sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 10.7k | content stringlengths 1 200k |
|---|---|---|---|---|
54d1771dc71bf1fee857ee1ccef692779212ff9b3ce70b43698cf292828c4935 | Shell | 3,044 | 97 | #!/bin/sh
###
# compare current branch with origin develop branch and list the changed files
###
curr_branch=$(git rev-parse --abbrev-ref HEAD)
files_to_be_checked=($(git diff --name-status $curr_branch..upstream/develop | awk '{ print $2 }'))
###
# define files to be checked
###
EXTENSIONS_TO_CHECK=("m" "sh" "csh")
... |
6cfce12cd284f0fb5b4ae098b719fc57179654450bc7ce7978a78e25e5382ed0 | Shell | 3,056 | 50 | #!/bin/bash
caret_command -file-convert -sc -is GS gradient_data/templates/Q1-Q6_R440.L.midthickness.32k_fs_LR.surf.gii \
-os CARET gradient_data/templates/fiducialL.coord gradient_data/templates/closedL.topo FIDUCIAL CLOSED \
-spec gradient_data/templates/fileL.spec -struct LEFT
caret_command -file-convert -sc -... |
581f362c4d5cc7e5324ca6289ea36485780287b4c72773bebaa7c1a2bab9dd90 | Shell | 3,065 | 96 | #!/bin/bash
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, mo... |
aec50d4b0081b91576537dd8bdf854ea944d67fe95119e27cf7973391c07941d | Shell | 3,068 | 77 | ###
#!/bin/bash
#$ -cwd
#$ -l bluejay,mem_free=30G,h_vmem=32G,h_fsize=100G
#$ -pe local 1
#$ -N bam_split
#$ -o logs_split_layer/bam_split.$TASK_ID.txt
#$ -e logs_split_layer/bam_split.$TASK_ID.txt
#$ -m e
#$ -t 1-76
#$ -tc 16
module load samtools
module load python/3.6.9
SUB=/dcs04/lieber/lcolladotor/with10x_LIBD001... |
65b28be5fef7a46ceca87d95e160c74603705cf59bea4cbe14cbe5437ae65460 | Shell | 3,092 | 81 | #!/usr/bin/env bash
# configure.sh — point the release at your own copy of the data and your own interpreters.
#
# Every script in this release was written against absolute paths on the authors' machine. Rather
# than rewrite 300 scripts by hand (and risk changing behaviour), the release ships them with the
# two machi... |
c99c73936675fb3c5322d5b3d1642cccc1f65bdb5fec7bba04d30919dca73d2b | Shell | 3,098 | 94 | #!/bin/bash
# Bash script to run compiled MATLAB code
# Requires MATLAB R2018a runtime library which can be downloaded from
# https://www.mathworks.com/products/compiler/matlab-runtime.html
#
# Example:
# bash SINGE.sh PATH_TO_RUNTIME standalone data1/X_SCODE_data.mat data1/gene_list.mat Output data1/default_hyperpara... |
b91c197217bba0dba22ef76818c3b186c29aa2b8f54e41f74202ad673d42d470 | Shell | 3,104 | 86 | #!/bin/bash
# Script to compare CNN, RNN, and SPIDNA across three population size scenarios:
# 1. Abrupt change
# 2. Linear decline
# 3. Linear growth
# Navigate to the experiments directory (scripts are now here)
cd /home/adkern/popgensbi_snakemake/experiments/variable-popn-size
# Create output directory
OUTPUT_DI... |
44161b91d86770ef3e7bd37515eb1100a7e584fd7f091877f51915ce48181bba | Shell | 3,136 | 78 | #!/usr/bin/env bash
# Verify that the Miniforge installer provisions the base environment using ONLY
# the packages embedded in the installer, i.e. with NO network access at all.
#
# This is a regression guard for issues such as
# https://github.com/conda-forge/miniforge/issues/883
# where the bundled mamba/micromamb... |
4e493fdfa364001de6bb355590afd47f58ae945373c80792e858048deec2d462 | Shell | 3,154 | 94 | #!/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.
