sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
176bb34b0a41a787ab3b962195eb170f3c7a5c52c98a579bc337665c42571a4c | R | 36,172 | 798 | #' Create a list for differential genes for all pairwise cell types in the a reference data set.
#' Using this significantly reduces computation time for the 'de' variable gene method.
#'
#' @param ref_data the reference dataset gene expression matrix
#' @param types labels for each column in ref_data
#' @param n numbe... |
23db41f5f0d0a855dbfcb8ecdaae15f8198937d53d20131c9819843b3e356827 | R | 36,410 | 802 | #!/usr/bin/env Rscript --vanilla
# This code was copied and modified from the github
# broadinstitute/gatk and tgen/tCoNut repositories.
suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(data.table))
#### Preset Options For Readability ####
# Homo_sapiens_assembly38 primary c... |
c1964e668c64ced69ce32b0261b0463506fd88dbf9d4c849192cc672640b0736 | R | 36,694 | 740 | ---
title: "Mid-Spectral Initialization"
date: "December 31 2024"
---
## Introduction
The
[initialization article](https://jlmelville.github.io/uwot/articles/init.html)
describes some ways to initialize the embedding process. Really you have two
options: a spectral initialization (the default) and PCA, which is what... |
6abce02f455345384a9827643c542e71b42860b9a8c8431e831ad66dc1e6886d | R | 37,418 | 1,074 | library(tidyverse)
library(cowplot)
library(ggforce)
#========================================================================================================
# here I will bin positions based on KL-divergence and find the aa distributions within each bin.
#===========================================================... |
830cf5119a079ee2cbcd930880f62a37e0e66b1cf823b794d105a4fbc65599cd | R | 37,439 | 750 | library(shiny)
library(shinyhelper)
library(data.table)
library(Matrix)
library(DT)
library(magrittr)
sc1conf = readRDS("sc1conf.rds")
sc1def = readRDS("sc1def.rds")
### Start server code
shinyUI(fluidPage(
### HTML formatting of error messages
tags$head(tags$style(HTML(".shiny-output-error-validation {col... |
80c4850eeb71ba0a2f3220e17ad6751ee2f8e8190380b7d7e6ac8b982d2e3e37 | R | 38,733 | 737 | ---
title: "Leopold: Lightweight Estimate of Preservation of Local Density"
subtitle: "Approximating densMAP"
date: "February 16 2022"
---
## densMAP
[densMAP](https://doi.org/10.1038/s41587-020-00801-7) is a variation on UMAP
that attempts to preserve the differences in density in the original data by
adding a new c... |
29a5dd7bca79449a31deaeb57b4447ebb82836e2e93ff4446aa03daad087ffed | R | 39,603 | 1,115 | ## io.R from cmapR verison 1.0.1 (2018-01-30)
########################################
### GCT class and method definitions ###
########################################
#' An S4 class to represent a GCT object
#'
#' @slot mat a numeric matrix
#' @slot rid a character vector of row ids
#' @slot cid a character vector... |
bdec2e6f5f0396b8885dfda848050217fa5c0022c68f88b4d51b6e0c319e72a0 | R | 40,765 | 1,071 | get_sce_sparsity <- function(sce){
# Computes sparsity of the counts matrix of a SingleCellExperiment
require(Matrix)
# (double divide rather than divided by (row*col) so it can handle large
# matrices without integer overflow)
return(1 - (Matrix::nnzero(counts(sce))/nrow(sce)/ncol(sce)))
}
get_dataset_spa... |
4af68b0f66a154ebed7b68788865ab18bb0dd9fccd5e8c7e966334794054b448 | R | 42,071 | 1,253 | library(tidyverse)
library(cowplot)
library(ggforce)
#===============================================================================
# Analysis for protein engineering applications.
#===============================================================================
# Looking at wt/consensus accuracy as a function of CNN... |
da18557b6228d649b2f329b4bad795a37e86e739e971436ecc05e9b1668005a8 | R | 42,864 | 912 | #!/usr/bin/env Rscript --vanilla
# Load required modules
suppressPackageStartupMessages(require(tidyverse))
suppressPackageStartupMessages(require(optparse))
# Define Options
option_list = list(
make_option(c("-i", "--samtoolsStatsFile"),
type="character",
default=NULL,
hel... |
0e3e39f3777179ed0fec0bb3e946c4498050e9b5b26cd5aad15fcdc116ddacea | R | 43,587 | 1,240 | ################################################################################################################
## Filename: plots.R
## Created: February 06, 2015
## Author(s): Karsten Krug
##
## Purpose: plotting functions for Protigy app.
##
###########################################################################... |
ef0bc9ca9f59444d5aa40877ff7f0b8bd4765b2ae3eb4f6003b44f415b1d673c | R | 45,866 | 1,041 | #############################################################################
## forked from GitHub repos 'raivokolde/pheatmap'
##
#############################################################################
lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, ... |
8e810bdb194232f5e9a0314692aeb11224fc95e6ddc217102590631bf8f5d0d2 | R | 46,611 | 842 | #' Dimensionality Reduction with UMAP
#'
#' Carry out dimensionality reduction of a dataset using the Uniform Manifold
#' Approximation and Projection (UMAP) method (McInnes et al., 2018).
