sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 10.7k | content stringlengths 1 200k |
|---|---|---|---|---|
261062bb41caf8a456600233d27618dfdb1119440835ef7ea8cfb39e44e23baf | Shell | 5,595 | 134 | #!/bin/sh
# MIT License
#
# Copyright 2018 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modi... |
cf7a93759a44275990ebab3db085ce3ee6b2b82e54cc816cb5b4d114f7d452e2 | Shell | 5,738 | 185 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# raw glue data as downloaded by glue download script (https://gist.github.com/W4ngatang/60c2bdb54d156a41194446737ce03e2e)
if [[ ... |
2855048072a0b251c9bdc29eb9458b098f8f20d19b7ac1c550fb97f7742db2fe | Shell | 5,830 | 58 | #!/usr/bin/env bash
##
# @file train_npc.bash
# @author Simon Yu
# @date 02/16/2024
# @brief Script for training NPC models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
# Joint optimization with data-driven PC
./train_npc.py -w "42.awa2.neural.resnet34mtl.2... |
968f8ae7799b306191a3af4b9495b2159aff42de8e01154a4b3f71300df35c88 | Shell | 5,875 | 111 | #!/usr/bin/env bash
#
# GPLv3 LICENSE INFO
#
# Copyright (C) 2020 Mario S. Valdes-Tresanco and Mario E. Valdes-Tresanco
#
# Project: https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU Gener... |
55acbba6e34b3728fe15a4b0bfba766457143c2609cd0e360539c7fc249684f1 | Shell | 5,878 | 172 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -d <docs> -t <setting> -k <no_topics>... |
b65073ae68fb01315a64d69e79d75e9df8c4cb1616bf997fda3e41b457800e96 | Shell | 5,895 | 180 | #! /bin/sh
# get the input file
file=$1
echo ""
echo "You are checking file: $file"
# check if the input file is a Matlab script
if [[ "`echo $file | cut -d '.' -f2`" != "m" ]]; then
echo "This file is not a Matlab script, quit."
exit 1;
fi
###############
# Move the comment block below the function name
###... |
99eff56ea0c10c699caff7ea08eedec9f616ade5cb480c1a725d59d402204c09 | Shell | 5,957 | 216 | #!/usr/bin/env bash
set -euo pipefail
# Lightweight end-to-end check for the public reproduction scripts.
#
# This is not a scientific reproduction run. It uses tiny datasets, one-epoch
# training, and dummy model weights where appropriate, so that dependency,
# path, TensorFlow weight-loading, data-generation, and p... |
8a1ff1f45120462755b86bfa562f33ed24c4229e362ee3982fa8d32040254d61 | Shell | 6,023 | 179 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function warps an input volumes to a target volume space with specified ANTs warp or inverse warp files
###########################################
# Main commands
###############... |
1f512ea0a89c45f227ece444768861d2ea2acaec2b07431870655227808b9908 | Shell | 6,025 | 185 | #!/bin/sh
#
# Example:
# sh ./CBIG_ASDf_unit_test.sh ~/storage/Temporaray/CBIG_ASDf_unit_test
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################################
# Set paths and create log file
###################################... |
241a5e9fadfed2a44720692044d7e91745d6cc9964c19a803232cbe516f6d316 | Shell | 6,063 | 196 | #!/bin/sh
# This script serves as a toy example of using the code in folder step1_FC2doc
# and step2_polarLDA in Tang2020_ASDFactors
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
#############################################
# Specify output director... |
306134e830ce98186c870f1ae09e48931d09d3357246df26d8b0cdb21c8840c4 | Shell | 6,110 | 186 | #!/usr/bin/env bash
# NEMO Benchmark Evaluation Script
# Runs NEMO evaluation on C4 database H5 files (requires spike times for 3D ACG)
set -euo pipefail
# C4 Database H5 files - loaded directly from S3 or local cache
# These are the original H5 files from https://www.c4-database.com/apps/download
# IMPORTANT: NEMO re... |
90289c142f3ca38a60f01caa6026b9e968ef3ad786424d3ab5ee3cdc681e1702 | Shell | 6,210 | 225 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#echo 'Cloning Moses github repository (for tokenization scripts)...'
#git clone https://github.com/moses-smt/m... |
02a2e48630cc6a6f4d18ef316f06642243c29f3169a663ee445db2ec830ae899 | Shell | 6,233 | 212 | #!/usr/bin/env bash