#
# This script produces the results from Table 1 in the following paper:
# Bag of Tricks for Efficient... |
2bdd421a20f38d115ce0228b74ebc647e51a88df11bf1ff695592ae1b98d152b | Shell | 3,172 | 100 | #!/bin/bash
# Following taken (almost) entirely from Rob Barry's use of AFNI' 3dWarpDrive in Neptune (MATLAB tool)
# 2022/05/09
if [ $# -ne 3 ] ; then
echo "Usage:" $(basename $0) "<input4D> <target> <mask>"
exit
fi
fbase=$(basename $1 .nii.gz)
numslices=$(fslval $1 dim3)
oneless=$(echo "$numslices - 1" | bc)
tpoi... |
0238b78e7e701bd45e697dceee6d4c0176a5b6de0c06edd90f2fe70d62b4832a | Shell | 3,184 | 111 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2023 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, ... |
7c7a97483ab7a286c5073aeb8633c9a71368e63da915f8e12c3330b5064de669 | Shell | 3,205 | 110 | #!/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: $0 -i <id_list> -t <T1_list> -p <PET_lis... |
92b12f0af04fbe7e282da41d44e44cfe9da938e6a6364b442a76931b8fcaeab4 | Shell | 3,238 | 78 | # Paths
dir="/root/dir"
sct_dir="/sct/dir/6.5"
# List of subjects
declare -a sub=("sub-SPAIN01" "sub-SPAIN02" "sub-SPAIN04" "sub-SPAIN06" "sub-SPAIN07" "sub-SPAIN08" "sub-SPAIN11" "sub-SPAIN13" "sub-SPAIN15" "sub-SPAIN16" "sub-SPAIN19" "sub-SPAIN20" "sub-SPAIN21" "sub-SPAIN24" "sub-SPAIN25" "sub-SPAIN26" "sub-SPAIN27"... |
4cf9fcbd8cc5576bb8052a94aa3596410c22f89e8ae92fa7ba05a4b273cd4528 | Shell | 3,240 | 98 | #!/bin/bash
SCRIPTS=mosesdecoder/scripts
TOKENIZER=$SCRIPTS/tokenizer/tokenizer.perl
NORM_PUNC=$SCRIPTS/tokenizer/normalize-punctuation.perl
REM_NON_PRINT_CHAR=$SCRIPTS/tokenizer/remove-non-printing-char.perl
BPEROOT=subword-nmt/subword_nmt
BPE_CODE=wmt18_en_de/code
SUBSAMPLE_SIZE=25000000
LANG=de
OUTDIR=wmt18_${L... |
8327a056902a9c0bf932b91080b9421b8db798f9f8e23e3f2092275515676d17 | Shell | 3,290 | 61 | set -e
#Bundle specific postprocessing
TractSeg -i tests/reference_files/peaks.nii.gz -o examples/BS_PP/tractseg_output --single_orientation --test
pytest -v tests/test_end_to_end.py::test_end_to_end::test_bundle_specific_postprocessing
#Bundle specific postprocessing
TractSeg -i tests/reference_files/peaks.nii.gz -o... |
13163833279db5fcfba283ab4dcf9f8c6d86b8e6b8bd5519c00a37a66208bce9 | Shell | 3,310 | 79 | #!/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.
#
set -e
normalize_text() {
sed -e "s/’/'/g" -e "s/′/'/g" -e "s/''/ /g" -e "s/'/ ' /g" -e "s/“/\"/... |
c583c150ed1c7ae4831ad96cc679354cc78b71f381a95e62f5be6d079dca3f3b | Shell | 3,315 | 103 | #!/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.