#'
#' This function behaves like \code{\link{umap}} except with some updated
#' defaults that make it behave more like the Python i... |
2373902356077a8355ca63452424803e8fe41e66d7b316f0a9ba60a0c441ec7c | R | 47,963 | 811 | # Last updated May 4, 2022 by Natalie Clark (nclark@broadinstitute.org) - v 1.0.1
############################
## UI part
printHTMLUI <- function(id) {
ns <- NS(id)
htmlOutput(ns("html"))
}
#############################
## server part
printHTML <- function(input, output, session, what, error=NULL, global.inp... |
dc9cf9999467f7faf47f566ef064d26b4a65aa78abc8212800062acd63f10f94 | R | 48,656 | 807 | # Intervene: is a tool for intersection and visualization of multiple lists and genomic region sets
# Author: Aziz Khan <aziz.khan@ncmm.uio.no>
# Date: January 30, 2017
#UI code for intervene
#====================================================#
## Sidebar content ####
#===============================================... |
c164caaf34b8d630cefc1818e3885cc397652be59559d4ad79bc7470c27bda30 | R | 49,235 | 1,320 | .reserved_cb_names <- c("names", "class", "call", "params", "niter", "nfeatures", "folds")
#' XGBoost Callback Constructor
#'
#' Constructor for defining the structure of callback functions that can be executed
#' at different stages of model training (before / after training, before / after each boosting
#' iteration... |
146f44167484fa4220c01e0148b3f9e22a38c209c65ab649d6063d2c6bf104fc | R | 51,310 | 1,132 | library(shiny)
library(shinyhelper)
library(data.table)
library(Matrix)
library(DT)
library(magrittr)
library(ggplot2)
library(ggrepel)
library(hdf5r)
library(ggdendro)
library(gridExtra)
sc1conf = readRDS("sc1conf.rds")
sc1def = readRDS("sc1def.rds")
sc1gene = readRDS("sc1gene.rds")
sc1meta = readRDS("sc1m... |
b9331511fd90053e549c3bd42f5939e676c60f484d89269477bb24336ae87f71 | R | 52,780 | 867 | #' @title Fit XGBoost Model
#' @description Fits an XGBoost model to given data in DMatrix format (e.g. as produced by [xgb.DMatrix()]).
#' See the tutorial [Introduction to Boosted Trees](https://xgboost.readthedocs.io/en/stable/tutorials/model.html)
#' for a longer explanation of what XGBoost does, and the rest of th... |
fcac1c3cf05c513c24297a4829ec993ee323d77e0d6308e22c986adf55edaa19 | R | 56,790 | 1,158 | ---
title: "Effect of Paracetamol on Neuronal Differentiation"
Authors: Ankush Sharma with contributions from Martin Falck
output:
date: "`r Sys.Date()`"
html_document:
df_print: paged
---
#==========================================================================================================
#Description:... |
8f686fed5c1ac33da2b242ed75ce2a9245f5f581ca35c5876d0128ad57425d15 | R | 61,466 | 1,631 | prescreen.objective <- function(objective) {
if (!is.null(objective)) {
if (!is.character(objective) || length(objective) != 1L || is.na(objective)) {
stop("'objective' must be a single character/string variable.")
}
if (objective %in% .OBJECTIVES_NON_DEFAULT_MODE()) {
stop(
"Objectiv... |
b995b73bc9a92248da1ee405db5d8791e03f1198e988b11b4233bc5a72180867 | R | 61,674 | 1,006 | #加载R包
library(Seurat)
library(tidyverse)
library(cowplot)
library(patchwork)
library(ggplot2)
###
data_dir <- "/Users/niuruize/Downloads/scRNA/scrna_Cont/44"
age44_matrix <- Read10X(data.dir = data_dir)
age1 <- CreateSeuratObject(counts = age44_matrix, project = "stage1", min.cells = 3, min.features = 200)
age1[["S... |
910dbfbb0d30d18bf099d11fead5d1983df52e455f4f97d20b0949b56f36c978 | R | 61,987 | 1,691 | #' The scAI Class
#'
#' The scAI object is created from a paired single-cell transcriptomic and epigenomic data.
#' It takes a list of two digital data matrices as input. Genes/loci should be in rows and cells in columns. rownames and colnames should be included.
