sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1fd411df276fe1abdfc5cdb20346ce24414be410f350e311dfe379da4ef8c087 | R | 67,967 | 1,687 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
library(destiny)
library(presto)
library(dtw)
filter <- dplyr::filter
select <- dplyr::select
setwd('~/projects/cutntag/')
mark_colors <- c('H3K4me3'='#CB9ACA', 'H3K27me3'='#3AAFC3', 'H3K2... |
db51ab7f95438344b0c31f36dfb79703a684cde2a61eb0503424b186af2a38fd | R | 69,940 | 688 | ###########################################################################
## Author: Youtao Lu <luyoutao@sas.upenn.edu>
##
## Copyright (c) 2021-2023, Youtao Lu and Junhyong Kim, Department of Biology, University of Pennsylvania
## Copyright (c) 2021-2023, James Eberwine, Perelman School of Medicine, University of ... |
2ffd85fad293c71d8f26d95f7c5a333f10f526a3ccc6c8144a2d2239420ba534 | R | 72,157 | 1,906 | #' Calculate gene negative specific score
#'
#' Calculate gene specific score in negative direction
#' @param scrna obj to use
#' @param gene gene to use
#' @param assay which assay to use in obj, default RNA
#' @param slot which slot to use, default data
#' @export
#' @examples
#' @return alpha before normalization
#'... |
bc8729f21ae7333710d00589ed10d8a7c67b13cfd21fbe1fb49f25014a5b933e | R | 73,312 | 1,886 | source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
Matrix <- Matrix::Matrix
setwd('~/projects/cutntag/')
#### Read data ####
marks <- read_rds('dat... |
086a8ad1f2eb65d5d651d7d172d0065d248ff0e60083fe203b63cc8b93f93e0d | R | 76,410 | 1,256 | #------------------------------------------------------------------------#
#############PROJECT: infection & child brain development#################
#------------------------------------------------------------------------#
# Author: Anna Suleri
### Parts in this script:
#' Part 1: Transformations, mixed model, with... |
9128237a370c9441153a3b34504c9b696133f3f2be50598a7eb86a9cd7fd59fa | R | 86,174 | 2,047 | ---
title: "CSF Experiment"
output:
html_document:
code_folding: hide
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
```
## 10X scRNA seq
All samples are initially processed using the 10X cellranger pipeline. This workflow aligns the reads to the reference genome and deconvolutes the cell b... |
d0efe1f951424b1d718e18d6c8d13d1939e6db272cf4b4b26bb711e88ce3b1a9 | R | 86,291 | 1,495 | library(splines)
library(Matrix)
library(slam)
library(spam)
##..........................................................
## R-functions required to fit, predict and plot the P-spline Hierarchical Curve Data Model
## used in the second stage of the two-stage approach described in the paper
##
## "A two-stage approach... |
9cde620951e94381598946c16f0cd10eb3bd06a45a15ad61795015e82f06d45c | R | 94,527 | 1,543 | ---
title: "*Drosophila* Time Series - Dataset Evaluation Sheet"
output:
html_document:
number_sections: true
toc: true
toc_float: true
keep_md: FALSE
---
<style type="text/css">
body .main-container {
max-width: 1800px !important;
}
h1.title {
font-size: 38px;
color: DarkRed;
text-al... |
23224db2fe387d016b7c0a100dfffe77e7bc7a020027a2b43024a3dc2220ba2e | R | 94,748 | 2,467 | library(tidyverse)
source('~/scripts/single_cell/de.R')
source('~/scripts/single_cell/atac.R')
source('~/scripts/perturbator/de.R')
library(Pando)
rename <- dplyr::rename
filter <- dplyr::filter
select <- dplyr::select
dist <- stats::dist
setwd('~/projects/cutntag/')
mark_colors <- c('H3K4me3'='#CB9ACA', 'H3K27me3'... |
db00147d0b45c10c1c423128fbe9bdbef68692aeb0e621f88f78d24b260358f5 | R | 96,233 | 2,131 | # _____________________________________________________________________________
# -----------------------------------------------------------------------------
# FUNCTION: create_design_table
# ARGUMENTS: sample_design_file_path
# DESCRIPTION: Reads in the design table from a given path
# --------------------... |
7c84748fe699b6df7034b411945c1fa9e89e08bbb7b00abaced788a6a22b0ac7 | R | 96,702 | 3,173 | # Changes by AH