#
source_lang=kk_KZ
target_lang=en_XX
MODEL=criss_checkpoints/criss.3rd.pt
SPM=criss_checkpoints/sentence.bpe.mo... |
7c40351b1f11935ab35b97768dc7d2543ad7cd195b0908da0e7557507887baf5 | Shell | 3,322 | 75 | # Paths
dir="/root/dir"
sct_dir="/sct/dir/7.0"
# 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" "sub-SPAIN27"... |
50c880154c6fdfdc20b99cc536bb1c36fa877e373a5c0ba6639e975084ee75fd | Shell | 3,328 | 89 | #!/bin/sh
#============================================================
# iso2mesh inline documentation to wiki convertor
#
# Author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
#============================================================
print_help()
{
awk '/^%/ {dp=1} /-- this function is part of iso2mesh/ {... |
d3e04278c1e3d8e91ff99ce226ac3fa25db26f70b60935f20e9d41d5e78a96c9 | Shell | 3,339 | 118 | #!/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.
echo 'Cloning Moses github repository (for tokenization scripts)...'
git clone https://github.com/moses-smt/mosesdecoder.git
SCR... |
7b7acc76f9b69cc99be5673672282c49e66f1df3b0f9331235ae96fced009a80 | Shell | 3,346 | 82 | #!/bin/bash
set -e # Stop on error
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
CONDA_ENV_PY3=encode-atac-seq-pipeline
CONDA_ENV_PY2=encode-atac-seq-pipeline-python2
REQ_TXT_PY3=${SH_SCRIPT_DIR}/requirements.txt
REQ_TXT_PY2=${SH_SCRIPT_DIR}/requirements_py2.txt
SRC_DIR=${SH_SCRIPT_DIR}/../src
conda... |
11b5b864fe17588f3172bcec86c42dec558f2c2da28236c748594b09739c5e54 | Shell | 3,356 | 107 | #!/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 -i <inDir> -d <idList> -r <reorientMa... |
024d48bfa001d70cbb0498704df8a93673f54882ede08ea848453192c14ae133 | Shell | 3,435 | 93 | #!/bin/bash
# Exp B: run transformer models with up to 3 parallel jobs (batch=128, ~5.9GB each, safe on RTX 4090)
# Picks up from where run_expB_resume.sh left off — skips all already-done runs.
# Run from: Kattn-sim-dev/src/simulation/
# Usage: bash run_expB_parallel.sh > /tmp/expB_parallel.log 2>&1 &
source env_setu... |
e89d94640d1b585297984eb6f732290311ae6d8617f0f484148095a592640a3b | Shell | 3,466 | 79 | #!/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.
timit_root=$1 # assume it is the upper-cased version
tgt_dir=$2
model=$3
set -eu
setups="matched unmatched"
splits="test valid ... |
03a3443d5e68fb8df7ee065835fad84cd0ef53e2dec80fde406b951036c18ae1 | Shell | 3,478 | 93 | #!/usr/bin/env bash
# Profile a clean --limit 200 -prof run; record epoch wall time, GPU utilization,
# and peak VRAM
#
# scripts/benchmarks/perf_baseline.sh <outdir> [limit] [epochs]
set -euo pipefail
OUT="${1:?usage: perf_baseline.sh <outdir> [limit] [epochs]}"
LIMIT="${2:-200}"
EPOCHS="${3:-3}"
PDM="${PDM:-$HOME... |
d329013d425aefd1eafa06974f7151a6f2243bc4b1f7f88e73bdf7b3b0501dfd | Shell | 3,489 | 114 | set -e
VCF_DIR="/sietch_colab/data_share/drosophila_melanogaster/vcf_output/"
OUT_DIR="/sietch_colab/data_share/popgen_npe/dromel-isolation/data"
# Parse subset of DroMel samples from VCF, remove nonsegregating
# and multiallelic sites
mkdir -p $OUT_DIR
rm -f $OUT_DIR/sample_list.txt
for VCF in $VCF_DIR/*.vcf; do
CH... |
1b42b4cf97ec135122d5451803a6ca0af1e9d098f0ed02cdc83393ff761149a5 | Shell | 3,513 | 88 | #!/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 -i <id_list> -t <T1_list> -p <PET_lis... |
729bea126e11763541053d6f9230fc132c2d68c2b300f6651dadae404ce298f8 | Shell | 3,531 | 85 | #!/usr/bin/env bash