#' The class provides functions for data preprocessing, ... |
e19caa3bf30af249a1702c1c817dd906de07171d657fe633633eb63cc69089e3 | R | 65,792 | 1,281 | ---
title: "Integration_paracetamol"
author: "MS"
date: "11/11/2020"
output: html_document
---
```{r setup,include=FALSE}
knitr::opts_chunk$set(include = TRUE, root.dir ="Paracetamol/Integration", echo = TRUE)
#rm(list=ls())
library("readr")
#devtools::install_github("PF2-pasteur-fr/SARTools", build_opts="--no-re... |
8e283aa95b6dc745143a2b56d3c2df1066d333a7181c12b996c8dfc1d6b6a1cd | R | 66,472 | 1,959 | ################################################################################################################
## Filename: global.R
## Created: October 09, 2015
## Author(s): Karsten Krug, Ozan Aygun
##
## Purpose: Shiny-app to perform differential expression analysis, primarily on proteomics data, to perform
## ... |
badaf4494bb5c474f3ce23eb17c9ac0fe9ff310967456e350c4555354f5d8966 | R | 69,734 | 2,204 | ---
title: "Whole Connectome Stats"
output:
html_document:
keep_md: true
---
# Whole Connectome Results
We are now going to see if there is anything in cortical-cortical connectivity by running the matrix of all possible connections instead of just subcortical-cortical stats.
```{r message=FALSE, warning=FALS... |
f7e9216a69857939b815f7eaf07031bb3c8d233927806b447149f966b4928619 | R | 72,046 | 2,171 | ---
title: "Whole Connectome Stats"
output:
html_document:
keep_md: true
---
# Whole Connectome Results
We are now going to see if there is anything in cortical-cortical connectivity by running the matrix of all possible connections instead of just subcortical-cortical stats.
Adding the Schaefer template data... |
60650112d4785557ab7380c14268d91615d4bc8ee85fb823eaf6cd31a5ea80a5 | R | 106,826 | 2,180 | ---
title: "DEseq2-paracetamol"
author: "MS"
date: "8/11/2020"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(include = TRUE, root.dir ="Paracetamol/RNAseq/Analysis", echo = TRUE)
#rm(list=ls())
#BiocManager::install("tximport")
library("tximport")
library("readr")
library(SARTools)
libr... |
8247c25a4669c86e47cdeafcbdd6ecb8b8f4b96901a1ed6e3af6d558fcf47225 | R | 107,692 | 2,078 | #### Master Script 06: Visualise study results for manuscript ####
#
# Shubhayu Bhattacharyay
# University of Cambridge
# email address: sb2406@cam.ac.uk
#
### Contents:
# I. Initialisation
# II. Figure 1
# III. Figure 2
# IV. Figure 3
# V. Figure 4
# VI. Supplementary Figures 5 and 6
# VII. Supplementary Figures 8 and... |
a6b907af4f8fa29371e50cc97bae7c3b4ca94225b1c99f5090566aed45eb7319 | R | 119,524 | 2,272 | #### Master Script 06: Visualise study results for manuscript ####
#
# Shubhayu Bhattacharyay
# University of Cambridge
# email address: sb2406@cam.ac.uk
#
### Contents:
# I. Initialisation
# II. Figure 1
# III. Figure 2
# IV. Figure 3
# V. Figure 4
# VI. Supplementary Figures 5 and 6
# VII. Supplementary Figures 8 and... |
93ff429bd13ac7b9db98d3be5600eb4fa39abda2c05210367b0decff6724e380 | R | 125,563 | 3,481 | ---
#==========================================================================================================
title: "Neuronal Differentiation Paracet scATACSeq Pipeline "
author: "Ankush Sharma"
date: "`r Sys.Date()`"
output: html_document
Description: This script analyzes the integrative single cell ATAC seq analys... |
d44c8a88a3af76287caeb91c4bfad6c99af94e3eb7f8a9f5908112818dd2f564 | R | 155,489 | 3,079 | ---
title: "Methylation Analysis - Paracetamol"
author: "MS"
date: "25/02/2022"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(include = TRUE, root.dir ="/Paracetamol/Methylation/bulkdata/analysis/AllSamples", echo = TRUE)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.p... |
fb1702a7c67804bbff5f75f9a904ccf005896aa800f49c78bf07bbbf27d95e64 | R | 200,000 | 3,698 | ################################################################################################################
## Filename: server.r
## Created: October 09, 2015
## Author(s): Karsten Krug, Ozan Aygun
##
## Purpose: Shiny-app to perform differential expression analysis, primarily on proteomics data, to perform
## ... |
f05bd9d5f038935be47b2196b27d8e8a870b495328650701537c669fe6ee356c | R | 200,008 | 3,819 | #' Dimensionality Reduction with UMAP
#'
#' Carry out dimensionality reduction of a dataset using the Uniform Manifold
#' Approximation and Projection (UMAP) method (McInnes et al., 2018). Some of
#' the following help text is lifted verbatim from the Python reference
#' implementation at \url{https://github.com/lmcinn... |
0126ed5f2d02b64201dc508cbc96b17f775c7883d3ba8bef268be303afafc044 | Rust | 57 | 3 | fn main() {
std::process::exit(datamonger::run());
}
|
718fc2707af52d620bde247df4e9930acfed5c2e30f01da547c3d71da6234597 | Rust | 330 | 8 | fn main() {
println!("cargo:rustc-check-cfg=cfg(local_core_v2)");
println!("cargo:rerun-if-env-changed=DM_R_CORE_PATH");
// The published vendor archive predates v2; local core tests exercise the new API.
