sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cdef925153b20d3abddc6e4722e0a0dde188bea51a61c82c94cfbcc37f0cd2b9 | R | 150,892 | 3,327 | # read in required libraries
libs <- c( 'gplots','stringi','reshape2','cowplot','RColorBrewer',
'sctransform','stringr','org.Mm.eg.db','AnnotationDbi',
'IRanges','S4Vectors','Biobase','BiocGenerics','clusterProfiler',
'biomaRt','Matrix','DESeq2','RcppThread', 'extrafont', 'openxlsx',
... |
0634d6047da455c254332e7aa3d5fe895b7a34c188248ab3011b63305ec5808c | R | 154,714 | 5,760 | library(loupeR)
loupeR::setup()
library(SeuratObject)
library(SingleCellExperiment)
#############################################################################
#
# Filtered data (S1M + 2M) ("mismatched" samples)
#
#############################################################################
countMatrices <- read... |
ce718abdbe726e909ce8eac5d311277769d111eecce9650b6deca555d6c39e63 | R | 163,034 | 2,466 | # Read in required libraries
libs <- c( 'gplots','stringi','reshape2','cowplot','RColorBrewer',
'sctransform','stringr','org.Mm.eg.db','AnnotationDbi',
'IRanges','S4Vectors','Biobase','BiocGenerics','clusterProfiler',
'biomaRt','Matrix','DESeq2','RcppThread', 'extrafont', 'openxlsx',
... |
7ae9764d1550dabe30ecf797dd80b4f4df524dbd5d6473cdc11657e0c7ca5e6d | R | 166,259 | 1,499 | library(shiny)
library(Seurat)
library(ggplot2)
library(tibble)
library(cowplot)
library(viridis)
library(dplyr)
library(ggsci)
library(ggrepel)
library(tidyverse)
library(plotly)
library(htmlwidgets)
library(reshape2)
library(Hmisc)
library(corrplot)
library(pheatmap)
library(grid)
library(MAST)
library(shinydashboard... |
2e7ee3048540aa39ab0280da6b2eb26e6947296b00f46bad80788bb6ac33e735 | R | 168,320 | 3,014 | ##Figure 1 (Physiology) ----
setwd("/Users/mallott/Dropbox/Projects/Gut_microbiome/mouse_inoculation/phys_data")
library(tidyverse)
library(ggpubr)
library(ggnewscale)
phys = read_csv("Phys_combined_update_072722_noinfant.csv")
physnew = phys %>%
mutate(Treatment = case_when(Treatment == "human_Adult" ~ "Human",... |
167cba69d343df0c79ea7b625c01753a3e32792eea71bf59c3c8494b6f711501 | R | 168,362 | 3,853 | ########################################
######### Li et al., 2025 ##############
######### Main Script ##############
########################################
#----- Prepare R environement
```{r}
packages <- c(
"dplyr", "Seurat", "SeuratData", "SeuratWrappers", "ggplot2", "patchwork",
"sctransform", "co... |
ce91a8a8a1ecaf27183cd7c81483c21973083344742b667daf8ae9a4a04fa476 | R | 184,895 | 5,168 | # Test olink_normalization ----
# this tests also all functions called norm_internal_* except from
# "norm_internal_preferred_names", "norm_internal_update_pref_name" and
# "norm_internal_update_df_names".
#
# Namely:
# - norm_internal_assay_median
# - norm_internal_reference_median
# - norm_internal_bridge
# - norm_i... |
04c15c4a0ddb8643be8b005e995acfef82b6753038d5a6c2616619dc1553bf17 | R | 200,000 | 3,927 | ---
title: "SGCE Interneuron"
output: html_notebook
---
# Setup
```{r message=FALSE, warning=FALSE, include=FALSE}
# Choose the correct library location for R packages installation and usage
# diffrent paths provided depending on system setup
# Uncomment the desired path to set library location
# LIBLOC<... |
101f1631da01c572954e0b5b8c7463a6a0b1d853c4c83c4761eef95f47792b08 | R | 200,000 | 6,700 | # Test olink_norm_input_check ----
test_that(
"olink_norm_input_check - works - bridge normalization",
{
skip_if_not_installed("arrow")
# no normalization column ----
bridge_samples <- intersect(x = npx_data1$SampleID,
y = npx_data2$SampleID) |>
(\(x) x[!grepl(pa... |
3af257fb73945fe93822072df702df7aefe302bbc5b17396f2efe45e4fdc6d22 | R | 200,000 | 6,609 | ---
title: "Pipeline_For GeoMX_Data_Analysis"
author: "Thomas Goralski"
date: '2022-07-22'
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
This pipeline is intended for expedient analysis of raw data from Nanostring's GeoMx spatial transcriptomics platform.
