL, c("x", "y")))
X <- data.frame(x = c("a", "b"), y = c(100, 10))
shp <- shapviz(S, X, baseline = 4)
mshp <- c(shp = shp, shp2 = shp + shp)
test_that("get_* functions work", {
expect_equal(4, get_baseline(shp))
expect_equal(S, get_shap_values(shp))
expect... |
6c502311ab759cf8d474b5ea4095ffb89cc0cf44f167a9785012278de778427f | R | 10,303 | 413 | ---
title: "Pa for WD, Control (Hand, Machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
... |
17532aa3646eaa04b9b1931456426782a039190740d414ec658f9da06bef6804 | R | 10,341 | 302 | # Author: Ziwei Liu, Karolinska Institutet
#
# SoupX-based functions below are adapted from the SoupX package and workflow described in:
# Matthew D Young, Sam Behjati. SoupX removes ambient RNA contamination from droplet-based
# single-cell RNA sequencing data (Open Access). GigaScience, Volume 9, Issue 12, December 2... |
b191b3fb8479951a9a30c69fb5955d5d76db0a15ac7f7e1f6fa724236ddad485 | R | 10,354 | 398 | ---
title: "Tidymodels"
bibliography: "biblio.bib"
link-citations: true
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Tidymodels and SHAP}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
---
This vignette explains how to use {shapviz} with {Tidymodels}.
XGBoost and LightGBM are... |
ec973ff3d62ee9b7816ba798862a973bf30a440421e83672c4bbed676546241c | R | 10,378 | 249 | library(SnapATAC)
library(viridisLite)
library(ggplot2)
library(ggdendro)
library(ggsci)
library(ggpubr)
library(chromVAR)
library(motifmatchr)
library(SummarizedExperiment)
library(BSgenome.Hsapiens.UCSC.hg38)
library(rGREAT)
library(GenomicRanges)
library(tidyr)
library(parallel)
library(stringr)
library(umap)
lib... |
6086d127c8bf3aee3a9fc186fe74b4add2dac2b76818e1c61e54d73281e92a27 | R | 10,453 | 216 | # Function to generate a permutation map from a set of cortical regions of interest to itself,
# while (approximately) preserving contiguity and hemispheric symmetry.
# The function is based on a rotation of the FreeSurfer projection of coordinates
# of a set of regions of interest on the sphere.
#
# Inputs:
# coord.l... |
87a58aa74eeb4e91f6e60282bf52b80eb3d5741077f02c9ff5b8c2b9dc18036a | R | 10,461 | 277 | ### this code is to run the ARI and LISI evaluation for the method outputs
library(data.table)
library(NbClust)
library(mclust)
ari_calcul_sampled <- function(myData, cpcs, isOptimal=FALSE,
method_use='resnet',
base_name='', maxiter=30,
... |
8c9ceee0fe655c97f6a49346e76443dffae428228c8328f18ae34da6513eec2e | R | 10,465 | 289 | context("GSEA analysis")
test_that("fgseaSimple works", {
data(examplePathways)
data(exampleRanks)
set.seed(42)
nperm <- 100
fgseaRes <- fgseaSimple(examplePathways, exampleRanks, nperm=nperm, maxSize=500)
expect_equal(fgseaRes[23, ES], 0.5788464, tolerance = 1e-7)
expect_equal(fgseaRes[2... |
9e233d09fd48f17d269290f78a90a38905266e20345dd64b40c80bfb1ac2edf8 | R | 10,472 | 203 | ---
output:
html_document:
keep_md: yes
word_document: default
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# CSIDE on the Slide-seq J20 Hippocampus
### Load in CSIDE Results and calculate significant genes
... |
ec2818db28134d67a45492ed6427ac7402637186bc159795284c30bc8f91b9a9 | R | 10,520 | 276 | ```{r library}
#BiocManager::install("BSgenome")
library("BSgenome")
#http://bioconductor.org/packages/release/bioc/vignettes/MutationalPatterns/inst/doc/Introduction_to_MutationalPatterns.pdf
#BiocManager::install("MutationalPatterns")
library("MutationalPatterns")
head(available.genomes())
#https://bioconductor.org/p... |