if std::env::var_os("DM_R_CORE_PATH").is_some() {
println!("cargo:rustc-cfg=local_core_v2")... |
96c1e046f26be300fa46f070b9e61e24cee95660c95bc1a148fbf9e7fbfab700 | Rust | 539 | 26 | use std::fmt;
#[derive(Debug)]
pub struct Error {
pub category: &'static str,
pub message: String,
}
impl Error {
pub fn new(category: &'static str, message: impl Into<String>) -> Self {
Self {
category,
message: message.into(),
}
}
}
impl fmt::Display for Erro... |
2480540e7606165e8c464b57e0c5c18dbcd22923a745012554c359c17b7b92b2 | Rust | 744 | 20 | // Generated by extendr: Do not edit by hand
fn main() -> Result<(), Box<dyn std::error::Error>> {
let wrapper_path = "../R/extendr-wrappers.R";
let header = "\
# Generated by extendr: Do not edit by hand\n\
# nolint start\n\
\n\
#' @usage NULL\n\
#' @useDynLib datamonger... |
5f2cbd53d0f64948469919e7dc035bb1a7433f472e2e1b9602d4ca61a7a9bb9f | Rust | 1,145 | 34 | use std::error::Error;
use std::fs;
use std::path::Path;
// Share the parser without exposing an API or linking documentation tools into the CLI.
#[allow(dead_code)]
#[path = "../src/cli.rs"]
mod cli;
fn main() -> Result<(), Box<dyn Error>> {
let check = match std::env::args().skip(1).collect::<Vec<_>>().as_slice... |
80135aa6e5118c463d7b58acdbded0f4d6c6ccb3fea3d3adc8673880b4e0a22d | Rust | 1,589 | 61 | use std::fmt;
/// Portable error categories for language bindings.
#[derive(Clone, Copy, Debug, PartialEq, Eq)]
pub enum ErrorKind {
/// An unsupported or inconsistent representation recipe.
UnsupportedDecoder,
/// Invalid artifact text or compression.
Decode,
/// Invalid canonical logical componen... |
ff0095c6d35d6f39bb6b457354a9d1bb91e89829b3f1ef114725c94e534ffa86 | Rust | 2,127 | 56 | //! Strict, streaming implementations of Datamonger revision 1.
//!
//! This crate decodes verified artifacts into language-independent buffers and
//! writes the canonical verification stream without materializing another copy
//! of the dataset. Retrieval, registry selection, and caching belong to clients.
//!
//! ``... |
e2e120abbf2b494ced205cbc5a0843265374e8544ccde805faf20eac1c12c4fe | Rust | 2,811 | 96 | /// The four revision 1 logical element types.
#[derive(Clone, Copy, Debug, PartialEq, Eq)]
pub enum DataType {
/// IEEE 754 binary64.
Float64,
/// Exact signed 64-bit integers.
Int64,
/// UTF-8 strings without normalization.
String,
/// Boolean values.
Bool,
}
/// Contiguous logical va... |
615a2c472e62de2df2a283edbc20ffbc20d264848b5326ca368f10da78bc3c33 | Rust | 3,978 | 111 | use std::path::PathBuf;
use clap::{Parser, Subcommand};
const CATALOG_URL: &str =
"https://raw.githubusercontent.com/jolars/datamonger/main/registry/catalog.json";
#[derive(Parser)]
#[command(
name = "datamonger",
version,
about = "Verified research dataset artifacts"
)]
pub(crate) struct Cli {
/... |
be885b56b2d7a8545b731d5882227bae224a44f4f6ba999728bc194a0c7d6c19 | Rust | 4,386 | 124 | use std::io::{BufReader, Read, Write};
use std::time::Duration;
use flate2::bufread::GzDecoder;
use reqwest::blocking::{Client, Response};
use reqwest::header::{ACCEPT_ENCODING, CONTENT_ENCODING};
use reqwest::redirect::Policy;
use crate::error::{Error, Result};
pub struct HttpClient(Client);
impl HttpClient {
... |
7902aaaef50ac6a83559a4e405540a37a83f1626030381aab1eb633d4625035e | Rust | 8,106 | 227 | use std::collections::HashSet;
use std::io::Write;
use sha2::{Digest, Sha256};
use crate::{Component, Control, Error, ErrorKind, Result, Shape, Values};
/// Maximum number of canonical bytes emitted in a single writer call.
pub const EMIT_BYTES: usize = 65536;
fn invalid(message: &str) -> Error {
Error::new(Err... |
905fa740cda5d98ee91556abe68f20078b7635c06146ecfdea2ef1944544f494 | Rust | 8,860 | 244 | use std::io::{self, BufRead, BufReader, Read, Write};
use crate::{Error, ErrorKind, Result};
/// Manifest-declared artifact compression.