# Profile representative training on an NVIDIA GB10 machine.
#
# Usage:
# bash scripts/benchmarks/profile_gb10.sh
#
# Optional environment variables:
# GB10_PROFILE_CONFIG training config (default: best known config)
# GB10_PROFILE_LIMIT documents per split (default: 500)
# GB10... |
a4c4f2b19cf5affb8353bfbb4bd9319ac4ca0a1f5430ba21933914e2f590af99 | Shell | 6,373 | 210 | #!/bin/sh
#
# Example:
# sh ./CBIG_ASDf_replication.sh ~/storage/Temporaray/CBIG_ASDf_replication
#
# Written by Siyi Tang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
########################################
# Set paths and create log file
################################... |
b8e62860b6055fe155f692a32d4bc5972f1763edc03304485340a446a3322876 | Shell | 6,622 | 132 | #!/bin/bash
# Paths
export data_folder=/egor2/egor/MovieProject2/bids_data
export stim_folder=/egor2/egor/MovieProject2/stimuli
export fs_folder=/egor2/egor/MovieProject2/bids_data/derivatives/freesurfer
# Maximum number of parallel jobs nad threads
max_jobs=8
export OMP_NUM_THREADS=3
# Extract subject IDs dynamical... |
4904b196a81bf191cd5982f2f4da413a74fdc341d05ecf6525bfa5c78f8ed958 | Shell | 6,658 | 203 | #!/usr/bin/env bash
#
# Copyright (c) 2016-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
DATADIR=${DATADIR:-data}
report_error() {
echo "Error on line $1 of $0"
}
myshuf() {
perl -MLi... |
727ec3e80aaf52cd43691f8f9051c92b69733c4be92349d7ba82ce6d35f4276d | Shell | 6,720 | 95 | #!/usr/bin/env bash
##
# @file test_baseline.bash
# @author Simon Yu
# @date 10/03/2025
# @brief Script for testing baseline models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
./test_baseline.py -r "42.awa2.baseline.abm.2024.12.13.7.6.PowerEdge-R720"
./tes... |
6e06c244943c5de74c636024be93813fca611daad68d48ede2f2f16c36786a02 | Shell | 6,798 | 215 | #!/bin/bash
dcm2niix 006_S_4485/*/*/*/*.dcm
dcm2niix 006_S_6209/*/*/*/*.dcm
dcm2niix 006_S_6234/*/*/*/*.dcm
dcm2niix 006_S_6277/*/*/*/*.dcm
dcm2niix 006_S_6375/*/*/*/*.dcm
dcm2niix 006_S_6500/*/*/*/*.dcm
dcm2niix 007_S_6120/*/*/*/*.dcm
dcm2niix 007_S_6255/*/*/*/*.dcm
dcm2niix 007_S_6310/*/*/*/*.dcm
dcm2niix 007_S_6323... |
5fd4a31831a84dffe1ad76da3593f9a09615b4d39297a5327466847d452fe995 | Shell | 6,803 | 175 | #!/usr/bin/env bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey)
# Apache 2.0
# Begin configuration.
stage=-4 # This allows restarting after partway, when something when wrong.
config=
cmd=run.pl
scale_opts="--transition-scale=1.0 --acoustic-scale=0.1 --self-loop-scale=0.1"
realign_iters="10 20 ... |
f830a18a81698b231e2dd0fc264d773f80fc1ebe970c3b6feb3a22cb56161ffd | Shell | 6,816 | 146 | #!/bin/bash
# This script will generate replication input data for:
# 1) group priors estimation
# 2) individual parcellation generation
# The user need to specify the output directory, which will later contain two folders:
# 1) estimate_group_priors
# 2) generate_individual_parcellations
# Written by Ru(by) Kong and ... |
31b94daa4293650dba0e53ac595312e712dc7a397095b960218ead5dfb69c723 | Shell | 6,868 | 195 | #!/bin/bash
#SBATCH --job-name=genome_design_pipeline
#SBATCH --output=/path/to/phage_analysis_%j.log
#SBATCH --error=/path/to/phage_analysis_%j.err
#SBATCH --time=48:00:00
#SBATCH --signal=B:USR1@300
#SBATCH --open-mode=append
#SBATCH --requeue
#SBATCH --partition=cpu_batch
#SBATCH --nodes=1
#SBATCH --cpus-per-task=96... |
adbd074271293fc7affb584f4ec3ae0718a4ad9f60c1d49f96f758107bbe40c2 | Shell | 6,943 | 215 | #!/bin/bash
################################################################################
# Garfield Ablation Study Runner
#
# This script runs comprehensive ablation studies for the denoised-graph branch
# and hyperparameter justification.
#
# Usage:
# bash run_ablation.sh --data-path /path/to/data.h5ad [options... |
de874a593094db6c85a781733183efe4c2a7975150bd411a1b980e51263e42f6 | Shell | 6,972 | 240 | #!/usr/bin/env bash
# scripts/characterize_segments.sh
# ------------------------------------------------------------------------------
# Auto-discover model directories under SEGMENTS_ROOT (e.g., segments/mincut_K128,
# segments/protygus_*, ...) and run characterization for each model + split.
#
# Assumes each model h... |
f378f956e4a97f5e9a0cc5ddd3fc832b7e17eaf0a809c0c7a75a7c8d3a84bde5 | Shell | 7,089 | 178 | #!/usr/bin/env bash