f8861a49a55335b1bfbc80c1f96ff0d035543b8e08b5bd9ec98e7f3e6de34f37 | R | 10,628 | 349 | ---
title: "SF, LR dW DW | 24H WD vs Control 1 groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_optio... |
044fe24d3c0e9ab19e6caad439d663fcd18470e598db859cfeb417aef0b342fb | R | 10,658 | 346 | ---
title: "SF, LR dW DW | Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_flo... |
5affff25186417eab48821627365865f356e5318b63b54cfcfb08661961d42c4 | R | 10,667 | 224 | ---
output:
pdf_document: default
html_document:
keep_md: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# Finding Spatially Variable Genes
```{r libraries}
library(spacexr)
library(Matrix)
library(ggplot2)
library(ggpubr)
lib... |
5d5cd24dee38b3b20963ca326ab6012a0c3bd4d0b15bb5f22c69330ce7123179 | R | 10,675 | 215 | ---
output:
pdf_document: default
html_document:
keep_md: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, cache.lazy = FALSE, results = 'hide')
```
# CSIDE on the Slide-seq cerebellum
### Setup
```{r fig-1, fig.height = 6, fig.width = 6, fig.align ... |
7bf26c90aadd2154024dbe0b848c1e5b5b1e09275ca1180085803223befca75f | R | 10,686 | 355 | ---
title: "SF, LR dW DW | WD vs Sp groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chu... |
c999d8a462115fe5f9f4c42b6307f16c40a00ce09c8de32b77b3f974738e284e | R | 10,686 | 325 | ---
title: "Individual Brain Atrophy Trajectories: Mixed-Effects Modeling and Bootstrap Grouping"
output:
html_document:
toc: true
toc_float:
toc_collapsed: true
toc_depth: 3
theme: paper
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
```
#... |
285ef62bdd622ced895d7b8b773d636b7ed6640ccb2cbc4d3f94d6da30706fd1 | R | 10,793 | 355 | ---
title: "SF, LR dW DW | WD vs Sp vs Control 2/3 groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor... |
42378da238e3e8bd0439a027d14e333d463cc59e68c1694b6b5d3cf294d43a41 | R | 10,849 | 296 | #https://github.com/alexcoad/Econometrics
###################################################################
# Lasso on scoreboard data
###################################################################
library(readxl)
sb_raw <- read_excel("SB2023_World2500.xlsx")
sb <- sb_raw
# take a first look at the data
d... |
8cddc52ea192905bf04c452d1932c63f2b9c0c561cfb4176a9f2286bff05bd68 | R | 10,942 | 357 | ---
title: "SF, LR dW DW | Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) groups: Bayesian regression of smoothed stretch forces"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_flo... |
3e27b04f57fb4ea34618f0b7ed9085905627f52770c17c5afbc726ff5111631e | R | 10,985 | 302 | #!/usr/bin/Rscript --vanilla
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation file... |
2048bcf7bb95a2553e039cfdc6821608914fc27036f741dc47073ab3789ed8dc | R | 11,070 | 254 | ---
output:
html_document:
keep_md: true
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
library(spacexr)
library(Matrix)
library(devtools)
library(ggplot2)
library(ggpubr)
library(reshape2)
library(dplyr)
library(gg... |
71bc098b542ca3fe1ec0a382541422846a5adc9c09918fa19a7408e3c1320caa | R | 11,181 | 286 | cowplotText <- function(text, style) {
ggdraw() + do.call(cowplot::draw_text, c(list(text=text), style))
}
cowplotLabel <- function(label, style) {
ggdraw() + do.call(cowplot::draw_label, c(list(label=label), style))
}
valueToExpExpression <- function(val, log2err=NULL) {
a <- floor(log10(val))
b <- v... |
7063e8bdc746adac6cc11135b0ffcc91a56d7985b76604861e469e2823e6f889 | R | 11,238 | 425 | # ==========================================================