The followin... |
4d677beb588e3cc895a95363e8bba50e86fb0457b7c7888ca4eb6b44408c80f9 | R | 200,000 | 2,480 | library(Seurat)
library(SummarizedExperiment)
library(ggplot2)
library(future)
library(scrattch.hicat)
library(data.table)
library(dplyr)
library(tibble)
library(pbmcapply)
library(SCISSORS)
library(MetaMarkers)
library(gplots)
library(SeuratWrappers)
library(SeuratDisk)
library(slingshot)
library(scales)
library(vir... |
634a75c7910f643a8ebd1c7e583c07e65112682067b65b471a0be7768978a214 | R | 200,000 | 4,311 | library(Seurat)
library(torch)
library(SummarizedExperiment)
library(ggplot2)
library(future)
library(scrattch.hicat)
library(data.table)
library(dplyr)
library(tibble)
library(pbmcapply)
library(SCISSORS)
library(MetaMarkers)
library(gplots)
plan("multicore", workers=10)
plan()
options(future.globals.maxSize= 387... |
6c362b81cee82b4afc0ea40688936b0da0dbda9960e88d200f2a7174eadde0fb | R | 200,000 | 5 | tissue_mapping <-
c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11)
N_tissues <- 80
W_sparse <-
structure(c(1, 1, 1,... |
a715cc5dc869557d39f12f8d6d81b02f2cc828d47215413815db73a3ef25a40c | R | 200,000 | 2,888 | # expected.coords.smooth <- coords(smooth(r.s100b), "all", ret="all")
# dump("expected.coords.smooth", "tests/testthat/helper-coords-expected-smooth.R_new")
expected.coords.smooth <-
structure(list(specificity = c(
0, 0, 0.0063876682047232314, 0.013341366018777919,
0.020344288637047729, 0.02732113845873314, ... |
b58939d7f0f4bdd0e57646dd9009554b69f2e0be9c8705326f2bd6a90071e33d | R | 200,000 | 5 | tissue_mapping <-
c(1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, ... |
c9b104078e9b83660b7b36cbf34bdb100c3aaab6c35fa8b19fcfe63b1290c6e0 | R | 200,000 | 7,379 | # Test read_npx_wide_split_row ----
test_that(
"read_npx_wide_split_row - works",
{
# variables that apply to all tests
olink_platform <- "Target 48"
n_panels <- 3L
n_assays <- 45L
n_samples <- 88L
show_int_ctrl <- TRUE
## NPX ----
# synthetic wide df
data_type <- "NPX"
sh... |
7f1c83cae3109cc7e8caeaac23a8a7b73e76e0d9ca1adacdb6554e68f61451dc | R | 200,001 | 4,928 | ---
title: "HeMoVal_Data_Analysis"
date: "2025-01-28"
authors: "Kevin Akeret & Raphael M. Buzzi. Statistical review: U. Held, D. Kronthaler"
output: html_document
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
library(Hmisc)
library(tidyverse)
library(table1)
library(scales)
library(ggb... |
b1871e172d30c817f563a5a10406abc29d2b1c93800f205caeb373f7442e575e | R | 200,001 | 4,756 | library(torch)
####################################
#Plot
####################################
library(ggplot2)
mytheme_classic <- theme_classic()+
theme(axis.text = element_text(size=14, color="black"),
axis.ticks = element_line(size=1),
axis.title = element_text(size=18, color="black"),
... |
d85897a401087e44f6cc3b7578bbb6fbd06947063b515269afe3b4cdae636f9f | R | 200,001 | 4,916 | ---
title: "HeMoVal_Data_Analysis - Additional explorative statistics (metHb)"
date: "2025-01-28"
authors: "Kevin Akeret & Raphael M. Buzzi. Statistical review: U. Held, D. Kronthaler"
output: html_document
editor_options:
chunk_output_type: console
---
```{r setup, include=FALSE}
library(Hmisc)
library(tidyverse)... |
98e41c2edb69bc525cac9d9b7d59dd7c72da24398cf2f1cb9515eb7200e9ebc0 | R | 200,016 | 4,255 | overall_start_time = Sys.time()
cat(file=stderr(), 'Loading dependencies...')
options(stringsAsFactors=F)
suppressMessages(library(tidyverse))
suppressMessages(library(janitor))
suppressMessages(library(binom))
suppressMessages(library(glue))
suppressMessages(library(lawstat))
suppressMessages(library(weights))
suppre... |
c6d187ab381e82c00baaa9c28efd73e6c53b69143897115cd17a836aaf38fcf7 | R | 200,019 | 4,359 | # The script is intended viewed in R studio
# Blocks are titled
# "=" symbol was used as an assignment operator
# Data processing and DE in initial cohorts is located in another file "Data_preprocessing_analysis/TRANSCRIPT_SUICIDE_PREPR_ANALYSIS_SCRIPT.R"
# Calculation of cohort-level moderators is located in "Moderato... |
ba3a1467f21e9e9ed1d682502b54e56bb663d3eacea5e6a6c9584b95455a0131 | R | 200,056 | 3,874 | # the purpose of this script is to find differentially expressed genes between conditions within cell-types
# load required libraries
libs <- c( 'gplots','stringi','reshape2','cowplot','RColorBrewer',
'sctransform','stringr','org.Mm.eg.db','AnnotationDbi',
'IRanges','S4Vectors','Biobase','BiocGen... |
054a71cba469c7e427da777e43dbb5cb5da444558add0fa492e8751b0f0b4dff | R | 200,089 | 4,666 | # Comments
# This code is intended to be viewed in RStudio and contains appropriate headings
# "=" symbol was used as an assignment operator
# Commands for STAR, fast, fastq tools and other command line tool/pythons scripts calls in the terminal is provided here as characters " <command code> "
setwd("/home/aleksandr... |
a8774494109da8a1cde3c184560403849b6455c234e5351bdb1f1858b78e5eb7 | R | 200,134 | 6,019 |
library(devtools)
library(monocle3)
library(Seurat)
library(SeuratWrappers) # For conversion helper
library(scater)
library(TSCAN)
library(slingshot)
library(tradeSeq)
library(scran)
library(ggplot2)
library(RColorBrewer)
library(grDevices)
library(DT)
library(pheatmap)
library(reshape2)
library(dplyr)
library(tidyr)... |
ee5564275aa1f18baeee83ff2a1dfdd0673116b6cb7513bf72d7fe9216fb4f20 | R | 215,997 | 5,505 | ---
title: "iscience_reverse"
author: "MM"
date: "2025-07-31"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
options(future.globals.maxSize = 10000 * 1024^2)
library(Seurat)
library(harmony)
library(dplyr)
library(scCustomize)
library(tidyr)
library(ggplot2)
l... |
fed9cfb12d26f8f863e56bef227d03225c75e2129cc8e5a0495ec651e7c51fb3 | Rust | 131 | 4 | ## A custom startup file for tests
## Run as if a system Rprofile, so no packages, no assignments
options(useFancyQuotes = FALSE)
|
dee9324880d89e4ad6b4bb9c3454b3bdcc9c675ccc5e265788ce4c4b97da77f6 | Rust | 699 | 30 | // Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use clap::Parser;
use yolov8_rs::{Args, YOLOv8};
fn main() -> Result<(), Box<dyn std::error::Error>> {
let args = Args::parse();
// 1. load image
let x = image::ImageReader::open(&args.source)?