# Trim Galore — Buckberry-scale benchmark driver.
#
# Reproducible perf comparison across:
# - Perl Trim Galore 0.6.11 + Cutadapt 5.2 (cores 1, 4, 8, 16; igzip + pigz)
# - Rust v2.1.0-beta.5 (cores 1, 4, 8, 16, 24) — pre-Buckberry-audit
# - Rust v2.1.0-beta.7 (cores 1, 4, 8, 16, 24) — post-M... |
aabe5a6a9e8a9c54c516832172a8689ee6c368daea3d8ac5dc8513f19357510f | Shell | 7,108 | 173 | #!/bin/bash
set -e # stop on error
#######################################################################################################################
#
# This is an example script for basic preprocessing of DWI images. It does the following steps:
#
# 1. Denoising
# 2. Remove Gibbs Ringing Artifacts
# 3. Remove ... |
6863c3b99b2bcd99947aa4488e428d80e175224e6e0024096a34598a333db95c | Shell | 7,189 | 148 | #!/bin/bash
##########################################################################################################
## This program computes connectomic outputs using seed region based on standard connectomes ##
## script by Andreas Horn, August, 2016. ... |
bfcc9b906bf3bf247916e7dd61c0febfe4ad0dee362f84aed28dded984f9eabe | Shell | 7,195 | 200 | #!/bin/bash
################################################################################
# Garfield Spatial Scalability Benchmark Runner
#
# This script runs the complete benchmarking pipeline:
# 1. Runs benchmarks on multiple dataset sizes
# 2. Generates visualization plots
# 3. Creates summary tables
#
# Usage:
... |
9708c4e83864e4d4e5ec2e0c0fc8e873328ef302d351cada37fe808bb21491f0 | Shell | 7,232 | 111 | # rely on twisst genomics_general
Scripts=./Scripts
ERICAPath=./ERICA
ERICAtrioPath=./ERICATrio
#################################################################
# 0. Data simulation of dataset with adaptive introgression
python ${Scripts}/FourTaxonSimulationAdaptive.py -o Adaptive --RepNum 100 -l 50000
python ${Scr... |
30431f99cf73645503586f6fcccbf06b560b8f2a9e9fc339ec44f40fc2c3759c | Shell | 7,299 | 238 | #!/usr/bin/env bash
set -euo pipefail
# End-to-end benchmark: optimized vs unoptimized fastp
# Tests both compressed (gz→gz) and uncompressed (fq→fq) modes.
# Usage: bash scripts/bench_e2e.sh [num_pairs] [threads]
NUM_PAIRS=${1:-10000000} # default 10M pairs (~1x human)
THREADS=${2:-4}
RUNS=3 # ... |
991500926eefeb90a4705cee8a2da3002df51f03f8b074bd2aaea2c36c720af9 | Shell | 7,941 | 198 | #!/bin/bash
# Option 2 for the document-level label noise: does down-weighting the
# class-negative false-negative mask beat hard abstention
# (run_negative_ablation.sh) or the untouched baseline?
#
# bash scripts/dec04_full/vm/run_downweight_ablation.sh
#
# Uses ModelConfig.class_negative_downweight — a float in [0,... |
68ad5518e7e5eb66872650f568b3840e9a580cf456342ea91d401a6150256e83 | Shell | 7,980 | 53 | # lsf22-gpu01
screen -dm bash -c ". ~/load_env_torch224.sh && CUDA_VISIBLE_DEVICES=3 nnUNetv2_train 3 3d_fullres 0 -tr nnUNetTrainer_noDummy2DDA -p nnUNetResEncUNetMPlans --disable_checkpointing"
screen -dm bash -c ". ~/load_env_torch224.sh && CUDA_VISIBLE_DEVICES=4 nnUNetv2_train 4 3d_fullres 0 -tr nnUNetTrainer_noDum... |
b45c63e6cf04818da243737bf1b2854fa53fc4a08a5db28a82237027912b3804 | Shell | 8,121 | 126 | #!/bin/sh
#
# Use as
# package.sh <sourcedir> <destinationdir>
SOURCE=$1
DESTINATION=$2
if [ -e ${SOURCE} ]; then
SOURCE=${HOME}/matlab/fieldtrip
fi
if [ -e ${DESTINATION} ]; then
DESTINATION=${HOME}/matlab/cifti
fi
echo Copying from ${SOURCE} to ${DESTINATION}
# update the version
REV=`cd ${SOURCE} && git rev-pa... |
a9419287639c7a44d8a8fc3b7283f3e8dc3716ac49268f7e15967f84802415c5 | Shell | 8,171 | 244 | #!/bin/bash
data_path=$1
lr=3e-5
echo "The provided data_path is $data_path"
for seed in 42
do
for data in H3 H3K14ac H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K79me3 H3K9ac H4 H4ac
do
python train.py \
--model_name_or_path zhihan1996/DNABERT-2-117M \
--data_path $data_path/GUE/EMP/... |
21b8a6877331c5f050f4c1c7a66360a0d49a20936541cb6e945115d3af242fb7 | Shell | 8,317 | 80 | #!/usr/bin/env bash
##
# @file test_npc.bash
# @author Simon Yu
# @date 11/09/2024
# @brief Script for testing NPC models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
# Independently trained with data-driven PC
./test_npc.py -r "42.awa2.neural.resnet34mtl.2... |
ac27ca4ea05c2e3305763104985984433894ca27a2625ad61c2ee1aaed7343bb | Shell | 8,335 | 201 | #!/bin/bash
# submit_rc_tasks.sh — RC Task 1/2/3 学习曲线实验提交脚本
#
# Task 1: random_fix2 (40% PWM) — 6 models × 6 sizes × 5 seeds = 180 runs
# Task 2: random_fix1 (20% PWM) — 6 models × 6 sizes × 5 seeds = 180 runs
# Task 3: random_rand (0% PWM) — 补全至 5 seeds = 148 runs
#
# Model-specific resources:
# KNET... |
0495f52b4be31e8c7ff789f93922731a2e42e4e1b5dffb4c375660deab779e5d | Shell | 8,345 | 202 | #!/bin/bash
# Example:
# sh CBIG_ArealMSHBM_replication_wrapper.sh ~/storage/Temporary/CBIG_MSHBM_replication_wrapper
#
# Written by Ru(by) Kong and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################
# Specify output directory
##########################... |
22c8b31e5b9742cf36d450e63adb64a8af4c40f6bde2b30420ecef5305204f40 | Shell | 8,379 | 223 | SCRIPT=$(dirname $(readlink -f "$0"))
object='train'
mode='both'
THREADS=32
RETRIES=3
help_message="
Usage: $(basename "$0") [-w <work_path>] [-a <aim_vcf>] [-b <bam_file>] [-r <ref>] [-q <vcf>] [-m <mode>] [-j <object>] [-p <phase>]
Options:
-w, --work_path Working directory path.