# changed from cex.lab=2 to cex.lab=1
# revised on 2-20-10
# - fix error in pass.structure: reverse rank.combined, so that big sig.value
# are ranked with small numbers (1, 2, ...)
# - fix error on get.ez.tt.all: get ez.cutoff from sorted e.z
#
# modified EM procedure to compute empirical CDF more p... |
5fc102685d721ad1cf4f851b0aecfd8c269cbdd13d6cc11a6446b97861d7b3cf | R | 98,614 | 3,348 | ---
title: "Codes for Figures"
author: "Zhe Fei"
date: "2023-06-12"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
```
## Figure 1: Dog AROCM
```{r}
datN12all = read.csv("/Users/feiz/Dropbox/N12.2018-9238DogBloodOstrander/SampleSheetAgeN12final.csv")
datN... |
7ee596722c9f6e9500947ce85fb9cf3cdf338b221606920be599f0d963661672 | R | 106,324 | 1,438 | ---
title: "Investigating the impact of vascular risk factors on the progression of white matter hyperintensities"
author:
- Frauke Beyer, PhD [1][2]
- Laurenz Lammer [2]
- Markus Loeffler [4][5]
- Steffi Riedel-Heller [5][6]
- Stéphanie Debette [1]
- Arno Villringer, Prof. [2][7]
- A. Veronica Witte, PhD... |
008a9d8161c33b7e242465ea582640c009fe0099fd7bb0100b103b4ad2d57e44 | R | 107,357 | 2,770 | ---
title: "PD_Fingerprinting"
---
```{r read in data & check for demo diff between groups}
library(dplyr)
library(ggplot2)
library(RColorBrewer)
library("ggpubr")
library(BayesFactor)
library(corrplot)
library(ggseg)
cbbPalette <- c( "#90319D","#E25987","#FFBF00","#3A3AA4", "#31CD71", "#F0792C", "#6C3ABF")
# read d... |
3a5460eea0cdd86b6647a8e44e51b85ccac5ed0fc827429fe7c7f7094e0b8ffb | R | 113,693 | 2,291 |
library(ggplot2)
library(reshape2)
library(cobs)
##SUMMARY: Compile and load the C libraries for faster core routines.
system("R CMD SHLIB -Wall permFDR.c")
dyn.load("permFDR.so")
##SUMMARY:
permFDR=function(
##SUMMARY: df or path_to_file containing true p-values
full_data,
##SUMMARY: column of full_data where actua... |
3c4aad7943510f7ce2257ae3916583f3add15b4253075c9e0d15601e4d9d48ec | R | 115,195 | 2,927 | ---
title: "PD_Fingerprinting"
---
```{r DONE setup & check for demo diff between groups}
library(dplyr)
library(ggplot2)
library(RColorBrewer)
library("ggpubr")
library(jtools)
library(BayesFactor)
library(corrplot)
library(ggseg)
cbbPalette <- c( "#90319D","#E25987","#FFBF00","#3A3AA4", "#31CD71", "#F0792C", "#6C3A... |
19f5478d9ad6e93f743a02c58200911ab8ebd171b741cbb37f1dc49d77d72535 | R | 116,468 | 2,001 | ######
# Parameters
#
path_home <- './R'
# Working directory with temperature data
setwd(path_home)
# Libraries to use
library(readr)
library(tidyr)
library(purrr)
library(ggplot2)
library(lubridate)
library(jsonlite)
library(dplyr)
library(stats4)
library(gridExtra)
library(grid)
library(stats4)
library(bezier)
libr... |
8a5f4fd0eb5c2410026e958285cd816d3f27a1249d7229b69d256e5933d8d248 | R | 126,704 | 2,573 |
## ---------------------------
##
## Purpose of script: Generate figures for thesis
##
## Author: Prakhar Bansal
##
## Date Created: 2022-03-27
##
## Copyright (c) Prakhar Bansal, 2022
## Email: pbansal@uchc.edu
##
## ---------------------------
##
## Notes:
##
##
## ---------------------------
## ... |
f3fc76df27e56d12b9931391f032b9f0fe24596c6ad4cf589da2ffa0b70e6bef | R | 172,171 | 5,033 | #!/usr/bin/env Rscript