# 07_baseline_and_longitudinal_analysis.R
# Purpose: First real ADNI analysis after biomarker merge
# ==========================================================
needed <- c("tidyverse", "janitor", "openxlsx", "lme4", "lmerTest", "lubridate")
missing ... |
7d9369a49574854b45e84af336f72502596e30ca6290868264b2e5b40bd38b34 | R | 11,289 | 297 | #!/usr/bin/Rscript --vanilla
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation file... |
680d95cbc30aca37d233ec1c817fcefee2293c83ef169046ccd8b6b18a4b0afb | R | 11,336 | 349 | ---
title: "HCA for Kinkopf et al. Intraskeletal Variation"
author: "KMKINKOPF"
date: "`r Sys.Date()`"
output:
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(warning = FALSE, message = FALSE)
```
#Libraries
```{r Before you Begin - Load libraries and/or set u... |
630e46cbb6c8915f4dd0e9234fa6d0ae2c5c35b9338c990e6911062625d7eff8 | R | 11,369 | 165 |
process_cell_type_info <- function(reference, cell_type_names, CELL_MIN = 25) {
message("Begin: process_cell_type_info")
message(paste("process_cell_type_info: number of cells in reference:", dim(reference@counts)[2]))
message(paste("process_cell_type_info: number of genes in reference:", dim(reference@count... |
b92da990f1246477a6f8bb8b45f02c2425ac47adb764751f458b846caa75d26f | R | 11,392 | 183 | ---
title: "Applying RCTD to Spatial Transcriptomics Data"
author: "Dylan Cable"
date: "March 17th, 2021"
output:
html_document:
keep_md: yes
rmarkdown::html_vignette:
keep_md: yes
vignette: >
%\VignetteIndexEntry{spatial-transcriptomics}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
... |
4a6690a34574f3cf8f42908855060306281a8d7334bb928568ccd3ed0a047d6f | R | 11,427 | 406 | # ==========================================================
# 06_merge_selected_biomarkers.R
# Purpose: Merge selected ADNI biomarkers with clinical core
# ==========================================================
library(tidyverse)
library(janitor)
library(openxlsx)
library(readr)
project_dir <- "R:/ADNI... |
761be2fb5cbbc3e9b0adb3148bfdb1ecb65214de2e6fe30cba6e5fb14dcb3ef7 | R | 11,444 | 223 | ---
title: "HERV and IFN Gene Expression in Microglia: Correlation with Braak Stage"
author: "Raquel Garza"
output:
html_document:
df_print: paged
---
## Overview
This notebook analyzes the expression of **upregulated HERVs** and **IFN-related genes** in microglia. The objectives are:
1. To **compare expressio... |
9156418db2de017df656fbfa923154b3987b5ed3d6bb3d62212aafcc1522c2cd | R | 11,543 | 199 | #"F:\OneDrive - NTNU\R-4.3.2\bin\Rscript.exe" C:\Users\animeshs\OneDrive\Desktop\Scripts\diffExprSeq.r L:\promec\Animesh\TK\hg38lall\star_salmon\
args = commandArgs(trailingOnly=TRUE)
print(paste("supplied argument(s):", length(args)))
print(args)
#setup####
#install.packages("BiocManager")
#install.packages("phe... |
a11e0589e5159839f127a23f122e194a607d3edb3f617b216640f945fb4ee965 | R | 11,607 | 417 | ---
title: "PAS WD vs Control (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
s... |
6ac876658e93379820e5d4013a9f2a87b3094b40d2160bcf48311607f25ee806 | R | 11,616 | 193 | #C:\users\animeshs\R-4.4.0\bin\Rscript.exe diffExprTestTmatrix.r "L:\promec\Qexactive\LARS\2022\juli\toktam\PDv2p5\Beer\220706_toktam1_Proteins.txt.Abundance.Normalized..log2.csv" "L:\promec\Qexactive\LARS\2022\juli\toktam\PDv2p5\Beer\GroupsR1.txt" Sample Class Rem
#setup
#install.packages(c("readxl","writexl","svglite... |
8b4dab1924f2cacdccea5f03a3ee9916cfed6abf03933f6ee12bb0450ab322cf | R | 11,634 | 400 | #' Prints "shapviz" Object
#'
#' @param x An object of class "shapviz".