-a, --aim_vcf Aim VCF file... |
a589e082cf20e7717a5cd9d4b40578325941a5e128321b34ff696ab4adec4296 | Shell | 8,478 | 202 | #!/bin/sh
# CBIG_IndCBM_replication_wrapper.sh <output_dir>
# This function intends to replicate the published result in this study, which involves the individual cerebellar
# parcellations for 2 subjects.
# Note that this eplication is only avaliable within CBIG lab.
# Input:
# output_dir: Path of output folder.
... |
04c9bc0aa97dae5e0d70b74af4f3d83a2734401d45daecaf8929b101adff97a2 | Shell | 8,557 | 247 | #!/bin/bash
################################################################################
# Garfield Weight Parameter (ω) Ablation Study Runner
#
# This script runs ablation experiments for the weight parameter that controls
# the balance between spatial and expression connectivity.
#
# Usage:
# bash run_weight_a... |
3d0eae4ab662cef405265789a91eb2474d587dfea9c38348850ba1d4a5cd2918 | Shell | 8,591 | 169 | #!/bin/bash
# Paths
export data_folder=/egor2/egor/MovieProject2/bids_data
export stim_folder=/egor2/egor/MovieProject2/stimuli
export fs_folder=/egor2/egor/MovieProject2/bids_data/derivatives/freesurfer
# Max number of parallel jobs and threads
max_jobs=8
export OMP_NUM_THREADS=3
# Extract subject IDs dynamically f... |
7299181edbfa29fb01c97f19c7336c43bd2dee448ea085becdbb899b71f37ae1 | Shell | 8,647 | 230 | #!/bin/sh
# MIT License
#
# Copyright 2018 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modi... |
ad0574987785c1179414b4017e2d023aca81e5e016cb86a47a1bfda52b0db219 | Shell | 8,660 | 253 | #!/bin/bash
# This is your argument
data_path=$1
kmer=$2
echo "The provided kmer is: $kmer, data_path is $data_path"
# sh scripts/run_dna1.sh 3 ; sh scripts/run_dna1.sh 4 ; sh scripts/run_dna1.sh 5 ; sh scripts/run_dna1.sh 6
for seed in 42
do
for data in H3 H3K14ac H3K36me3 H3K4me1 H3K4me2 H3K4me3 H3K79me3 H3K9... |
ae744bd5f67d2af1eda1420e3cec81adff340e1408c5471304f1277ce805786b | Shell | 8,718 | 140 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
d6c3b31f250da72d57a981eb3f82cc93ed3a47062919f49c39f1dbfc3d715657 | Shell | 8,767 | 216 | #!/bin/bash
# submit_markov_tasks.sh — Markov Task 1/2/3 学习曲线实验提交脚本
#
# Task 1: markov_0_75 (entropy=0.75, easiest) — 6 models × 6 sizes × 5 seeds = 180 runs
# Task 2: markov_1_0 (entropy=1.0, medium) — ALREADY COMPLETE, skipped
# Task 3: markov_1_25 (entropy=1.25, hardest) — 6 models × 6 sizes × 5 seeds = 180 runs
... |
445b3c5db049443e860f6c726dabd62325242fbf331e8770148d716c2c1e5467 | Shell | 8,980 | 176 | #!/bin/bash
##########################################################################################################
## This program computes connectomic outputs using seed region based on standard connectomes ##
## script by Andreas Horn, August, 2016. ... |
21fc2a58076547c8f462b1e48ca011ed2a5c28d427620cfaa360388555ba1b8e | Shell | 9,196 | 230 | #!/bin/bash