###############################################
#loading libraries
###############################################
cat("loading libraries...\n")
require(scales)
library(devtools)
library(Seurat)
library(dplyr)
library(tidyr)
library(data.table)
library(simpleCache)
library(ggplot2)
library(pat... |
4b85844d72a20e1208cea326e76b133ad4f72df701606d0dbba516d32bcb8859 | R | 179,851 | 3,170 | #-----------------------------------SETUP------------------------------
#Study 2 Figures
#HCPD, HBN, & UT datasets
#Written by M. Peterson under MIT License 2023
#Nielsen Brain and Behavior Lab
#load libraries
library(mosaic)
library(dplyr)
library(ggpubr)
library(broom)
library(tidyverse)
library(rstatix)... |
5d69225b3a80d3363ce36311d29383de1a49a555397a5c7a7f71aac9c66f123b | R | 190,555 | 2,973 | ## Colors and abbreviations ####
#' @title Tissue abbreviations
#' @description Tissue abbreviations used in tables and figures
#' @format Unnamed character vector
"TISSUE_ABBREV"
#' @title Tissue colors
#' @description Tissue colors used in figures. Values are hex codes and names are tissue abbreviations [TISSUE_... |
4a413efbbb77e85634e12d4df9848094fd45fb3287fb43a9de0fd3a9c8d34a21 | R | 200,008 | 3,431 | ---
Author: "Amin Haghani"
Paper: "DNA Methylation Networks Underlying Mammalian Traits"
Authors: "Amin Haghani1, 2 †*; Caesar Z. Li3, 4 †; Todd R. Robeck5; Joshua Zhang1; Ake T. Lu1, 2; Julia Ablaeva6; Victoria A. Acosta-Rodríguez7; Danielle M. Adams8; Abdulaziz N. Alagaili9, 10; Javier Almunia11; Ajoy Aloysius12; Nab... |
af4365fd2cd573fe48b661a3d9b378787d53195971047663dda5c29b59dcadd7 | Shell | 26 | 2 | #!/bin/bash
pip install .
|
0e69bc6a9754b4035a22c56940fce99c1fae946dbe2fadb2318c9e48a956258b | Shell | 27 | 2 | #!/bin/bash
pymol 2P0R.pml
|
10259058e48ce86a66be4d1c5d6d8f4ba6cebe1b3fb2631ae44c0f7778ef3fed | Shell | 27 | 2 | #!/bin/bash
pymol 3LKF.pml
|
3a10b769f07fbce8947f88a0cbb2c053de3f375cf74b621994efb93e941f2e6f | Shell | 27 | 2 | #!/bin/bash
pymol 6X3P.pml
|
6f0461a82317cc3d6e2ed889a1e3969f9cf6ab05c87e5037ad78db602b66152e | Shell | 27 | 2 | #!/bin/bash
pymol 1ATP.pml
|
6f5bb4717ef4eba9d084db09a2c3b6728127793134e4e2323d4961f19f5a1dc7 | Shell | 27 | 2 | #!/bin/bash
pymol 1UYD.pml
|
8f480d047297b786d75482d0ebc5450673176f7a21dbf66395ef218604311544 | Shell | 27 | 3 | #!/bin/sh
quarto render .
|
93dd6a619b52eb86c9f4a9a6ab64da2abfc0a4fe816613cf92ebaa617e1ec0bb | Shell | 27 | 2 | #!/bin/bash
pymol 4URL.pml
|
9ba23e270bc91063d6b70908c14376eeac2b38513d9feb7c2bc6d9c241f74719 | Shell | 27 | 2 | #!/bin/bash
pymol 5WA6.pml
|
f5d9d0ad5b6fc6b11a7c0c4f5d4cd395a5b92c0574efe79f43891de116b4f1c9 | Shell | 27 | 2 | #!/bin/bash
pymol 7TAA.pml
|
095b3078760b024c448d5d39b607c0e1b57cc55898864bc5de0d98b2040d30df | Shell | 31 | 2 | #!/bin/bash
pymol 6TL9_cif.pml
|