#' @param ... Further arguments passed from other methods.
#' @returns Invisibly, the input is returned.
#' @examples
#' S <- matrix(c(1, -1, -1, 1), ncol = 2, dimnames = list(NULL, c("x", "y")))
#' X <- data.frame(x = c("a", "b"), y = c(100, 10))
... |
beaedefc9173d4020b89923389f6fbae9f21dd49b34b87b0711bcff1661143a2 | R | 11,655 | 329 | #' SHAP Importance Plots
#'
#' This function provides two types of SHAP importance plots: a bar plot
#' and a beeswarm plot (sometimes called "SHAP summary plot").
#' The two types of plots can also be combined.
#'
#' The bar plot shows SHAP feature importances, calculated as the average absolute SHAP
#' value per feat... |
9f19428d6991041788581b0aafaa45ae434e472f0ec446b26a63ea0297f2f966 | R | 11,676 | 379 | #' SHAP Dependence Plot
#'
#' Scatterplot of the SHAP values of a feature against its feature values.
#' If SHAP interaction values are available, setting `interactions = TRUE` allows
#' to focus on pure interaction effects (multiplied by two) or on pure main effects.
#' By default, the feature on the color scale is se... |
48ec2caa1d9c539e1462ed974d0278b6bb6fa9bfcac534c5ca1dca0c4fb7b42f | R | 11,683 | 431 | ---
title: "MPA WD vs Sp (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
source... |
c66da18d80332d930ca88e070ed29ec5bdea72f0dd94666b78942e77ef1612b9 | R | 11,710 | 274 | ```{r data, echo = FALSE}
inpD <-"L:/promec/Elite/LARS/2018/november/Rolf final/txt/"
data <- read.delim(paste0(inpD,"proteinGroups.txt"),row.names=1,sep="\t",header = T)
summary(data)
```
```{r clean, echo = FALSE}
decoyPrefix="REV"
dataClean<-data[-grep(decoyPrefix, rownames(data)),]
dfNoRev = data[!data$Reverse=="... |
55f05c9ab5cd8ea05036f5e13d60bbe094e727b27173b9e0cedc115938759237 | R | 11,729 | 433 | ---
title: "PAS WD vs Sp (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
source... |
849b9e0f8bda0ff77b559d914af8c0b94d631978f07256ed9537920fb0f31b6a | R | 11,814 | 499 | # ==============================================================================
# 08b. Monocle 3 graph test and pseudotime-associated gene modules
#
# Description:
# This script performs graph_test() on one or more ordered Monocle 3 CDS objects,
# selects genes using q-value and Moran's I thresholds, identifies gene m... |
7c5fe064159a2b28f57f2e174ad697bfa0ba53e56801fa9e647a321324955e45 | R | 11,825 | 236 |
fake_coords <- function(counts) {
coords <- data.frame(as.matrix(Matrix(0,nrow=dim(counts)[2],ncol=2)))
colnames(coords) <- c('x','y')
rownames(coords) <- colnames(counts)
return(coords)
}
#' Creates a SpatialRNA object from a 10x Genomics Visium `outs` directory
#'
#' Given a SpatialRNA directory 10x Genomi... |
5badb7637ec2f78634951707881a93ee4d1f04cbbb164d9a1d85b1494bc54a76 | R | 11,849 | 206 | ---
output:
html_document:
keep_md: yes
word_document: default
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# CSIDE on the Visium Lymph Node
### Load in CSIDE results
```{r prelude}
# Load in spatialRNA dat... |
d61c784450cddd6e9485905dad3ecba0b9ff09a3c9987272f217001f9154c8f1 | R | 11,853 | 284 | # ==========================================================