#
# labgascore_run_headless.sh -- publish LaBGAS analysis reports without a display
#
# USAGE
#
# labgascore_run_headless.sh -d <projdir> -s <setup_script> <script> [<script> ...]
#
# ALL OPTIONS MUST COME BEFORE THE SCRIPT NAMES. Anything after the first
# script name is treated as another script.
#
... |
9a679d38665871ff96b48edd8ea32e42306980e2060724d6e2e224f4ca1c8d58 | Shell | 9,205 | 224 | #!/bin/bash
#
##########################
# define a helper function
##########################
warn_msg () {
# only output warning msg when the shell is interactive
if [[ $- == *i* ]]; then
echo $1
fi
}
####################################################
# export paths for subdirectories of CBIG repositor... |
f12ea38e932b761401234308d7727ec2a88c633bd94d99c48afde9c1797ad77b | Shell | 9,263 | 187 | #!/bin/bash
./trnSuvr.sh 0767 /root/data_fbb/bids111423helen/
./trnSuvr.sh 4485 /root/data_fbb/bids111423helen/
./trnSuvr.sh 4835 /root/data_fbb/bids111423helen/
./trnSuvr.sh 4856 /root/data_fbb/bids111423helen/
./trnSuvr.sh 6001 /root/data_fbb/bids111423helen/
./trnSuvr.sh 6005 /root/data_fbb/bids111423helen/
./trnSu... |
1415b0d35254efb7f8ed6c29ddcfaded3696367c1d9d3a4d477e67cef4ce9ed9 | Shell | 9,363 | 239 | #!/usr/bin/env bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey)
#
# LDA+MLLT refers to the way we transform the features after computing
# the MFCCs: we splice across several frames, reduce the dimension (to 40
# by default) using Linear Discriminant Analysis), and then later estimate,
# over mul... |
62fd64afd333d592267c262d99b226211f3c1a99194d1178f164c33225e221c3 | Shell | 9,418 | 245 | #!/bin/bash
# Example:
# sh CBIG_gwMRF_unit_test.sh ~/storage/Temporary/CBIG_gwMRF_unit_test
#
# Written by Yang Qing and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
user=`whoami`
###############################
# Set paths and create log file
#############################... |
29ecb2c0da0a432410e73814160cd050355f152ef62ec9bf8d3b29b981ed4a0b | Shell | 9,423 | 196 | #!/bin/bash
cd 006_S_4485 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 006_S_6209 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 006_S_6234 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 006_S_6277 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 006_S_6375 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 006_S_6500 && dcm2niix ./*/*/*/*.dcm && cd ..
cd 007_S_6120... |
669e2df0d4b7f42f897e6e0fca0cb3306fb12e2a3e80667fc15989230226a6b9 | Shell | 9,625 | 211 | #!/bin/bash
# The measurement run.sh's full-split run left untaken: does removing the
# document-level false-negative label noise (class_negative_abstention) buy
# anything, once it is actually removed rather than merely carried?
#
# bash scripts/dec04_full/vm/run_negative_ablation.sh
#
# Requires the earlier run.sh ... |
8435de9a956a37ef0e7e6d9a78456f11df9de0e34f9fa8c80358767e34d8e1e6 | Shell | 9,657 | 291 | #!/bin/bash
# This script was developed and tested under bash 5.0.17(1)-release
echo "The script was developed and tested under bash 5.0.17(1)-release"
echo -e "Your version of bash is $BASH_VERSION\n"
# Heudiconv
echo "The script was developed and tested under heudiconv 1.3.0"
heudiconv_version=$(docker run --rm ni... |
a3e80bf9a308ebb2d858d0d49538325e35c1128485c35e7342f486fe4784756c | Shell | 9,700 | 296 | #!/bin/bash
data_path=$1
m=$2
if [ "$m" -eq 0 ]; then
model=InstaDeepAI/nucleotide-transformer-500m-1000g
run_name=NT_500_1000g
elif [ "$m" -eq 1 ]; then
model=InstaDeepAI/nucleotide-transformer-500m-human-ref
run_name=NT_500_human
elif [ "$m" -eq 2 ]; then
model=InstaDeepAI/nucleotide-transforme... |
6536b45c10d0573f50dcd177b9fa87824805b3cbd6d6abec3e00d91165067238 | Shell | 9,713 | 246 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environment varia... |
3547d34e64afaf44cf43f8147aa846a1e8b6cec02dabb4f57802c52740494488 | Shell | 9,944 | 234 | #!/usr/bin/env bash
#
# Copyright 2024 Bjorn Neergaard
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
#
# This script is used to automatically create backport pull requests. It is
# smart enough to require no arguments if run against a PR branch, a... |
5e946249c57018213bcfa68f2a0fb04c403462d69c8df1f1982c8128869b1f89 | Shell | 10,037 | 212 | #!/bin/bash
# This script will generate example input data for 3 examples:
# 1) generate gradients
# 2) group priors estimation
# 3) indidividual parcellation generation
# The user need to specify the output directory, which will later contain two folders:
# 1) generate gradients
# 2) group priors estimation
# 3) in... |
ef78f888baa309e464e911cc6c79fde005f8c3d2a2ca6362fe5175ae580f17ab | Shell | 10,525 | 265 | #########=================connect afni and suma===================###########
subj=S01
input_dir='/Users/guofanhua/Desktop/gfh/work/experiment/ASL_Mesoscopic2025/SUMA'
cd ${input_dir}/${subj}/CBF
cd ${input_dir}/${subj}
@SUMA_Make_Spec_FS -sid ${subj}
cd ${input_dir}/${subj}/CBF
mripy_create_hd_mesh.ipy -i ../SUMA -o... |
823ee5ffd418128cd3285cd3d81518700776034df55329d4f3770bde3e1c7029 | Shell | 10,558 | 255 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "This script installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
echo
echo "Supported genomes: hg19, mm9, hg38 and mm10"
echo
echo "Usage: ./b... |
d42cdbd9ad1d85738954303207bf90cc238b609e8ba28af69256b82ddedd4a96 | Shell | 10,559 | 255 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "This script installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
echo
echo "Supported genomes: hg19, mm9, hg38 and mm10"
echo
echo "Usage: ./b... |
8e0a79623c15d8863513aecd4aa57cd7e866f0bb8fc5b5818ca36d7a05ce1cdd | Shell | 10,635 | 201 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "This script downloads/installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
echo
echo "Supported genomes: hg19, mm9, hg38 and mm10"
echo
echo "... |
143394d1e3876c61c29078c0e47310e726e1f5bd42739fe92df9ece65711655f | Shell | 10,727 | 366 | #!/bin/sh