66086301daf82a40abb25740e6e3f532de4501c82acb75ef02a3bee8a5f47abc | Shell | 31 | 2 | #!/bin/bash
pymol 5RGF_cif.pml
|
713ce40d6552bd54d442ccf6f782b6c9087493c314cf07d4d6779c6c2c9b74e7 | Shell | 31 | 2 | #!/bin/bash
pymol 3VI4_cif.pml
|
7f565cb469d0e65094a5f4bfd5fb0e9f63a94f30fffce28c1efeac9e7987adeb | Shell | 31 | 2 | #!/bin/bash
pymol 2P0R_mod.pml
|
bda3cd57b83bd78334a1e415f9c11ca7e735f34fe6df711417a8b6ee33f263de | Shell | 31 | 2 | #!/bin/bash
pymol 6X3P_cif.pml
|
fcecb92bbb3f0f2a7042596848353a156ad22e4d10c902d6a03d51bdc6d529e6 | Shell | 31 | 2 | #!/bin/bash
pymol 1QNH_cif.pml
|
0f3b3aaa084ac84425f02757794d35e9c3b589ba19e833f44d4541a8df364bd4 | Shell | 33 | 3 | #!/bin/sh
mkdir RSEM_reference/
|
0bfc1adb538c899f59d4ed85e72a64723c5a87a693261035bb060885f6587ce4 | Shell | 41 | 2 | #!/bin/bash
vmd 3LKF_out.pdb -e 3LKF.tcl
|
10c7daa878fcb1567a1b258ee5a3b9523d7243271c824a30f9809fffd332fff6 | Shell | 41 | 2 | #!/bin/bash
vmd 5WA6_out.pdb -e 5WA6.tcl
|
25acae94eef70c4722f9d8949d3bc070e0eb696a32024bec91948a989642f43f | Shell | 41 | 2 | #!/bin/bash
vmd 2P0R_out.pdb -e 2P0R.tcl
|
4b510df97d85b123cebb20121c84ce9f25efde86216178f54a29abcd9fe3ed52 | Shell | 41 | 2 | #!/bin/bash
vmd 7TAA_out.pdb -e 7TAA.tcl
|
5b73255fc86b25c3524970a885ae98fc7be3e821e5b806c2675a6b12ec3e4cf7 | Shell | 41 | 2 | #!/bin/bash
vmd 1ATP_out.pdb -e 1ATP.tcl
|
b8baa1080aad9e96fcaa21b5999766752db0cfe616eb086df325ce9369994117 | Shell | 41 | 2 | #!/bin/bash
texcount -merge frontiers.tex |
e90504ebf8713663f0c5b1b1cf23903ceb99723669de9862e8741c7bca3c24a9 | Shell | 41 | 2 | #!/bin/bash
vmd 4URL_out.pdb -e 4URL.tcl
|
f36cdccd4b3ea4e031bce82fe0dd990ceca46133392633f575af63ceb597111c | Shell | 41 | 2 | #!/bin/bash
vmd 1UYD_out.pdb -e 1UYD.tcl
|
f894daa775bd71ca5d24ac89d250915f2639efa73e6a6925797e0cca732ef5bf | Shell | 41 | 2 | #!/bin/bash
vmd 6X3P_out.pdb -e 6X3P.tcl
|
2ff40cdba414b4302254b0863d10f7ee5078d427f0941aaab7cd6c698742f718 | Shell | 45 | 2 | #!/bin/bash
vmd 6TL9_out.cif -e 6TL9_cif.tcl
|
422601f59031a263a98a62f2ba7aa649daccaa01f46fe98b01642543cc9732eb | Shell | 45 | 2 | #!/bin/bash
vmd 1QNH_out.cif -e 1QNH_cif.tcl
|
8b2c8e3c065946188875dd7bea9177e7d9b0b2714471210e69cadf359bcb7295 | Shell | 45 | 2 | #!/bin/bash
vmd 5RGF_out.cif -e 5RGF_cif.tcl
|
a60a59ac240a0c51909121e19c0a0793d81e688950e29ed3bb8b240f98b5a563 | Shell | 45 | 2 | #!/bin/bash
vmd 6X3P_out.cif -e 6X3P_cif.tcl
|
b7f467b9aa2348de0b8f7f5e2c8a67b567550aa285e488082a3c59bc1320b6f3 | Shell | 45 | 2 | #!/bin/bash
vmd 3VI4_out.cif -e 3VI4_cif.tcl
|
1845e884363bd249674ad3904cfe5d291d33aa532ac7db495356e85b9395be84 | Shell | 49 | 2 | #!/bin/bash
vmd 2P0R_mod_out.pdb -e 2P0R_mod.tcl
|
8263755ceaff49fa5523565d3d4392f3e48718b8982c68ee317c50d352415a8f | Shell | 51 | 3 | #!/usr/bin/env bash
jupyter lab "$@" --allow-root
|
a551863e896117cca7dab7497b8992eda56cacc55b14a881f449e90b2d2eff09 | Shell | 54 | 3 | cd $BIOEMUS_PATH/firmware
sudo make
sudo make install
|
64e12de2511b2c41b231b9b68ff939883dbaa8d8d81dfe73af1e2edc8b325965 | Shell | 55 | 5 | #!/usr/bin/env bash
mkdir build
cd build
cmake ..