.with_guessed_format()?
.... |
218af586e8840f8d5e4db91be7c519449b91ee158d1898d6448a3650f3d6bc56 | Rust | 726 | 19 | // in build.rs
//use clap_generate::{generate_to, generators::*};
include!("src/cli.rs");
fn main() {
/*
// creates an error with cargo publish and then installing
let mut app = Cli::into_app();
let outdir = std::path::Path::new(env!("CARGO_MANIFEST_DIR")).join("target/");
for bin_name in ["rb", "r... |
97d529590849b84f41464f1694eee69ce9296b9ba0f8f06b19eed0733c1e33fb | Rust | 1,028 | 36 | //! # Command line interface for rustybam
//! [rustybam command line interface, subcommands, and options.](cli::Commands)
//! # README for rustybam
#![doc = include_str!("../README.md")]
/// Annotation of bed files.
pub mod annotate;
/// Calculate stats from sam/bam/cram and paf files.
pub mod bamstats;
/// Bed file ut... |
9ea90781a8d5c575c943511ce4cad6d6a6e8b5aa25b885c2eca9bb78b8770b42 | Rust | 1,424 | 44 | use rustybam::paf::PafRecord;
/// A line with fewer than 12 columns must return an error.
#[test]
fn short_line_returns_err() {
assert!(PafRecord::new("").is_err());
assert!(PafRecord::new("A 1 2 3 + B 1 2 3 10 11").is_err());
}
/// A tag token that is too short must return an error.
#[test]
fn short_tag_retu... |
bed0679ef4ed20e721e9800af084539ea84a4a10495c84f07650feb6a207ba05 | Rust | 1,450 | 45 | use super::myio;
use needletail::{parse_fastx_file, parse_fastx_stdin, parser::LineEnding};
/// Split a fasta file across outputs
/// ```
/// use rustybam::fastx;
/// fastx::run_split_fastx(&["-".to_string()], ".test/large.test.fa.gz")
/// ```
pub fn run_split_fastx(files: &[String], infile: &str) {
// open the ou... |
079a627400f405d69f41347aa541cad8cbe7f0b45041281d82f742df8f4bc035 | Rust | 1,485 | 46 | use super::bed;
//use rayon::prelude::*;
use num_format::{Locale, ToFormattedString};
use std::collections::HashMap;
pub fn bed_stats(bed: &str, readable: bool, column: Option<u8>) {
let rgns = bed::parse_bed(bed);
match column {
Some(c) => {
let mut dict = HashMap::new();
for r... |
a8ebb3ccc85bba0cdb3a1288f1f9b2d78d8fd0c53d532253e2db4cea87c65a67 | Rust | 1,838 | 89 | // Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use clap::Parser;
use crate::YOLOTask;
#[derive(Parser, Clone)]
#[command(author, version, about, long_about = None)]
pub struct Args {
/// ONNX model path
#[arg(long, required = true)]
pub model: String,
/// input path
#[arg(l... |
468f5af286edfb213d35aa56b0336d37977561d311c4064576dac819212ec48f | Rust | 2,092 | 63 | use bio::data_structures::interval_tree::{Entry, IntervalTree};
use bio::io::*;
use itertools::Itertools;
pub trait IntervalTreeExt<N: Ord + Clone, D> {
fn find_bed_overlaps(&self, rec: &bed::Record) -> Vec<Entry<'_, u64, bed::Record>>;
}
impl IntervalTreeExt<u64, &bed::Record> for IntervalTree<u64, bed::Record> ... |
791af895bd6c260f4e777abb62bad74aa12b38c13951c02eb23ea6e01f919033 | Rust | 2,146 | 58 | use super::*;
use bio::alphabets::dna::revcomp;
use bio_types::strand::Strand::{Forward, Reverse};
use rust_htslib::faidx;
use std::str;
pub fn fetch_fasta(reader: &faidx::Reader, chrom: &str, start: usize, end: usize) -> Vec<u8> {
// rust-htslib 1.0 fetch_seq returns an owned Vec and frees the
// htslib buffe... |
a7b255ff0442b8bf1183208d4d2171a793a57f9314652e2f143f69bb9b4b842d | Rust | 3,514 | 98 | use anyhow::Result;
use flate2::read;
use gzp::deflate::Bgzf; //, Gzip, Mgzip, RawDeflate};
use gzp::BgzfSyncReader;
use gzp::Compression;
use gzp::ZBuilder;
use std::error::Error;
use std::ffi::OsStr;
use std::fs::File;
use std::io::{self, BufRead, BufReader, BufWriter, Write};
use std::path::{Path, PathBuf};
type Dy... |
4869d2399f70dc9f9a387492d0d24e3daff8abfe7284c52c3e9bf54256f0b829 | Rust | 3,995 | 108 | use linear_map::LinearMap;
use log;
use rust_htslib::bam::header::HeaderRecord;
use rust_htslib::bam::{self, Header, Read};
use std::collections::HashMap;
pub fn header_from_hashmap(hash_header: HashMap<String, Vec<LinearMap<String, String>>>) -> Header {
let mut header = Header::new();
for (key, values) in ha... |
87ef43606b33f83739fd43d86ddf2ae01527786f1c06dd237be526bf4b95b09d | Rust | 4,268 | 152 | use super::bed::*;
use rust_htslib::bam;
use rust_htslib::bam::Read;
use std::convert::TryFrom;
use std::fmt;
pub struct Nucfreq {
pub name: String,
pub pos: u32,
pub a: u64,
pub c: u64,
pub g: u64,
pub t: u64,
pub id: String,
}
impl fmt::Display for Nucfreq {
fn fmt(&self, f: &mut fmt... |
7c18f2a9d51e94c5dd46758e657c0cb5a038a440308ed12395094e371c49a5a8 | Rust | 4,721 | 153 | #![allow(clippy::type_complexity)]
// Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use std::io::{Read, Write};
pub mod cli;
pub mod model;
pub mod ort_backend;
pub mod yolo_result;
pub use crate::cli::Args;
pub use crate::model::YOLOv8;
pub use crate::ort_backend::{Batch, OrtBackend, OrtConfig, O... |
bb48fef23571c55a803f8eed235373da748e6360359c3902d7a283339fa5f17c | Rust | 5,186 | 186 | use super::paf::*;
use log;
use rust_htslib::bam::record::Cigar::*;
use std::cmp::{max, min};
/// Walk compressed CIGAR to compute per-position scores for query range [q_start, q_end).