#
# ZLIB compilation script for the OS/400.
#
#
# This is a shell script since make is not a standard component of OS/400.
################################################################################
#
# Tunable configuration parameters.
#
##############################... |
00abbc5f37f066808151d02a9c3a39b24de332e6214c571a6349551d9f4302df | Shell | 10,811 | 421 | #!/bin/sh
# Copyright 2019-2021 René Ferdinand Rivera Morell
# Copyright (C) 2005, 2006 Douglas Gregor.
# Copyright (C) 2006 The Trustees of Indiana University
#
# Distributed under the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or http://www.boost.org/LICENSE_1_0.txt)
# boostinspect... |
8b7ff249b467ca3c004c9a16eb77b41e2ef5fbb7c51063c28d08ecbc8350822b | Shell | 10,907 | 237 | #!/bin/sh
datadir="/media/sf_MRI-Data/Projects"
project=${1}
vnum=${2}
hum_num=${3}
datadir=${datadir}/${project}/${vnum}/${hum_num}
bids=${vnum}_${hum_num}
echo ${datadir}
echo "Calculating transmit bias for TurboSTEAM sequence on TIM TRIO"
echo "Calibration by A.Lutti, WTCN, London: MRM submitted"
echo ""
# cal... |
d74e88490178e19b379d1820b592ed0dcc84fe6d55cd0f60bf24910d401605e3 | Shell | 11,069 | 100 | #!/bin/bash
OUTPUT_DIR="./xenium"
mkdir -p $OUTPUT_DIR
# Last dataset update: 2026-04-14
ZIP_REMOTE_PATHS=(\
"https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Breast_Cancer_FFPE/Xenium_Prime_Breast_Cancer_FFPE_outs.zip"\
"https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Kidney_FFPE... |
b28e5143500ba9e1a9605e3dd95824662ee5b33938c45e7d07c03c45c2bc8bf2 | Shell | 11,113 | 301 | #!/bin/bash
set -e # abandon script on error
BASEDIR="$(dirname "$(readlink -f "$0")")" # set env variable for current directory (utils/)
ROOTDIR="$(dirname "$BASEDIR")" # parent directory of BASEDIR (repo root)
BUILD=false
HELP=false
REMOVE_LOCAL=false
REMOVE_GRNBEELINE=false
VERBOSE_VALUE="-q "
# Images ... |
ca1a5703166cb54bd74328644228177f4f42525a86205c833405ca850c8ed2bf | Shell | 11,595 | 281 | #!/usr/bin/env bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey). Apache 2.0.
# This does Speaker Adapted Training (SAT), i.e. train on
# fMLLR-adapted features. It can be done on top of either LDA+MLLT, or
# delta and delta-delta features. If there are no transforms supplied
# in the alignmen... |
ea6fbb9509d112dc8faef59a0f47eed105ca713c800e60a95cdbd4a1638a69cb | Shell | 11,857 | 169 | # Path of the folder containing all data
dir="/root/dir"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "su... |
b6c4251c7a0a93fae1ba784aa9f668ca273939cfe9c9e5e52ff0f4ca3a5ba6a9 | Shell | 12,070 | 223 | #!/bin/bash
# This script will generate replication input data for:
# 1) group priors estimation
# 2) individual parcellation generation
# The user need to specify the output directory, which will later contain two folders:
# 1) estimate_group_priors
# 2) generate_individual_parcellations
# Written by Ru(by) Kong and ... |
3d6a287ec20c5efc1d24e998e23198361d92804e5c0afed17df0d256417636f2 | Shell | 12,281 | 334 | #!/bin/bash
# The token-loss weighting re-measurement on the VM, end to end.
#
# bash scripts/feat10_recall/vm/run.sh
#
# Three arms differing in one config line — `token_loss_weighting` — each
# trained on the full split and then scored with `evaluate`, whose per-type
# detection block is the number the predicted-si... |
8c7d638b4dd1d599578eb260af79101b940082715bf67dd5b218d3d8d185f0e3 | Shell | 13,082 | 201 | #!/bin/bash
mkdir -p /root/data_fbb/bids111423helen/sub-6443/ses-baseline/pet
mkdir -p /root/data_fbb/bids111423helen/sub-6116/ses-baseline/pet
mkdir -p /root/data_fbb/bids111423helen/sub-6577/ses-baseline/pet
mkdir -p /root/data_fbb/bids111423helen/sub-6580/ses-baseline/pet
mkdir -p /root/data_fbb/bids111423helen/sub... |
1cd70e46a4b355dd3d77d976bfc81e9771f1ebec6ca1b0375cd3e5038e5e5af1 | Shell | 14,111 | 350 | #!/bin/bash
# The token-supervision falsification test on the VM, end to end.
#
# bash scripts/dec04_full/vm/run.sh
#
# Stages run in order and each records a stamp in $OUT/stamps; a rerun skips
# the stages already stamped, so an interrupted run resumes where it stopped.
# Force one with `rm $OUT/stamps/<stage>`, or... |
0d0bf570177fc47b860f7bd08766ab0d819ac988bd41528d55cee1f119213cca | Shell | 15,465 | 320 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "ACTIVATE PIPELINE'S CONDA ENVIRONMENT BEFORE RUNNING THIS SCRIPT!"