make
|
7fa534016b1bd483a3a0c710143b0ca96908d844dd45a64bfabc8fb5e0c108a7 | Shell | 55 | 4 | #!/bin/bash
python ../scripts/state_specific_info.py
|
5a63897cfb64ce373ca622c1a52e963ad0517cf59362ed9731af6c68e5509e39 | Shell | 59 | 3 | #!/usr/bin/env bash
# properties = {properties}
{exec_job}
|
c8317024ae7c8eed50a97d86fde59a3a288fc2547e35db439e939c3d6443e67f | Shell | 60 | 4 | #!/bin/bash
if make debug test clean
then ./tests/utest
fi
|
c9ebe293eabcfaac62120e948995c9f4296ea2275198eac69bfeb9e513146fef | Shell | 62 | 4 | #!/bin/sh
PYTHONPATH="./:$PYTHONPATH"
python3 bin/scanatk.py
|
9d1d53cddba39aeded0dd716c1a93f914a71d6f245b8931bfd6d6cda12244b38 | Shell | 73 | 4 | #!/bin/bash
python ../scripts/get_tutorial_datasets.py -d "./mor-data"
|
5ccff42e434c37638f88e4e6402785eb4bc7498997dea7836ad761615836b12b | Shell | 75 | 3 | #!/bin/bash
GCR_PROJECT_ID=devenv-215523
DOCKER_IMAGE_NAME=psychscreen-app
|
8f443423237f4133b1aa0d6937bb864135aef6fa815610c58c5c36b10fbfbc1c | Shell | 80 | 3 | sudo rmmod dma_proxy
sudo xmutil unloadapp
sudo xmutil loadapp k26-starter-kits
|
2f2ca4ea7303c273544bcd915ad21f95ccba9e7bfcd72bb89de0ca00642bb7a6 | Shell | 82 | 2 |
$PYTHON setup.py install --single-version-externally-managed --record=record.txt
|
e7402deea7cf1573338cabcbaf33a0942ef1585ea6d9129e80d72d47a2fe3173 | Shell | 84 | 5 | #!/bin/sh
IN=$1
perl -F"\s+" -lane 'print $F[0] if $_ !~ /^\#/' ${1} | sort | uniq |
2c27e7d812617d35e62e50460ac7ab9d6d074b634afb26dbff526024852efda4 | Shell | 85 | 2 | #!/bin/bash
echo ">> Executing shell script before running the docker container ..."
|
4e1e0539bdb6689fff8fbb6e681297b25c1aa21eb77c2535e3a0303b46f0755e | Shell | 87 | 3 | set -e
python support_extract_disease_specific_cohorts.py
python support_preprocess.py
|
6f9455b5c2ed68ef26ed76461828e40bae6b31b38e98019c0061c1756c43de78 | Shell | 90 | 3 | rm dist/*
rm build/*
python3 setup.py sdist bdist_wheel && python3 -m twine upload dist/*
|
a70f99f5e46dd94a8dad1504166fe9b2910e9062049c944d33550a7ae7ac09e9 | Shell | 90 | 5 | #!/bin/env bash
rm -rf 1ns_lig*
rm -f out_*.{stderr,stdout}
rm -f parsed-*-template.yaml
|
d417b82f477387dd41b0d49c9b757e333c55737ee7bb581da82a224448b7a5d2 | Shell | 90 | 7 | #!/bin/bash
# properties = {properties}
# exit on first error
set -o errexit
{exec_job}
|
a95f2933cf3aacf9f29fe9caecafbb95792bc1fb50a701449ca1d059167c53eb | Shell | 96 | 8 | #!/bin/bash
#python ../scripts/hbond_featurizer.py
python ../scripts/density_featurizer.py
|
d4f27c4d99cc280043bb571a550ae836350a255808b773920c9a93189852e18b | Shell | 98 | 10 | #!/bin/bash
# compile PALM output into a single file
for i in *.csv; do
echo $i
cat $i
done
|
b4783e4ab3a6ee98af2061aa931e1ea8a678feaf49f7682af3775cd04d0ff1dd | Shell | 101 | 2 | set -ex
python train.py --dataroot ./datasets/colorization --name color_pix2pix --model colorization
|
562c793656763206e72d0513986c634ee566f915890989c144ad23b9d5ca3c99 | Shell | 102 | 5 | #!/bin/bash
echo ">> Executing shell script right after running the docker container ..."