/// O(n_cigar_ops + overlap_length) — no expansion to 1-bp resolution.
fn compute_overlap_scores(
paf: &PafRecord,
q_start: u6... |
48d608f7a1fdda27399d15e5b4b7ecff016e0b5434944cea091d642414afc35d | Rust | 5,489 | 242 | // Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use ndarray::{Array, Axis, IxDyn};
#[derive(Clone, PartialEq, Default)]
pub struct YOLOResult {
// YOLO tasks results of an image
pub probs: Option<Embedding>,
pub bboxes: Option<Vec<Bbox>>,
pub keypoints: Option<Vec<Vec<Point2>>>,
... |
37755dac823b0c42ac1b5e9881d53b0e5f23f37917a8ed6b08b2b2ade7bdb494 | Rust | 6,030 | 238 | // Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use anyhow::Result;
use clap::Parser;
use usls::{
models::YOLO, Annotator, DataLoader, Device, Options, Viewer, Vision, YOLOScale, YOLOTask,
YOLOVersion, COCO_SKELETONS_16,
};
#[derive(Parser, Clone)]
#[command(author, version, about, long_... |
5f64088af9de6852206425d71cfca0e8e429f8b98599865c03bb83710325bb07 | Rust | 6,554 | 235 | use crate::myio;
use bio::io::bed;
use lazy_static::lazy_static;
use regex::Regex;
use std::cmp::{max, min};
use std::fmt;
use std::str;
lazy_static! {
static ref BED_RE: Regex = Regex::new(r"([^\s]+)\t([0-9]+)\t([0-9]+)\t?([^\s]+)?.*").unwrap();
static ref RGN_RE: Regex = Regex::new(r"(.+):([0-9]+)-([0-9]+)")... |
8f7662bd3d8b07b0338730d44e49934db1e35df4f1bdfe3821b6ab48a8a6d7c7 | Rust | 7,733 | 270 | use super::bed;
use needletail::parse_fastx_file;
use num_format::{Locale, ToFormattedString};
use rayon::prelude::*;
use rust_htslib::bam::{self, Read};
use std::fs;
use std::io::{self, BufRead};
use std::path::Path;
fn read_bam(file: &str, threads: usize) -> Option<Vec<usize>> {
let mut lengths = Vec::new();
... |
d2b351e919bb2da1855a256d81299dee92639c6b87d8f96036225ade731527ff | Rust | 8,932 | 276 | use super::bed;
use rust_htslib::faidx;
use std::collections::HashMap;
/// Represents k-mer counts for a specific region category
#[derive(Debug, Clone)]
pub struct KmerCounts {
pub name: String,
pub kmer_counts: HashMap<String, u64>,
}
/// Generate reverse complement of a DNA sequence
fn reverse_complement(s... |
039f00d7506585cdf1dd6ed31e78c95d412c734cc18501a9d0bfd75a565b6f3c | Rust | 10,396 | 297 | use bio::alphabets::dna::revcomp;
use bio::data_structures::suffix_array::{lcp, shortest_unique_substrings, suffix_array};
use bio::io::fasta;
use std::{fs::File, io::BufReader};
static END_CHAR: u8 = b'$';
static END_CHAR_STR: &str = "$";
pub struct Genome {
pub names: Vec<String>,
pub starts: Vec<usize>,
... |
37b9ffea71bf783640c9c11207213a799ba0e53f28ba233d59976002cf35e3d0 | Rust | 11,323 | 367 | use colored::Colorize;
use env_logger::{Builder, Target};
use itertools::Itertools;
use log::LevelFilter;
use rayon::prelude::*;
use rust_htslib::bam;
use rust_htslib::bam::Read;
use rust_htslib::faidx;
use rustybam::cli::Commands;
use rustybam::fastx;
use rustybam::paf::paf_swap_query_and_target;
use rustybam::seq_con... |
59c293873c108613c11725886215f1f7f13afe41132ecb1aa18435c92ec57bd5 | Rust | 12,375 | 304 | use clap::IntoApp;
use clap::{AppSettings, Parser, Subcommand};
#[derive(Parser, Debug)]
#[clap(
author,
version,
about,
propagate_version = true,
subcommand_required = true,
infer_subcommands = true,
arg_required_else_help = true,
help_expected = true
)]
#[clap(global_setting(AppSettin... |
9dceaa7163e0249d7853dc5a1e104dbde47839331ab9854e646112c115463f22 | Rust | 12,416 | 402 | use super::paf;
use bio_types::strand::ReqStrand::*;
use colored::Colorize;
use lazy_static::lazy_static;
use regex::Regex;
use rust_htslib::bam::record::Aux;
use rust_htslib::bam::record::{Cigar::*, CigarStringView};
use rust_htslib::bam::Header;
use rust_htslib::bam::HeaderView;
use rust_htslib::bam::Record;
use std:... |
5f93cf2ca7a527f141bbd483f0d61d4dafc5441e7507d2a689b2da516a35e9e9 | Rust | 13,731 | 445 | use super::bed;
use super::paf::*;
use colored::Colorize;
use itertools::Itertools;
use rayon::iter::ParallelBridge;
use rayon::prelude::*;
use rust_htslib::bam::record::Cigar::*;
use rust_htslib::bam::record::CigarString;
use std::cmp;
pub enum Error {
PafParseCigar { msg: String },
PafParseCS { msg: String },... |
56006e860fd7a44fe7f5556cdac6c50623b0d5b124620efaf144b34ab2372bfc | Rust | 19,958 | 609 | // Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use anyhow::Result;
use clap::ValueEnum;
use half::f16;
use ndarray::{Array, CowArray, IxDyn};
use ort::execution_providers::{
CPUExecutionProvider, CUDAExecutionProvider, ExecutionProvider, ExecutionProviderDispatch,
TensorRTExecutionProvide... |
607f8f807bedf979b833be981c3b430d29160830ac060fd83508ecdd924a8343 | Rust | 22,962 | 652 | #![allow(clippy::type_complexity)]
// Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
use ab_glyph::FontArc;
use anyhow::Result;
use image::{DynamicImage, GenericImageView, ImageBuffer};
use ndarray::{s, Array, Axis, IxDyn};
use rand::{thread_rng, Rng};
use std::path::PathBuf;
use crate::{
gen_t... |
508d06fedfd61676f8ac937e44a88b7d4d9a7866bd4cbf4613bbf891ccb79b98 | Rust | 51,926 | 1,279 | //! Visual test cases for rustybam's liftover, trim, and break-paf operations.