echo
echo "This script installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
e... |
d03acf8f5abb10f352b6968a011650aad4879a0ab72b6b5bd9055f0d5388a4bc | Shell | 15,591 | 570 | #!/bin/bash
base=$(echo `dirname \`pwd\``)
echo $base
datdir=$base/data
resdir=$base/results
pltdir=$base/plots
scrdir=$base/scripts
onClust=$2
#---------------------- choose which analysis
analysnum=1 # 1-5
#---------------------- choose analysis step
step=$1 # 1-XX
#--------------------
# main analysis o... |
1533f80ad48e71301195e55ddd261d6df59acd6688d837b5bea121b2e1bd8654 | Shell | 16,719 | 265 | #!/bin/bash
# Stop on error
set -e
if [[ "$#" -lt 2 ]]; then
echo
echo "This script downloads/installs data for genome [GENOME] on a directory [DEST_DIR]."
echo "A TSV file [DEST_DIR]/[GENOME].tsv will be generated. Use it for pipeline."
echo
echo "Supported genomes: hg19, mm9, hg38 and mm10"
echo
echo "... |
1aedf2adb58be6fed3c7552ccde8f8385cf73548c9b4592e2e2101b7613a1e5e | Shell | 17,219 | 201 | #!/bin/sh
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This script will overlay $in_vol on the $underlay_vol with $colormap and concat different slices horizontally.
# The cropping parameters assume FreeView's "1 big 3 small" mode, window fully expan... |
d3662a59a2b13638484304fb5c98944e2e976424134a2f14593b163d762b2e64 | Shell | 23,814 | 547 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environment variable... |
36aec8a78dcf7ecc9656080de6e88610e39512c704ebcc6386bcfcf991197bae | Shell | 28,366 | 359 | # rely on ms msms Seq-Gen genomics_general twisst
Scripts=./Scripts
ERICAPath=./ERICA
ERICAtrioPath=./ERICATrio
# three taxa with an outgroup
# 0. Data simulation of training dataset D1
for i in {1..12}
do
python ${Scripts}/FourTaxonSimulation.py -o Training_dataset_R${i} --RepNum 10000
done
for i in {1..12}
do
mkd... |
db6c369ebc77b2cd719578f252c1896b40a27bd69eae8cd001bd5c35c107cf6e | Shell | 29,448 | 414 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
4c946defea7550e51b1597b03c6e9f5a8de3ad15e3dd5685e19e58fa2d48640b | Shell | 34,672 | 200 | #!/bin/bash
mv '/root/data_fbb/fbb198/tmp/6443/I1044158_Florbetaben_Dyn_4x5min_2Di_336_2z_AllPass_(AC)_20180829152603_3.nii' /root/data_fbb/bids111423helen/sub-6443/ses-baseline/pet/sub-6443_ses-baseline_pet.nii
mv '/root/data_fbb/fbb198/tmp/6116/I1262873_PET_AC_20191204153243_5.nii' /root/data_fbb/bids111423helen/sub... |
f0b753ca0840ea365f18388593e7d8698e3ebbf8f60ffd8876526cef36e9346b | Shell | 35,068 | 200 | #!/bin/bash
mv '/root/data_fbb/fbb198/tmp/6443/I1044158_Florbetaben_Dyn_4x5min_2Di_336_2z_AllPass_(AC)_20180829152603_3.json' /root/data_fbb/bids111423helen/sub-6443/ses-baseline/pet/sub-6443_ses-baseline_pet.json
mv '/root/data_fbb/fbb198/tmp/6116/I1262873_PET_AC_20191204153243_5.json' /root/data_fbb/bids111423helen/... |
df3664c7cbd2576977c8ae021365e3affc5e4a3f6c328b359819cc8d30031769 | Shell | 35,801 | 375 | #!/bin/bash
cp '/root/data_fbb/ADNI_FBB/006_S_4485/Brain_ADNI3_Florbetaben_LM__AC__FBB/2019-10-29_16_24_03.0/I1252060/I1252060_Brain_ADNI3_Florbetaben_LM_(AC)_20191029160501_4.json' /root/data_fbb/fbb198/tmp/4485
cp '/root/data_fbb/ADNI_FBB/006_S_6209/Brain_ADNI3_Florbetaben_LM__AC__FBB/2018-02-27_16_26_40.0/I971640/I... |
bd0645ca3cf8fd4394346e6584ec3a55df2e7cc993cd27167f6ce4baa0de6a3f | Shell | 41,222 | 195 | #!/bin/bash
mv '/root/data_fbb/ADNI_T1/006_S_4485/MPRAGE/2012-02-01_09_52_27.0/I281882/I281882_WIP_MPRAGE_SENSE_20120201092932_601.nii' /root/data_fbb/freesurfer/fsT1forFbb/sub-4485_I281882.nii
mv '/root/data_fbb/ADNI_T1/006_S_6209/Sagittal_3D_Accelerated_MPRAGE/2018-02-14_11_18_47.0/I963926/I963926_Sagittal_3D_Accele... |
c9a5364eb28b15dee43203760d080e788af4a5c4ea23bd512211e6a6de072236 | Shell | 41,606 | 195 | #!/bin/bash