# 19_extract_creatinine_from_adnimerge.R
#
# ADNI's laboratory table is wide with coded column names such as
# RCT392, and the readable descriptions live in the data
# dictionary rather than in the column names. Script 17 searched
# column names, so it found ... |
50598043d66a07e7f0df724f471863ba07505ee8e3c8afd1522b742c70c1bbf6 | R | 11,854 | 221 | ---
output:
html_document:
keep_md: yes
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T)
```
# Finding Astrocyte Genes Dependent on Cellular Colocalization
```{r libraries}
library(spacexr)
library(Matrix)
library(ggplot2)
library(gg... |
818e086dd1fc02ab19d52ca9143375228038af30d5f9715d7ea1dfbac2848f76 | R | 11,888 | 204 | test_single_beads <- function(puck, gene_list, cell_type_info, trust_model = FALSE, constrain = T, OLS = F) {
cell_type_names = cell_type_info[[2]]; n_cell_types = cell_type_info[[3]]
beads = t(as.matrix(puck@counts[gene_list,]))
weights = decompose_batch(puck@nUMI, cell_type_info[[1]], beads, gene_list, constrai... |
550efaf30f1df94be2d8795e3bae5877ae959e19f469dbc905e18abba1e636cf | R | 11,936 | 235 | #decompose with just two cell types
#if score_mode, then returns the objective function score
#if denoise, then it fits a "noise" dimension as the mean of all the data
decompose_sparse <- function(cell_type_profiles, nUMI, bead, type1=NULL, type2=NULL, score_mode = FALSE, plot = F, custom_list = NULL, verbose=F, constr... |
bbef2712ddd9664cc100d2dd2a56a93c211d7543b3ff4e52b3c681b00ac070e3 | R | 11,942 | 213 | ---
output:
html_document:
keep_md: true
pdf_document: default
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# CSIDE on the Slide-seq KP tumor (immune cell-dependent DE)
### Load in CSIDE Results and calculate significant genes
`... |
cd6ed3a9a0f3006d4111ab7d182d876dc3a289e1b81278456f8eb6954ef76157 | R | 12,142 | 466 | ---
title: 'SF: Read and preprocess raw stretch force measurements 1 and 3'
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: i... |
51db7f10c049908c5213106b5f3da2427a307b5980b83bac78ac97dfa3715706 | R | 12,170 | 303 | #!/usr/bin/env Rscript
# ============================================================
# Minimal, reproducible pipeline retained from the original scripts:
# Raw 10x Xenium/CellRanger count matrix
# -> Seurat QC + clustering (for CM cluster selection)
# -> sgRNA assignment (single-KO cells)
# -> perturbat... |
ebd44df9233be9916ed4a58ea27f90baca3d91e2d757f7a95efe6de669422d11 | R | 12,214 | 188 | ---
title: "Applying CSIDE to Spatial Transcriptomics Data: Differential Expression with Multiple Experimental Replicates"
author: "Dylan Cable"
date: "December 21st, 2021"
output:
html_document:
keep_md: yes
pdf_document: default
rmarkdown::html_vignette:
keep_md: yes
vignette: |
%\VignetteIndexEntry{C... |
3b536bbdd4bbc9af22ef2470351b12d8959703309a2a91115cfbc1e1564b927f | R | 12,217 | 358 | #R script for immunihistochemistrey data###########################
#Packages
# Core Data Science, Plotting & Estimation Stats
library(tidyverse)
library(dabestr)
# Frequentist Modeling & Distribution Fitting
library(fitdistrplus)
library(car)
library(permuco)
# Bayesian Modeling & Post-Hocs
library(b... |