//!
//! Each test contains an ASCII diagram showing the alignment, the region being
//! operated on, and the expected result. This makes it easy to verify correctness
//! by visual inspection.
use rustybam::bed::Region;
use rustybam::liftov... |
6befaa4e3df0198f76c12c700a7a18d06680eb39c2ff97ce817ac0910064a164 | Rust | 61,352 | 1,735 | use super::bed;
use super::getfasta;
use super::myio;
use super::trim_overlap::trim_overlapping_pafs;
use bio::alphabets::dna::{complement, revcomp};
use core::fmt;
use itertools::Itertools;
use natord;
use rust_htslib::bam::record::Cigar::*;
use rust_htslib::bam::record::CigarString;
use rust_htslib::bam::record::*;
u... |
055a1e4134f45e71f19e88812e0a90372361f0287d660b7a773f5ebbfb717493 | SAS | 72 | 3 | %macro rm_macro_debug;
options nomprint nosymbolgen nomlogic;
%mend;
|
f626054beb0a79e00ddfbe5780f7fe1b70abc04890b75f414d43c9d082926ff1 | SAS | 72 | 4 | %macro linuxtest;
proc print data=sashelp.cars(obs=20);
run;
%mend;
|
60a9d0a84a1e9526e2d2dfe94fe192950e00e500c9f4e4e9fd50d0bc36f54b8a | SAS | 118 | 3 | %macro getdsdvarsfmt(dsdin,fmtdsdout);
proc contents data=&dsdin out=&fmtdsdout(keep=name format) noprint;run;
%mend;
|
057065223ffaa686f74e9618088ea9fb59798b42cc2a9089f42c1ff905f7fb81 | SAS | 127 | 4 |
%macro ntokens(list);
%eval(1 + %length(%sysfunc(compbl(&list))) - %length(%sysfunc(compress(&list))))
%mend ntokens;
|
f064b31df916df537cdd552184703076a05895bb1b6dae05124d2c153daf00cf | SAS | 135 | 10 | %macro ClearLib(Libname);
proc datasets lib=&Libname kill nolist memtype=data;
quit;
%mend ClearLib;
/*
%ClearLib(work);
*/ |
ee472d25578311f432bf84e4adbc88b8f974612453ddca87cc44fc6a4321b202 | SAS | 136 | 9 | %macro getsystemseparator;
%if (&sysscp=WIN) %then %do;
%str(/)
%end;
%else %do;
%str(\)
%end;
%mend;
|
79ba5a596177a903b9fc6d1ab9e7414f0b7dc587022dbd9103a1e3182726caf5 | SAS | 144 | 7 | %macro isBlank(param) ;
%sysevalf(%superq(param)=,boolean)
%mend isBlank ;
/*Demo:;
*check whether the macro var is blank;
%isBlank(&xxx);
*/
|
f6aca1dd0968ac3b3af411064c866715706528f29222a00212282729edb70af5 | SAS | 145 | 7 | %macro shuffle_rows(dsdin,var,dsdout);
proc sql;
create table &dsdout as
select &var from &dsdin
order by rand('uniform');
quit;
%mend;
|
7dceec3d146c88cf64c80c5c5313b90b2a8ff7956434062d3004b23459b063ce | SAS | 151 | 9 | %macro delete_dir(dir);
filename del_dir "&dir";
data _null_;
rc=fdelete('del_dir');
put rc=;
msg=sysmsg();
put msg=;
run;
%mend;
|
d108bc300da266564058ff0fa3268d6bc14f3ccbf4c7142e9d9c919111f01a40 | SAS | 152 | 8 | %macro import_fam(file,out);
proc import datafile="&file"
dbms=dlm out=&out replace;
delimiter=' ';
getnames=no;
guessingrows=2000;
run;
%mend;
|
a646eaf8ab59b5c1eb931806d69027cfdc499aa6fc2f2b06df307997a0c93e8d | SAS | 170 | 10 | %macro import_plink_ped(
pedfile=,
out=x
);
proc import datafile="&pedfile" dbms=dlm out=x replace;
getnames=no;
delimiter=' ';
guessingrows=10000;
run;
%mend;
|
20573d5565f4da5919771c381a1339cdf85c3e3599e31ec2f9f9b9c0099859a8 | SAS | 181 | 10 | %macro delete_file_or_dir_with_fullpath(
file_or_dir_fullpath=
);
filename fileref "&file_or_dir_fullpath";
data _null_;
rc=fdelete('fileref');
run;
filename fileref clear;
%mend;
|
e5ae6a3e5b67b192045e019959e534ff85c20646afc0f60a30db6fe9a26cf50d | SAS | 197 | 6 | %macro importmacroslinux;
%let MacroDir=/project/fas/gelernter/zc254/SAS/SAS-Useful-Codes/Macros;
%include "&MacroDir/ImportAllMacros.sas";
%ImportAllMacros(MacroDir=&MacroDir,filergx=.*);
%mend;
|
9cb188cb4c5fddae8082e9fe59c7c65e1aff39f0562cce606122f68016992adc | SAS | 199 | 8 | %macro del_file_with_fullpath(fullpath);
data _null_;
rc=filename("fname","&fullpath");
if rc=0 and fexist("fname") then
rc=fdelete("fname");
rc=filename("fname");
run;
%mend;
|