/bin/bash
|
8d9522d6b470321b89e3cbbded0ec67ae19cc1ee34c73a860ef05f14c53b06b0 | Shell | 102 | 1 | g++ -std=c++11 render_balls_so.cpp -o render_balls_so.so -shared -fPIC -O2 -D_GLIBCXX_USE_CXX11_ABI=0
|
127b3e2cfa9af9f1c0b5c2faa027bf96d76640b0a4ab9a0c84ef1e541430b3c4 | Shell | 107 | 5 | #!/usr/bin/env bash
# properties = {properties}
PATH="$HOME"/miniconda3/bin:"$PATH"
export PATH
{exec_job}
|
e8423742dabead17023f7333c52205c8cf23a354841de4096ff94bd36b860cf7 | Shell | 113 | 3 | sudo xmutil unloadapp
sudo xmutil loadapp kr260-bioemus
sudo insmod $BIOEMUS_PATH/drivers/dma_proxy/dma-proxy.ko
|
64acc0d4e67587cc0a02915a2343a63b57493c1136030292bbd301b5c698f60a | Shell | 118 | 2 | set -ex
python train.py --dataroot ./datasets/maps --name maps_cyclegan --model cycle_gan --pool_size 50 --no_dropout
|
687dbbf19fd509ae4705843335d6beec06398a6069b00b7e4d7f92e2837515b4 | Shell | 118 | 4 | #!/bin/bash
singularity exec ../../../../../singularity_containers/bernardo_article_analysis.sif ./get_new_reads.R
|
b7844041994708cc4fcb48008cd873eabac1e6063ad3858791cf25d6b09f5b3e | Shell | 121 | 5 | #!/bin/bash
export MODEL_FILE=$(pwd)"/src/test/resources/test-model.cpsign"
mvn clean package jetty:run-war -DskipTests |
e333fe6e3384fe938c9e01daad1a8a6fda594390b95f4a7b28b3e7f58234b499 | Shell | 123 | 3 | FOLDER=datasets/consortium/00_download/
xargs -a $FOLDER/SRR_Acc_List.txt -n 1 -P 8 prefetch -O $FOLDER/prefetch {}
exit 0
|
ba5127a06c8099673296efe5064d87ac3e6657a387b71494b11c3bb6cd24b908 | Shell | 124 | 6 | #!/bin/sh
set -eux
mkdir blastdb_${2}
cd blastdb_${2}
makeblastdb -in ${1} -out ${2} -dbtype prot -hash_index -parse_seqids |
ab62ea45fc1834227e0788b9b900c082c52cc2939e2f36289820928ad89b9d9d | Shell | 129 | 6 | #!/bin/bash
zcat $1 | \
awk 'OFS="\t" {if ($3=="gene") {print $1,$4-1,$5,$14,$10,$7}}' | \
tr -d '";' | \
bgzip > $2 |
64ef9085c7fd88ec5960b51a27500d23a0ed3a03d38bf5d4108f11ff90081435 | Shell | 135 | 1 | python generate_gexf_from_prov.py ../../outputs/provenance/R2G_PSD_all_subjects.ttl ../../outputs/provenance/R2G_PSD_all_subjects.gexf
|
c1da2ed3ef0bac91ef2e43ecbb66302f12bad4d173bf72e167bf5d6ec7d1e833 | Shell | 136 | 5 | #!/bin/bash
singularity exec ../../../singularity_containers/bernardo_article_analysis.sif ./make_volcano_plots_AD_vs_CT_no_intron.R
|
5f6301daffa5ddf2ad8b652fbe04b4ba5f4539995ea33aa75754e2725b8c652c | Shell | 137 | 5 | #!/bin/bash
wget https://huggingface.co/datasets/sywang/CNNDetection/resolve/main/progan_val.zip
unzip progan_val.zip
rm progan_val.zip
|
956095d4ce739820951cc6b5b75db5b700a5ce1980e356f0b6be2badab1f5d8a | Shell | 137 | 6 | #!/bin/bash
export MODEL_FILE=$(pwd)"/src/test/resources/test-model.cpsign"
#clean package
mvn clean package jetty:run-war -DskipTests |
8c9e966a8631850a6bf773f77d11fecf99aa176650c49c363698774acba14c73 | Shell | 138 | 10 | #!/bin/bash