#[derive(Clone, Copy, Debug, PartialEq, Eq)]
pub enum Compression {
/// Uncompressed bytes.
None,
/// Gzip compression.
Gzip,
/// Bzip2 compression.
Bzip2,
}... |
e56d17240d49be6a86bd0ef4e65d8fd1828ced2163aa491d05fefa335608a237 | Rust | 10,967 | 344 | use std::fs;
use std::io::{Read, Write};
use std::net::TcpListener;
use std::path::Path;
use std::process::{Command, Output};
use std::thread;
use std::time::{Duration, Instant};
use flate2::Compression;
use flate2::write::GzEncoder;
use serde_json::{Value, json};
use sha2::{Digest, Sha256};
use tempfile::TempDir;
co... |
d91c20a47a0d9e8dbdaecc28914fd73d1f8a3e9be65b4c3aee23a12f9b940aa3 | Rust | 12,912 | 392 | use std::collections::{HashMap, HashSet};
use std::fs::{self, File, OpenOptions, TryLockError};
use std::io::Read;
use std::path::{Path, PathBuf};
use std::time::UNIX_EPOCH;
use serde::Serialize;
use sha2::{Digest, Sha256};
use tempfile::NamedTempFile;
use crate::error::{Error, Result};
use crate::registry::{BUNDLED_... |
157517b5bc8b11e1d2ea8e77be50dcb46d06ad9b282db640d588474195368022 | Rust | 12,978 | 357 | //! Private Python conversions around the language-independent decoder.
use std::fs::File;
use std::path::PathBuf;
use datamonger_core as core;
use numpy::{IntoPyArray, PyReadonlyArray1};
use pyo3::exceptions::PyValueError;
use pyo3::prelude::*;
use pyo3::types::{PyBytes, PyTuple};
pyo3::import_exception!(datamonger... |
e1e0d0fc6c732cb7c779caf89fa06ac21b9c8d59fef7cb9f39d9cacea112697f | Rust | 15,302 | 465 | //! Private R conversions. The reusable decoder has no dependency on this crate.
use std::ffi::{c_int, c_void};
use std::fs::File;
use std::io::Cursor;
use datamonger_core as core;
use extendr_api::prelude::*;
extern "C" {
fn R_CheckUserInterrupt();
fn R_ToplevelExec(fun: Option<unsafe extern "C" fn(*mut c_v... |
e5c2547d619490d34cd3657813b4c3e19f9c3613cda8da2af472e35ad69df927 | Rust | 17,581 | 546 | //! C ABI 1. The public contract and ownership rules are in include/datamonger.h.
//!
//! Unsafe code is confined to borrowing caller-owned slices and result handles.
//! The decoder and canonical encoder themselves live in the safe core crate.
#![allow(clippy::missing_safety_doc)]
use std::ffi::c_void;
use std::fs::F... |
53ffabe5077f315367886b29bc3e81a19a486f1f6907b3cdce64dc4d7cf2e685 | Rust | 18,446 | 501 | use std::collections::HashSet;
use std::fs;
use std::path::Path;
use jsonschema::Registry;
use reqwest::Url;
use serde::{Deserialize, Serialize};
use serde_json::Value;
use sha2::{Digest, Sha256};
use crate::error::{Error, Result};
pub const BUNDLED_INDEX: &[u8] = include_bytes!("../assets/index.json");
const BUNDLE... |
1913002789bfbf8089e3b1d97906c247050d7667778fd16547beacd2f7aef8b6 | Rust | 18,504 | 591 | use std::fs::File;
use std::io::{BufReader, Cursor, Read, Write};
use std::path::{Path, PathBuf};
use datamonger_core::*;
use serde_json::Value;
fn fixtures() -> PathBuf {
Path::new(env!("CARGO_MANIFEST_DIR")).join("tests/fixtures/conformance")
}
fn document(path: &str) -> Value {
serde_json::from_reader(File... |
b51c861f88061bd733130287cc5977ba377379707e439ce85ebbf73b20a02386 | Rust | 18,697 | 529 | mod cache;
mod cli;
mod error;
mod http;
mod registry;
use std::collections::BTreeMap;
use std::fs;
use std::io::{Seek, SeekFrom, Write};
use std::path::{Path, PathBuf};
use clap::Parser;
use serde_json::{Value, json};
use tempfile::NamedTempFile;
use crate::cache::{CachedFile, default_root};
use crate::cli::{CacheC... |
d9cdd1d2d200eb5ed1c9fc95a2f33e69b16fb6a9c4b04fcca18f9affbd3be1ec | Rust | 19,045 | 590 | use std::collections::HashSet;
use std::io::BufRead;
use crate::{Component, Control, DataType, Error, ErrorKind, Result, Shape, Values};
/// A declared delimited-text column.