3618b120a263a8689f787cd2f89b1d4179b06180d314562db04f806cb6416b08 | SAS | 210 | 10 | %macro print_x_cmd_via_pipe(xcmd=);
/*Note: do not include double or single quotes in the xcmd argument*/
filename FX pipe "&xcmd";
data _null_;
infile FX;
input;
put _infile_;
run;
%mend;
|
3f9369553edd9191ed7b079a2224b17f7fc30a530ce16f7cc350cf281452329f | SAS | 212 | 8 |
%macro opends(name);
%if %sysfunc(exist(&name)) %then
%let dsid=%sysfunc(open(&name,i));
%else %put Data set &name does not exist.;
%mend opends;
/*%let dsname=sasuser.houses;*/
/*%opends(&dsname);*/
|
d3a3646463b6f23cd03d3ffef13daeec941fe4532369564b7123e835d591d303 | SAS | 213 | 9 | %macro findxy(dataname,xx,yy,outdsd=outa);
proc univariate data=&dataname noprint;
var &xx &yy;
output out=&outdsd min = minxx minyy max = maxxx maxyy;
proc print data=&outdsd;
run;
%mend findxy;
|
a6bb88d612360464c8053007ea27e5dc4fea0426adaf455ba00680829948f750 | SAS | 214 | 10 | %macro abort_when_file_not_exit(filepath);
%if %FileOrDirExist("&filepath") eq 0 %then %do;
%put no file for &filepath;
%abort 255;
%end;
%else %do;
%put file &filepath exists!;
%end;
%mend;
|
ec1e313e4f3e19ce48f7983af998ac45ac474a9de758783e29827df1b86ce820 | SAS | 241 | 10 | %macro Only_Keep_noduplicates(inputdsd,key,outputdsd);
proc sql noprint;
create table &outputdsd as
select * from &inputdsd
group by &key having count(*)=1;
quit;
%mend;
/*
%Only_Keep_noduplicates(inputdsd,key,outputdsd);
*/
|
15eb8b1b4bcf0375e8ad6accecf97570fd38eaf5774047dccff993af18fbb254 | SAS | 242 | 9 | %macro systran(prog,pathin,pathout,dsname);
options xwait;
%sysexec("&prog." &pathin.&dsname..sas7bdat &pathout.&dsname..dta /Y);
options xwait;
run;
%mend;
*%systran(C:\Program Files\StatTransfer7\st.exe,c:\data\,d:\data\,tempx);
|
c8495b2fb414860585d30c4dd54b636f04950403f0b6804c3844364eec7cb22a | SAS | 244 | 13 | %macro chdir(dir);
%let dir=%sysfunc(prxchange(s/\\/\//,-1,&dir));
%if "&sysscp"="WIN" %then %do;
x "cd /d &dir";
%end;
%else %do;
data _null_;
rc=dlgcdir("&dir");
put rc=;
run;
%end;
%put changed into the &dir;
%mend;
|
933a08012cadfcdcbef35e19341d1c041693ef80d6698ed6b7ba69158a563dbe | SAS | 252 | 12 | %macro list2sql_by_grps(
list=A B C /*Replace blank spaces with comma using %str or %nrstr or %nrbquote*/
);
%sysfunc(prxchange(s/ +/%str(,)/,-1,&list))
%mend;
/*Demo codes:;
%let new_list=%list2sql_by_grps(list=A C);
%put &new_list;
*/
|
043af703dfcf0981c0a11099c9136a77387ba968a2ecb320992aec735bdc78e4 | SAS | 257 | 12 | %macro numargs(arg);
%if &arg= %then %do;
0
%end;
%else %do;
%let n=1;
%do %until (%qscan(&arg,%eval(&n),%str( ))=%str());
%let n=%eval(&n+1);
%end;
%eval(&n-1)
%end;
%mend numargs;
|
493076fc0028cda89d588d36bb106779a621cc4cac5a54528ce9d2ef212f9376 | SAS | 262 | 11 | %macro make_global_vars_with_prefix(vtot,varname=var_si,value4var=-9);
%do vi=1 %to &vtot;
%global &varname.&vi.;
%let &varname.&vi.=&value4var;
%end;
%mend;
/*Demo codes:;
%make_global_vars_with_prefix(vtot=20,varname=var_si);
%put &var_si1;
*/
|
4e179f13bca3f3c674dff966c567bf2dec31cdb51dc46688d0469df74a9ab013 | SAS | 263 | 18 | %macro debug_macro(
undebug=0 /*give 1 to reset macro debugging parameters;*/
);
%if &undebug=0 %then %do;
options mprint symbolgen mlogic;
%end;
%else %do;
option nomprint nosymbolgen nomlogic;
%end;
%mend;
/*Demo:
%debug_macro;
%debug_macro(undebug=1);
*/
|
63c6bad6e3cec38b4ffc63a9be33aaa6de36ffd0531637076f14b999d4d6ed41 | SAS | 282 | 12 | %macro LoadMacros;
%let macrodir=%sysfunc(pathname(HOME))/Macros;
%include "¯odir/importallmacros_ue.sas";
%importallmacros_ue;
%mend;
/*Demo codes:
*Load these macros;
options mprint mlogic symbolgen;
%include "%sysfunc(pathname(HOME))/Macros/LoadMacros.sas";
%LoadMacros;
*/
|
dd5322c18947ade3fc5b2d2baf5f71964252c0e687a7abe735a4497790479221 | SAS | 284 | 8 | %macro DoseVCF2Plink(DoseVCF,GP,PlinkOut);