90ebc0ec8c85c38854ef7501cfb8b875c51a4fd8c61ade29c23c05d35eb0729c | R | 12,219 | 542 | ```r
# ==============================================================================
# 01. Load and merge single-cell RNA-sequencing datasets
#
# Description:
# This script loads neonatal mouse brain immune-cell datasets from
# preconstructed Seurat objects or 10X Genomics filtered feature-barcode
# matrices. I... |
0f31af9ea6fc19daacfd0a3c5a8af4512e99041f42bc3994df3491ec34cf7811 | R | 12,228 | 213 | ---
output:
pdf_document: default
html_document:
keep_md: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# Spatially localizing 27 interneuron subtypes
```{r libraries}
library(spacexr)
library(Matrix)
library(ggplot2)
library... |
2ffca762fad07bb9357f42144d6bf532de1bbdebd433cbd1cbae1c0561c41fa3 | R | 12,331 | 431 | ---
title: "MPA WD vs Sp vs Control 2/3 (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, includ... |
c6bf0b8396a2cf9271c2211bec4b57d5c00855ec1b3fb1f55cb8d1fd890f1543 | R | 12,332 | 375 | ---
title: "Reproduction of Figure 3"
output:
html_document:
df_print: paged
toc: true
toc_depth: 2
toc_float: yes
number_sections: yes
code_folding: show
---
# Setup and Libraries
```{r message=FALSE, warning=FALSE}
library(recoRdseq)
library(SummarizedExperiment)
library(S4Vectors)
library... |
e4d5d0d254b722a132ece26732e652116b3dee3faac1e632a1f2c2615f4f9f69 | R | 12,359 | 434 | ---
title: "PAS WD vs Sp vs Control 2,3 (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, includ... |
73640795b6a62fa21e79fbdf0ec6f5d5d736972efa90628e00951fcc79fd9ad3 | R | 12,371 | 434 | ---
title: "MPA Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_typ... |
40355e53aa62a0c7a57d2c42a4bee068148e7042cf4016c3f817215d44008e76 | R | 12,415 | 436 | ---
title: "PAS Measurement 1 (24H WD) vs Measurement 3 (SSR, Conivaptan) (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_typ... |
edef6973c41516d15405e0f3e2a4e7b362373ed00405c93c67e06cbba8b3eb82 | R | 12,529 | 433 | ---
title: "MPA WD vs Control (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{r setup, include=FALSE}
s... |
51465fe66a5069705a57183e7ddee622c8a9e4d8d337faada41fe52647f651de | R | 12,585 | 329 | ---
title: "scisorseqr: Standard Workflow"
#output: rmarkdown::html_vignette
output: pdf_document
vignette: >
%\VignetteIndexEntry{Vignette Title}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
The... |
9f76e015d68aa0e0deadb210b30efcc1de3247586ddbf1236b45a4848ee9eea4 | R | 12,768 | 480 | suppressPackageStartupMessages({
library(clusterProfiler)
library(DESeq2)
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(org.Rn.eg.db)
library(forcats)
library(ggplot2)
library(SeuratObject)
library(Seurat)
library(SeuratWrappers)
library(patchwork)
library(tximeta)
library(stringr)
lib... |
f1423355e1042bc00c3fd76be513be97ac0990a5da650c19568648fb64775ab0 | R | 12,805 | 295 | #' Runs preranked gene set enrichment analysis.
#'
#' This feature is based on the adaptive multilevel splitting Monte Carlo approach.
#' This allows us to exceed the results of simple sampling and calculate arbitrarily small P-values.
#' @param pathways List of gene sets to check.