#[derive(Clone, Debug)]
pub struct Column {
/// Exact header and component name.
pub name: String,
/// Declared logical type; no in... |
9ea83b1cba78918a9d5bd8920c058b24b7fe9a92cdfed0b86708ad89550fc1fb | SAS | 1,170 | 43 | /* jconfig.sas --- jconfig.h for Amiga systems using SAS C 6.0 and up. */
/* see jconfig.txt for explanations */
#define HAVE_PROTOTYPES
#define HAVE_UNSIGNED_CHAR
#define HAVE_UNSIGNED_SHORT
/* #define void char */
/* #define const */
#undef CHAR_IS_UNSIGNED
#define HAVE_STDDEF_H
#define HAVE_STDLIB_H
#undef NEED_BSD... |
c82b383c7b8b47649544b43e2c32c7da9ce43236007d132edef972e7a10be389 | SAS | 3,252 | 119 | *SCRIPT TO ANALYZE HEAD MOVEMENT PARAMETERS OF PROJ-EMOSYMP
AUTHORS: LUKAS VAN OUDENHOVE
@DARTMOUTH, APRIL 2021
-----------
DATA IMPORT
-----------;
%let path=C:\Users\lukas\Dropbox (Dartmouth College)\fMRI_emotion_Giao\BIDS\qc;
%let outputdir=C:\Users\lukas\Dropbox (Dartmouth College)\fMRI_emotion_Giao\BIDS\qc;
proc... |
659ccf7679c239df3d5c34674957d14a7f806d8928b9642218937fd4f23b5964 | SAS | 13,028 | 259 | # Makefile for Independent JPEG Group's software
# This makefile is for Amiga systems using SAS C 6.0 and up.
# Thanks to Ed Hanway, Mark Rinfret, and Jim Zepeda.
# Read installation instructions before saying "make" !!
# The name of your C compiler:
CC= sc
# You may need to adjust these cc options:
# Uncomment the... |
6984f18bd2ef91b1008fbe60472849b9180d369ceaebed25d6fdaa8d3edd69e7 | Scala | 2,624 | 80 | /*
Copyright (c) 2024-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
ed69f1a21341670a44a1a54c95ea796a9ce78be8de1d658d77efcc8078d3db2c | Scala | 2,640 | 67 | /*
Copyright (c) 2014-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
a748f8e2c640a6bcd56a845f3bd440c66575518a111a049c0771b626d8da7a09 | Scala | 4,662 | 138 | /*
Copyright (c) 2014-2024 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
4876fe87885e48d2e210c49459a8a851474310acbfa0a1e1f72a0ad49114e53e | Scala | 8,373 | 210 | /*
Copyright (c) 2014-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
c4e71ed3544d1e98a28f3890031590c57878a8550adb6cd7a43a3c6058acdc02 | Scala | 12,207 | 319 | /*
Copyright (c) 2014-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
219cb31969b086fc9555aa6a841499188ebe7fe45978880c736afdb773a8d298 | Scala | 17,348 | 459 | /*
Copyright (c) 2024 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, so... |
6790909f87503e8b1b3b2f1a7f54b4c4ae64d34fbe4b75fb9479a96551b29e3c | Scala | 27,254 | 756 | /*
Copyright (c) 2024-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
c3406ea62326cc42bc2e332e7d38820d7dc8fbe726ead2b0d3347dc64a226ac1 | Scala | 40,105 | 1,063 | /*
Copyright (c) 2024-2026 by Contributors
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writin... |
3687c54588adca5f3021419c9ace43f878d912d200d6d6f506a09db4fe92d082 | Shell | 32 | 1 | nohup python -u run.py >> log &
|
e23d3be6fe487b78eed63ccf4b3c05a6af5b57e4c10d0c813a67c8ef1a4d2bbb | Shell | 66 | 4 | #!/bin/bash
bash zUMIs/zUMIs.sh -y yaml/zUMIs_yaml_example.yaml
|
bd3bf738920748fe8809c1826019fdafff100cfe0277d8ee87c5323982069381 | Shell | 68 | 3 | #!/bin/sh
/usr/bin/python3 /opt/algorithm/processor.py 2>/dev/null
|
7069fe6c90d37bdcbf47886121987af6c735e3272416b71825e80271a2958369 | Shell | 70 | 4 | #!/usr/bin/env bash
pip install -r requirements.txt
pip install -e .