data _null_;
call system("plink1.9.exe --vcf &DoseVCF --vcf-min-gp &GP --make-bed --out &plinkOut");
run;
%mend;
/*
%DoseVCF2Plink(DoseVCF=E:\Yale_GWAS\GWCIDR_GWGO\GWGO_GWCIDR.1kg_phase3_v5.chr13.dose.vcf.gz,GP=0.9,PlinkOut=Tmp);
*/
|
d154fff1c96bdacb7670db7b0acc1b227fce08d493b974a48d19e9c5f85fecd6 | SAS | 288 | 17 | %macro startxl;
filename sas2xl dde 'excel|system';
data _null_;
file sas2xl;
run;
options noxwait noxsync;
%if &syserr ne 0 %then %do;
x '"C:\Program Files (x86)\Microsoft Office\Office12\excel.exe"';
data _null_;
x=sleep(2);
run;
%end;
%mend startxl;
/*
%startxl;
*/
|
d704b05182a49c79446a128f9f7b4ab86c876589388a6173ac470c12f51450de | SAS | 315 | 17 | %macro dbquote_vars(vars);
/*%let &vars=CEU YRI;*/
%let re=%sysfunc(prxparse(s/ +/" "/oi));
%let var_list=%sysfunc(prxchange(&re,-1,"&&vars"));
%syscall prxfree(re);
%put &var_list;
&var_list
%mend;
/*Demo codes:;
data y;
set sashelp.cars;
where make in (%dbquote_vars(vars=Acura BMW));
run;
*/
|
e0c9bff2e26a644ccb5623262ac6c6a27ebdf2d4c6fa1efe5db24f20dc334c92 | SAS | 316 | 25 | %macro BMI(WgtPd_Var,HgtIN_Var);
%if &HgtIN_var= or &WgtPd_var= %then %do;
.
%end;
%else %do;
&WgtPd_var*0.45/(&HgtIN_Var*0.025)**2
%end;
%mend;
/*
options mprint mlogic symbolgen;
data a;
input Wgt Hgt;
BMI=%BMI(Wgt,Hgt);
cards;
125 63
;
run;
data b;
set a;
x=%BMI(Wgt,Hgt);
run;
*/
|
93f0a8ba67a63ba5477a2fec470f0a91943a4828711a53c2c25853c107550bca | SAS | 333 | 15 | %macro GetCWD;
/*Get current working directory;*/
%global cwd;
%let cwd=%qsubstr(
%sysget(sas_execfilepath),
1,
%length(%sysget(sas_execfilepath))-%length(%sysget(sas_execfilename))-1
);
%put %sysget(sas_execfilepath);
%put &cwd;
%mend;
/*Demo: Require the running sas script having been saved;
%GetCWD;
%pu... |
a8498ea35410358994ef92615e9523833d6dbabf343685226cad19da09443fd8 | SAS | 335 | 19 | %macro assign_str4missing(Inval,NewVal);
%let Updated_Val=;
%if %eval("&Inval"="") %then %do;
%put New value &NewVal is updated for your input string "&Inval";
%let Updated_Val=&NewVal;
&NewVal
%end;
%else %do;
&Inval
%end;
%mend;
/*Use it in macro ONLY;
%let X=%assign_str4missing(Inval=,NewVal=X... |
c4b2105cb800b91d8a911538142a984b4b9590ecfface8bcc53d3c01bb6ddbac | SAS | 339 | 15 | %macro UniHetGeno(dsdin,geno,dsdout);
data &dsdout(drop=Het);
retain Het '00';
set &dsdin;
&geno=strip(left(&geno));
if substr(&geno,1,1)^=substr(&geno,2,1) and Het='00' then Het=&geno;
if substr(&geno,1,1)^=substr(&geno,2,1) and Het^=&geno then &geno=Het;
run;
%mend;
/*
%UniHetGeno(dsdin=topsnp,geno=geno... |
321f5da561e2536c8fe317172ba4d605f29369609e2f773f13c54256a204fa22 | SAS | 342 | 29 |
%macro chk_sas_dsd(lib=work,dsdname=_last_);
%if %sysfunc(exist(&lib..&dsdname))
%then %do;
1
%end;
%else %do;
0
%end;
%mend;
/*Demo:
options mprint mlogic symbolgen;
data x;
input y ;
cards;
10
;
run;
%let chk=%chk_sas_dsd;
%put &chk;
libname sc "/home/cheng.zhong.shan/data";
%let chk=%chk_sas_dsd(lib=sc,dsdname... |
0a809bf73c4905335128a49f720746f583f2b989b87f1bfcbae926c999436168 | SAS | 343 | 13 | *options symbolgen mprint mlogic;
%global list;
%macro Quote_Varlist(list);
%let re=%sysfunc(prxparse(s/ /" "/oi));
%let list=%sysfunc(cat("%sysfunc(prxchange(&re,-1,&list))"));
%put macro variable list=&list;
%syscall prxfree(re);
%mend;
/*
options mprint macrogen mlogic symbolgen mfile;
%Quote_Varlist(lis... |
f977ae85f28ccb15aab0badf192d6e5344ed06fb14493aaa50ff66adbcd7235d | SAS | 343 | 21 | %macro BedCount(bed,st,end,out);
proc sql;
create table &out as
select sum(&end-&st+1) as total
from &bed;
quit;
data &out;
set &out;
WGS_Pct=total/2897310462;
/*hg19=2897310462 (non-N bases)*/
run;
%mend;
/*Demo:
libname G "G:\";
%BedCount(bed=G.promoter
,st=var2
,end=var3
... |
a19b07f610352d6fdaaddbb90db0b67e9e9c2e55289dfd4bb53a5090909d73b4 | SAS | 357 | 20 | %macro pname;