#' @param stats Named vector of gene-... |
3b143ddde1e18001a444a83a6cda51f99b03d4f8137492f667c1e3f43c8cba62 | R | 12,853 | 434 | ---
title: "MPA WD vs SSR vs Conivaptan vs Control 2/3 (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{... |
7ea24f4d11957a57fb7a0cebfd666f1e3ccaf2e462b018a329bc0836089cf20e | R | 12,912 | 436 | ---
title: "PAS WD vs SSR vs Conivaptan vs Control 2/3 (hand, machine)"
author: "Yaromir Kobikov <kobikov.yaromir@gmail.com>"
date: "Date: `r format(Sys.time(), '%d/%m/%Y')`"
output:
word_document: default
html_document:
toc: true
toc_float:
collapsed: false
editor_options:
chunk_output_type: inline
---
```{... |
ed0efc89898fbea7f5b1d2907b0dd77537d0235c7c73335a236d18ee622327ba | R | 13,027 | 395 | # ------------------------------------------------------------------------------
# Title: Figure 5 - hdWGCNA Co-expression and Module Hub Analysis
# Author: Haofei Wang
# Date: March 24, 2025
# Description:
# This script performs weighted gene co-expression network analysis (hdWGCNA) on
# single-cell data, identifies ... |
6fecafa2d419452e6cbd64cadc266b17ff27001b03d88eaf79bebb9970845c05 | R | 13,143 | 263 | get_n_sig_genes_Z_test <- function(cell_type, cur_cell_types, myRCTDde, X2,puck, fdr = .01) {
final_df <- get_Z_test_res_ct(cell_type, cur_cell_types, myRCTDde, X2,puck, fdr = fdr)
return(dim(final_df)[1])
}
get_Z_test_res_ct <- function(cell_type, cur_cell_types, myRCTDde, X2,puck, fdr = .01, log_fc_thresh = 0.4,... |
4c4e00c6ab015c230516085866f0d29389d60cd225b6249c300b004188b5f050 | R | 13,150 | 380 | # Function to create a list of Seurat objects from multiple input directories
create_seurat_objects <- function(in_data_folders, SoupX = TRUE, min.cells = 3, min.features = 200, project = "Developing ENS", fig_dir, verbose = TRUE) {
seu_list <- list() # Initialize an empty list to store Seurat objects
# Read 10X d... |
501323b529450af9f4094a6b24c9b40805361a162afd96204facb2c815b109d4 | R | 13,296 | 258 | library(Seurat)
library(dplyr)
library(ggplot2)
library(patchwork)
library(CellChat)
library(ggalluvial)
library(ComplexHeatmap)
library(NMF)
library(circlize)
options(stringsAsFactors = FALSE)
options(future.globals.maxSize= 891289600)
setwd("/mnt/alamo01/users/gbb/NDMG_snRNA/seurat/Myeloid/ELSA_out/")
MM <- read.tab... |
3e8f2a45ecf3b0b572f487a7bb22c47d52dc51699282a54f75610c9e952d0f3b | R | 13,510 | 295 | # ------------------------------------------------------------------------------
# Title: Post-Cytospace Analysis and Visualization of Cell-Type Assignments
# Author: Yiran Song
# Date: March 18, 2025
# Description:
# This script processes the output from Cytospace, and performs correlation
# analysis between measured... |
a1efad8f8b80a794b7e21965061cb1a5ba1de33eb5e39a9b1e94eb22534c4aaf | R | 13,518 | 416 | #K+ dynamic analysis
#Packages
# Core Data Science, Plotting & Estimation Stats
library(tidyverse)
library(dabestr)
# Frequentist Modeling & Distribution Fitting
library(fitdistrplus)
library(car)
library(permuco)
# Bayesian Modeling & Post-Hocs
library(brms)
library(emmeans)
#######################... |
836f307991f36c5603c0bddb4652791af3b31ed34c6d34d14ee2b7b1dfcdda96 | R | 13,526 | 214 | ---
output:
pdf_document: default
html_document:
keep_md: true