|
9b9708610fc5503e52156d5d39154c5e45cd865bc3d149b8970b19b69d6db98f | Shell | 75 | 7 | #!/bin/bash
for i in {1..3}
do
sbatch $i.sh
echo "Job $i submitted"
done |
97ecd59a93fb7f88c2a6707d4809044c9e23efaa37ae5b96bd2517048ce1b4ba | Shell | 76 | 4 | #!/usr/bin/bash
source ~/.venvs/cleanenv/bin/activate
python3 $@
deactivate
|
b4f15234ae527ca61df4e1747f5ec0b0279685a8ea5da085ee855efdccb29798 | Shell | 79 | 1 | awk 'OFS="\t" {print $2"."$3+1"."$4, $2, $3+1, $4, "."}' peaks.tsv > peaks.saf
|
469823443766bd98e6bfe69c094c47d9c4fef325c5c52bed6690b8f0bd29013f | Shell | 81 | 5 | #!/bin/bash
NUM_PROC=$1
shift
torchrun --nproc_per_node=$NUM_PROC train.py "$@"
|
22d63b69f8346eafb02ccd98a580e5134e20fc83491271928cf0e847101bf1d1 | Shell | 82 | 1 | $PYTHON setup.py install --single-version-externally-managed --record=record.txt
|
5b8067b820325979cae8dd2bb0e713bb8bb08a68df5b6330f3857a871cd27c91 | Shell | 84 | 2 | MYPATH="./data/"
annotatePeaks.pl $MYPATH/peaks.tsv hg38 > $MYPATH/annot_homer.tsv
|
734761500448f2d057d3e829e30364d1ab1d3301e185d7694b77cc76f81fbc3d | Shell | 87 | 4 | #!/bin/bash
NUM_PROC=$1
shift
torchrun --nproc_per_node=$NUM_PROC legacy_train.py "$@"
|
c353bc3e06d2e9aea938890d952fd0346d9e5348dff159b089f8f806e3d60dcf | Shell | 89 | 9 |
FILE=./exprs/tmp/tmp.txt
while [ ! -f "$FILE" ];
do
sleep 10
done
echo "Finished." |
040586c0c27215227d240eb104b463ad731b94f5096bc841b490c73eaea34b92 | Shell | 100 | 5 | #!/bin/bash
#./gfcne_training.sh 5ch 1
./depth_pos_training.sh 5ch 1
./cmp_more_training.sh 5ch 1
|
7eac82d034e45bc3950f1b09e54d0343be1bdbde120c9ea2ac38e369c98036fe | Shell | 101 | 3 | python3 test_zy.py --test_mode\
--dataroot ./five_cross_valid/fold_0\
--savepath ./result/fold_0\ |
dcf0f549a02b89cc48028554ac866ed9d8e3f121fe1ab4df66f3ba4b4f789a35 | Shell | 112 | 5 | cd ~
mkdir mmvt_root
cd mmvt_root
git clone https://your-github-user@github.com/mmvt/mmvt.git
mv mmvt mmvt_code
|
010cf76dd8d2de455a62daf070c55c5449bc110240b0630f463f6a5819c1365d | Shell | 120 | 8 | #!/bin/sh
set -x
libtoolize --force --copy
aclocal -I ./m4
autoheader
automake --foreign --add-missing --copy
autoconf
|
bc3dd23334ccd65cd321e3cb2bf1b53a97aa4d323bc5731ff92a71f2f8ee2c65 | Shell | 125 | 5 | # install MMVT
cd mmvt_code
python -m src.setup
#updated src.setup should account for
#all operating systems inclusing osx
|
58fb2e35c3b88d51e9f7969398f5233642030911f1cc30f2f171dc9e411934e9 | Shell | 126 | 7 | #!/bin/bash
CONFIG_FILE="${config.yaml}"
export CUDA_VISIBLE_DEVICES=${DEVICE}
python main.py --config_file ${CONFIG_FILE} |
6af87c5cef0eed426903001d00ada53f687fba73efeddb8745eb050f2c6089d2 | Shell | 126 | 6 | #!/bin/sh
#
# Basic sanity check for tiffdump
#
. ${srcdir:-.}/common.sh
f_test_reader "${TIFFDUMP}" "${IMG_MINISWHITE_1C_1B}" |
0d31225860ea21a2f8c9fdf4a76fc3ee2fd2056119dfb84b4dbcaa08a3633e35 | Shell | 136 | 5 | python3 train.py --name PETAV45\
--nEpoch 60\
--dataroot ./five_cross_valid/fold_0\
--savepath ./result/fold_0\
--gpu_ids 0,1,2 |
51ff1d586e1fe61141552baddbd1841c2a14b7fe2def87bbdc03b16c8b41e9bb | Shell | 136 | 8 | # Build documentation from scratch.