source ~/.bashrc
conda activate pwmml_ioannis
clf_id=$1
final_lvl_clf=$2
python -u pu_learning.py $clf_id $final_lvl_clf
|
3d46db07662b5bac8e5f1741bd558a2079dabeb2e0bdf72c930b0643e2a07c53 | Shell | 141 | 7 | git pull upstream main
cd ../NDViewer
git pull upstream main
cd ../NDTiffStorage
git pull upstream main
cd ../AcqEngJ
git pull upstream main
|
8ecbeefd1fb3e1ac32f785661852e85c55e6f1091b8d877801b2a02efdea096a | Shell | 141 | 3 | #!/bin/bash
bcftools annotate -a $1 -c CHROM,FROM,TO,GENE -h <(echo '##INFO=<ID=GENE,Number=1,Type=String,Description="Gene name">') $2 > $3 |
d53967dbc8469e36b3fb7a82a2797f751caa5728bd6bca8e3b58069efc144c21 | Shell | 148 | 4 | #!/bin/bash
set -eu
python3 compare_with_annotations.py -a annotations_FC_2021Nov/corrected_z40.nrrd -s predictions/labels32_z40.nrrd -o `pwd`/val
|
4a5cb7b6087466836fe91ac3310182f78e2e846f607d18027e4c7856ad57d66e | Shell | 156 | 4 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
exec "${PYTHON_BIN:-python3}" "$SCRIPT_DIR/pipeline.py" "$@"
|
f44db30f78cd62bba14d6e6801de977f4556529e9a138dc84fb93c2f30463dc1 | Shell | 157 | 8 | #!/bin/bash
set -euo pipefail
set -x
bam=$1
sam=${bam%bam}sam
samtools view -h $bam | bismark_bam_UMI_format.awk >$sam
samtools view -b -o $bam $sam
rm $sam
|
59b98992f0741eb78fea672240900cc8ff318da53e1c4f314816e3401da3e1fa | Shell | 158 | 5 | #!/bin/bash
wget https://huggingface.co/datasets/sywang/CNNDetection/resolve/main/CNN_synth_testset.zip
unzip CNN_synth_testset.zip
rm CNN_synth_testset.zip
|
10a59f7a541ff3ca69a3b52c5e9e701c7074a66e527b1081bde5fdcf468b10d8 | Shell | 160 | 8 | #!/bin/bash
singularity exec ../../../singularity_containers/bernardo_article_analysis.sif ./01_create_new_gtf_for_fastas.R
./02_create_fastas_for_meme.sh
|
635c9ab05dbf8f8787cbc9d794dd2b8513aaedd36b8d359b084ce448368c7cf7 | Shell | 163 | 6 | # code to substitute code in job files.
filename='job_sub-0101007_ses-1.sh'
search='N4_reg --anat_autobox'
replace='no_reg'
sed -i "s/$search/$replace/" $filename |
de499fd32592da6ed8b152be3950366fbb7606f0aa73f7bc9f9a9ef306d40d29 | Shell | 164 | 6 | case $CI_OS in
windows*)
eval "$(${CONDA}/condabin/conda.bat shell.bash hook)";;
*)
eval "$(${CONDA}/condabin/conda shell.bash hook)";;
esac |
9e193dcf8dea0d5eca4876e17994da5c6e700e4c512f600f849e30af9b92a80c | Shell | 166 | 7 | #!/bin/bash
cd /home/pi/piPaw/
until python3 -u piPaw_amplitude.py &>>log.txt; do
echo "'piPaw program' crashed with exit code $?. Restarting..." >&2
sleep 1
done
|
d926205babf39313de33d2359d07fdcfbc8f435093793c8bf84c6ab5f745a5e5 | Shell | 171 | 6 | #!/bin/bash
source parse_yaml.sh
eval $(parse_yaml ../config.yaml CONF_)
docker build -t $CONF_project_docker -f $CONF_project_root_host/$CONF_project_name.Dockerfile .
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.