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = T, warning = F, message = F, cache = T, results = 'hide')
```
# RCTD on the Slide-seq cerebellum
```{r libraries}
library(spacexr)
library(Matrix)
library(ggplot2)
library(ggpubr)
lib... |
84334e38dcf5941b64efcfd9f1bcac3c55dbce13a1c919e3c04de0cba44cf498 | R | 13,628 | 429 | ---
title: "Longitudinal ComBat Harmonization of Brain Volumetric Measures"
output:
html_document:
toc: true
toc_float:
toc_collapsed: true
toc_depth: 3
theme: paper
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE)
```
# Overview
This script... |
bcc479f9fbf5ca3cdc8dfdb538f13023e65f98f0ad9b82047a4c4c533f0abd59 | R | 13,693 | 412 | #!/usr/bin/env Rscript
##import packages
library(readxl)
library(tidyverse)
library(DESeq2)
library(ggfortify)
library(ggplot2)
library(pheatmap)
library(sva)
library(biomaRt)
library(DescTools)
library(ComplexHeatmap)
library(circlize)
# set working dir to the folder containing this script
setwd(dirname(rstudioapi::... |
b42a70f0166e30ca35a2e1db885c1d529efd0e052c38373c62ea105ccdaf611c | R | 13,780 | 262 | library(gplots)
library("RColorBrewer")
plot_heat_map <- function(data, file_loc = NULL, save.file = F, normalize = T, dendrogram = 'none') {
if(normalize) {
norm_conf = sweep(data, 2, colSums(data), '/')
norm_conf[norm_conf < 0] = 0
} else
norm_conf = data
if(save.file) {
png(file = file_loc)
... |
c49ea2b35a74848fb4b5d05a1511e164bafd60f2f4484dbf3018a4e029b24672 | R | 13,867 | 285 | ---
title: "QC and Exploratory Analysis of ASAP_PMDBS snRNA-seq"
author: "Raquel Garza"
output:
html_document:
df_print: paged
---
## Description
This script performs **quality control (QC) exploration and visualization** of the ASAP_PMDBS single-nucleus RNA-seq dataset.
It integrates multiple metadata table... |
24408cd4dac77fb6152d4347e44a808e3341da438d44a03b566fb9169d38a7ba | R | 13,870 | 327 | #!/usr/bin/env Rscript
library(optparse)
## The following code is copied from Tcseq package
## Wu M, Gu L (2021). TCseq: Time course sequencing data analysis. R package version 1.18.0.
## Modified as per requirement by Abhijit Chakraborty
clust <- methods::setClass("clust", slots = c(method = "character",
... |
0332013420eb973bf1c525857a17cec3f935ec9b4bc6952a6d0fbe976833b333 | R | 14,054 | 148 | ---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# spacexr (Spatial-eXpression-R): Robust Cell Type Decomposition (R... |
04a70ea80ebfddb5572cdac80ec58fc6a192ac9cdb78122fcfcb93a0b0f24fee | R | 14,190 | 336 | # ------------------------------------------------------------------------------
# Title: Figure 4 - Maturation Feature Mapping and GO Analysis
# Author: Haofei Wang
# Date: March 24, 2025
# Description:
# This script generates plots related to maturation features across Xenium timepoints.
# Includes:
# - ImageFeatureP... |
c582e8c4a01ef94e6c974a9bb63cf501b891d239e20144e1b35c9410eb5a17b9 | R | 14,381 | 270 | #C:\Users\animeshs\R-4.2.3\bin\Rscript.exe peptideGroups.r C:\Users\animeshs\230504_hela_test\combined\txtMC1
print("USAGE:Rscript peptideGroups.r <complete path to proteinGroups.txt file> <LFQ or SILAC if performed else it defaults to raw Intensity columns>")
#supplying input file for testing
#inpF<-file.path("L:/prom... |
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