rm -r source/generated &> /dev/null
rm -r source/auto_examples &> /dev/null
make clean
make html
|
36dfdd4bc9985116e26e25bfd313cd14f2ad30eb155500c6b49be65afc34cfd2 | Shell | 142 | 5 | #!/usr/bin/env bash
./build.sh
docker save doduo1.umcn.nl/bodyct/releases/dram-emph-subtype:1.0.0 | gzip -c > dram-emph-subtype_1.0.0.tar.gz |
599067aa70af5d9264d6f2a9475a756355739b729875bb377eb6ad46fb40002a | Shell | 143 | 6 | #!/bin/sh
#
# Basic sanity check for tiff2pdf
#
. ${srcdir:-.}/common.sh
f_test_stdout "${TIFF2PDF}" "${IMG_MINISWHITE_1C_1B}" "o-tiff2pdf.pdf" |
99a080bb53d1292ebf77155fa2c0bcd66eb4beb4d9932eeefa0f72440ea8ddec | Shell | 143 | 3 | #!/bin/bash
MYPATH="/home/eloiseb/data/ATAC-seq_2024/"
awk 'OFS="\t" {print $1"."$2"."$3,$1,$2,$3, "."}' $MYPATH/peaks.tsv > $MYPATH/peaks.saf
|
a5bffec25a037729fdcc9a6350e6c46956d20856a126b46a8f873ef43a76388b | Shell | 145 | 6 | #!/bin/sh
#
# Basic sanity check for tiffinfo.
#
. ${srcdir:-.}/common.sh
f_test_reader "${TIFFINFO} -c -D -d -j -s " "${IMG_MINISBLACK_1C_16B}"
|
c29d8bf5a17a39b00de6012e59cd00121d3327726e09f8caa09444e473808e6d | Shell | 153 | 4 | #!/usr/bin/env bash
SCRIPTPATH="$( cd "$(dirname "$0")" ; pwd -P )"
docker build -t doduo1.umcn.nl/bodyct/releases/dram-emph-subtype:1.0.0 "$SCRIPTPATH" |
6f0a225b5cfdf7c2df2849e30b689f76019d6d72e314f86d06d7d44c11e18aeb | Shell | 155 | 7 | #!/bin/bash
python3 -m venv $HOME/venv
module purge
module load devel/cuda/11.4
source $HOME/venv/bin/activate
pip3 install -r requirements.txt
deactivate
|
237bf06f73db2f53a787121a65f8b471e9cca618d93b054601255ed1ba424102 | Shell | 156 | 14 | #!/bin/bash
./upool_eval.sh 5ch 1
./depth_pos_eval.sh 5ch 1
./depth_eval.sh 5ch 1
./cmp_eval.sh 5ch 1
./gfcne_eval.sh 5ch 1
./cmp_more_eval.sh 5ch 1
|
2c381ee3b10b005a35651416e0c15ee5251d9e6bb18cc21cce7a899a924f765f | Shell | 167 | 9 | #!/bin/bash
## conda environment name
ENV_NAME=bds_atac
ENV_NAME_PY3=bds_atac_py3
conda env remove --name ${ENV_NAME} -y
conda env remove --name ${ENV_NAME_PY3} -y
|
1527770f38bcb92fea2839f16384d221ffe12d42b5efcb13bd329a40ce69cc3b | Shell | 168 | 6 | #!/bin/sh
#
# Basic sanity check for tiffcp with G4 compression
#
. ${srcdir:-.}/common.sh
f_test_convert "${TIFFCP} -c g4" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g4.tiff" |
a8d17ad1c52c27b6d6cfe6dd47f9f137f4445606971c653b8764e9d2f5396c22 | Shell | 168 | 6 | #!/bin/sh
#
# Basic sanity check for tiffcp with G3 compression
#
. ${srcdir:-.}/common.sh
f_test_convert "${TIFFCP} -c g3" "${IMG_MINISWHITE_1C_1B}" "o-tiffcp-g3.tiff" |
45c293601e643de08020d5e58d86206c4b650046494594b7dddd30d5ed8dad88 | Shell | 169 | 8 | #!/bin/sh
#parse pubchem molecules and construct 3d from SMILES.
#SBATCH -J pubchem
#SBATCH -o pubchem.out
#SBATCH -p cpuQ --qos=normal
#SBATCH -N 1 -n 48
python mp.py
|
80f432ab5e724df696479099ca27467d17d5ef6b7f39ab94e0a3f2af8339e463 | Shell | 170 | 6 | #!/bin/sh
./bci_walls_with_t_test.py -f &
./bci_walls_with_t_test.py -m &
./bci_walls_with_t_test.py -d &
./bci_walls_with_t_test.py -e &
./bci_walls_with_t_test.py -n &
|
9afdf0ab42979102a0f5e436ff80bd96023da5a36c7dd76bf7f88b3a0381d825 | Shell | 182 | 6 | #!/bin/sh
#
# Basic sanity check for tiffps with PostScript Level 2 output
#
. ${srcdir:-.}/common.sh
f_test_stdout "${TIFF2PS} -a -p -2" "${IMG_MINISWHITE_1C_1B}" "o-tiff2ps-PS2.ps" |
b62dd918fa40a1ec0aab5877c3d92a26c81e0a86dc07b4fd58fb46ffede8fa71 | Shell | 182 | 6 | #!/bin/sh
#
# Basic sanity check for tiffps with PostScript Level 3 output
#
. ${srcdir:-.}/common.sh
f_test_stdout "${TIFF2PS} -a -p -3" "${IMG_MINISWHITE_1C_1B}" "o-tiff2ps-PS3.ps" |
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