%global pgmname;
%let pgmname=;
data _null_;
set sashelp.vextfl;
if (substr(fileref,1,3)='_LN' or substr
(fileref,1,3)='#LN' or substr(fileref,1,3)='SYS') and
index(upcase(xpath),'.SAS')>0 then do;
call symput("pgmname",trim(xpath));
stop;
end;
run;
%mend pname;
/*
%p... |
4fce91f08f6ca0127d868c1c4101925e99769be3870c34425451592c54edda43 | SAS | 365 | 17 | %macro zscroe2p(dsdin,Zscore_var,dsdout);
data &dsdout;
set &dsdin;
pval= probnorm(&Zscore_var);
/*pval=cdf('normal',&Zscore_var);*/
if (pval > .5) then pval= 1 - pval;
pval= 2*pval;
*SAS only can obtain pval no more less than 1e-16;
if pval=0 then pval=1e-16;
run;
%mend;
/*
%zscroe2p(dsdin=both,Zscore_v... |
ab36edafb0fc77485713c1b8f52d6f49e7b0eed2029a0a3fc54be21c6a804900 | SAS | 368 | 23 | %macro delete_sas_dsd(dsdin);
%if %sysfunc(exist(&dsdin)) %then %do;
%put delete previous &dsdin;
%if %index(&dsdin,.) %then %do;
%let _lib_=%scan(&dsdin,1,.);
%let _out_=%scan(&dsdin,2,.);
%end;
%else %do;
%let _lib_=work;
%let _out_=&dsdin;
%end;
proc datasets lib=&_lib_ nolist;
delete &_out_;
run;
%en... |
2d781c4c87b30a7326f58fe4259a6127f87104af623a283b078871b75b33af68 | SAS | 370 | 16 | %macro totobsindsd(mydata);
%let mydataID=%sysfunc(OPEN(&mydata.,IN));
%let NOBS=%sysfunc(ATTRN(&mydataID,NOBS));
%let RC=%sysfunc(CLOSE(&mydataID));
%if "&NOBS"^="." %then %do;
&NOBS
%end;
%else %do;
0
%end;
%mend;
/*Demo:
%let nobs=%totobsindsd(sashelp.cars);
%put The total n... |
dc6848dfd89e359c7bd105b68b9f4b9f6cb7fa2567bf785bb1c3dc96eb59cd50 | SAS | 374 | 17 |
%macro Find_duplicates(inputdsd,key,outputdsd);
proc sql;
create table &outputdsd as
select * from &inputdsd as A1
where A1.&key in
(select &key from &inputdsd
group by &key having count(*)>1)
;
quit;
proc sort data=&outputdsd;by &key;run;
proc print data=&outputdsd;run;
%mend Find_duplica... |
43c17f805d087c4b7a74ee439b5c3c9f48184f12bc78f3dcb1215d88ceb984dd | SAS | 376 | 24 | %macro CloseSVG_Printer;
ods printer close;
filename out clear;
ods listing;
%mend;
/*Demo:
*Demo1:;
%OpenSVG_Printer;
*default svg figure will be saved into the $HOME dir with the name mysvgfilename.svg;
*It will recursively add numeric appendix to the svg filename;
*to avoid overwritting previous svg files;
*Pu... |
f4d81cd6e24ed8a70175b7b34d97f095d168196762ffa28dd04431a3afd718e8 | SAS | 379 | 14 | %macro figureit(a,b);
%let y=%sysevalf(&a+&b);
%put The result with SYSEVALF is: &y;
%put The BOOLEAN value is: %sysevalf(&a +&b, boolean);
%put The CEIL value is: %sysevalf(&a +&b, ceil);
%put The FLOOR value is: %sysevalf(&a +&b, floor);
%put The INTEGER value is: %sysevalf(&a +&b, int);
... |
db82d7ecc4b0958a27b2edf8c79c4f41634272a2de96a298c291899431884814 | SAS | 410 | 20 | %macro isDir(iPath=,iQuiet=1);
%local result dname;
%let result = 0;
%if %sysfunc(filename(dname,&iPath)) eq 0 %then %do;
%if %sysfunc(dopen(&dname)) %then %do;
%let result = 1;
%end;
%else %if not &iQuiet %then %do;
%put ERROR: ISDIR: %sysfunc(sysmsg());
%end;
%end;
%else %if no... |
3a72019ac06555895046e844ff32f37c3c34842c90a2d42041c4046f882d129b | SAS | 412 | 16 | %macro list_files_with_dopen(dir);
filename mydir "&dir";
data files;
did = dopen('mydir');
if did > 0 then do;
count = dnum(did);
do i = 1 to count;
fname = dread(did, i);
output;
end;
rc = dclose(did);
... |
b5eb207c6a1415b805a0ec65e63ae3774eca10be8f3aee5e6831743aceb2cb3c | SAS | 420 | 27 | %macro regression_estimator(dsdin=_last_,xvar=,yvar=,outdsd=PE);
ods graphics off;
proc reg data=&dsdin;
model &yvar=&xvar;
ods output ParameterEstimates=&outdsd;
run;
data &outdsd;
set &outdsd;
attrib Probt format=best32.;
run;
proc print;run;
%mend;
/*Demo:
*perform regression analysis with proc reg;
%regression_es... |
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