mv '/root/data_fbb/ADNI_T1/006_S_4485/MPRAGE/2012-02-01_09_52_27.0/I281882/I281882_WIP_MPRAGE_SENSE_20120201092932_601.json' /root/data_fbb/freesurfer/fsT1forFbb/sub-4485_I281882.json
mv '/root/data_fbb/ADNI_T1/006_S_6209/Sagittal_3D_Accelerated_MPRAGE/2018-02-14_11_18_47.0/I963926/I963926_Sagittal_3D_Acce... |
c1570b48b0e00996916b88dd05989c3c5c1a335d0c46bc62d09b0f7c83ddc2f5 | Shell | 43,721 | 375 | #!/bin/bash
mkdir /root/data_fbb/fbb198/tmp/4485 && cp '/root/data_fbb/ADNI_FBB/006_S_4485/Brain_ADNI3_Florbetaben_LM__AC__FBB/2019-10-29_16_24_03.0/I1252060/I1252060_Brain_ADNI3_Florbetaben_LM_(AC)_20191029160501_4.nii' /root/data_fbb/fbb198/tmp/4485
mkdir /root/data_fbb/fbb198/tmp/6209 && cp '/root/data_fbb/ADNI_F... |
2dc635645646d9a952eb794774e71c348af4e8e93722457be14e44b325a3e805 | Shell | 52,200 | 300 | cat /home/whatizit/monq/medline/2016/baseline/medline16n0001.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_annotated/medline16n0001.xml.gz
cat /home/whatizit/monq/medline/2016/baseline/medline16n0002.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_anno... |
2ac2d96355df5fb5be700effb2b2c1a7473a5b4c62d2507fdcc8fa52b30aaa45 | Shell | 62,466 | 359 | cat /home/whatizit/monq/medline/2015/baseline/medline16n0001.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2015/baseline_annotated/medline16n0001.xml.gz
cat /home/whatizit/monq/medline/2015/baseline/medline16n0002.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2015/baseline_anno... |
50d27a39716de93dcaaf332bcad1064a5bb31843c9c58326b864488500b48365 | Shell | 141,288 | 812 | cat /home/whatizit/monq/medline/2016/baseline/medline16n0001.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_annotated/medline16n0001.xml.gz
cat /home/whatizit/monq/medline/2016/baseline/medline16n0002.xml | sh preprocessMEDLINE.sh | gzip > /home/whatizit/monq/medline/2016/baseline_anno... |
273ca8df8a98edd95720d2ccd94827f98335656f362bbf14a2691dbee5657305 | Text | 20 | 2 | # DualAudioTagging
|
918bc2d6d5f28abcb09b98b28053bb1abb7e4193569100b234199754622032fc | Text | 21 | 1 | # SpaceHack2023_study |
af7dd470590de96b810af3d4ac9662c1108d35da55b6cf152e221eaec6fae484 | Text | 28 | 1 | # decision_making_fNRIS_data |
9e31b1fded034992a929c916fcce35a64cedbe52c486d6f8e90a940ce8615978 | Text | 40 | 1 | Code saves all results into this folder. |
60de65e88d53daa68afe3c45cb1994de997c2cbb4908a5afe68a3a1d2c836473 | Text | 42 | 1 | Code usd for the models in Majumder et al
|
0cae956cee56e1b933c924fd7524e0bde3c03f685b6c0ed33717fa2c8bd8e2ce | Text | 56 | 5 | nextpresso1.9.1
A pipeline for RNA-seq data analysis
|
f4014dd1348640bfdf5616f66939bb175014eb4246be0046bc29495f0076a509 | Text | 59 | 2 | # ieeg_sz_embedding
Seizure embeddings using deep learning
|
eceb18606465c8770fef8e1bdf09d4dd8d12d3ebefc7d6c3648987c16ff11c50 | Text | 74 | 1 | files in this folder are to be uploaded in Public repository of FCD paper
|
cee45e6c5d00fe4f646a466c9d54d30df41b2ff986b6347aa640220fcd01857d | Text | 81 | 2 | # SPLSM_version1.0
Standard sPace Lesion-Symptom Mapping(SPLSM): Version1.0 beta
|
15db0044bd5c7251383614580af8b06405852920383e6f3268131f6c86e6d5b6 | Text | 142 | 3 | # Multiphoton-Ratiometric-Measurements-Model
Mathematical Model for 2-color Multiphoton Ratiometric Measurements :
Data + MATLAB R2025b Code
|
cf3b061c2959c538b7aa20ee96f85fd940295392ab46e31db2bb7b3234383920 | Text | 179 | 2 | # Paul_Kay_Kronauer_2026
This repository contains code and example datasets for behavioral analyses developed by Alexander Paul and Tomas Kay and used in Paul, Kay et. al, 2026.
|
9b2b3931972cc6b6b0ff56264d8f074648bed14cbeac31af783af7f23e033e2f | Text | 185 | 2 | # nose-to-brain-anxiety-regulation
This repository houses the analytical code for the paper, "A Nose-to-Brain Circuit Underlies Anxiety Regulation by Nasal Afferent Frequency in Mice".
|
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