# Run wily without letting it check out revisions in the working tree.
#
# `wily build` walks the history with a real `git checkout` per revision, in
# whatever directory it was pointed at. Pointed at this repo it would swing the
# live tree through two hundred detached-HEAD checkouts: a concurrent ... |
32f62877ceaf9f6fff32eb14cf064f84d9886f1cd00c4371f04b19d067604cd9 | Shell | 3,556 | 52 | # In grip web workflow: upload demo_input3neuromark_sbm.zip and gift-bids-main.zip
# (github gets permission problems for gift-bids)
# Manual steps:
# start VM
# Open terminal
mkdir -p ~/vm_work/code
cd ~/vm_work/code
#not working git has no permission - git clone https://github.com/trendscenter/gift-bids
cp /mnt/vm-... |
631e4134f026ed811a9ae1541f478dafdeb6146a793d4eda9b878c9a2d863551 | Shell | 3,578 | 112 | #!/bin/bash
set -e
echo "=============================================="
echo " HydraRNA Environment Auto Installer"
echo "=============================================="
# ----------------------------
# 1. Create and activate conda env (with existence check)
# ----------------------------
echo "[1/10] Checking if... |
97eba825c7e74b4b1848a335c3e51cf43f450cc4cbe16ee86d297846e9706b86 | Shell | 3,583 | 109 | #!/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 -i <id_list> -s <script_dir> -o <out_... |
d998cadfe6dbc35acac0031129e25050663372d7cc6d841eccb9a0659d229ad6 | Shell | 3,591 | 87 | # Florian Bénitière - 21/03/2025
# This script processes unique SPARK gVCF files to filter SNPs, INDELs, and non-homozygous ref sites.
# It then retains only short variants (SNVs and Indels) that intersect between GATK and DeepVariant, preserving DeepVariant metadata in the output.
#!/bin/bash
# Exit immediately if a... |
961b5f89826145f9f4d1350ddbfd3f795a6a7590d77f66180a7975a120519e2b | Shell | 3,606 | 82 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -b <brainList> -n <nuisanceVars> ... |
8c5c40299a4404ce7f9ed1a58f07aa433740863a4b60be9fcf8faf0b8bc4dff0 | Shell | 3,649 | 97 | #!/bin/bash
# Copyright 2012 Johns Hopkins University (Author: Daniel Povey);
# Arnab Ghoshal, Karel Vesely
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.ap... |
c46beb5c2898a66ddf081a606381f3c9860efdc570fc5fad47d550eca3561ab2 | Shell | 3,683 | 115 | #!/bin/bash
# submit_expB_ext.sh — Exp B extension: new sizes (1k,2k RC; 2k Markov) + seeds 3&4 for all sizes
# Total: 210 new runs
# Usage (from Kattn-sim-dev/src/simulation/ on luminary, kattn-sim env active):
# bash submit_expB_ext.sh
#
# Partitions: alternates gpu2 / gpu32
LUSTRE=/lustre/grp/gglab/liut/K-attenti... |
307f79236ee310df46035bd72bab203520e893a5a47ce30e9801dd3e98ae8c5f | Shell | 3,698 | 44 | # rely on trimmomatic bowtie2 picard-tools GATK
Scripts=./Scripts
ERICAPath=../ERICA
ERICAtrioPath=./ERICATrio
# Heliconius analyses
## SNP calling
### aligning re-sequencing data to genome
for i in `cat samplename`
do
java -jar ${Scripts}/trimmomatic-0.38.jar PE -threads 10 -phred33 ${i}_1.fastq ${i}_2.fastq output_p... |
0792bc48be49de6a5ef3ae265e86df8c699185e36c51c1af48786639f73a2acd | Shell | 3,699 | 135 | #!/bin/bash
# Adapted from https://github.com/facebookresearch/MIXER/blob/master/prepareData.sh
echo 'Cloning Moses github repository (for tokenization scripts)...'
git clone https://github.com/moses-smt/mosesdecoder.git
echo 'Cloning Subword NMT repository (for BPE pre-processing)...'
git clone https://github.com/rs... |
26dc2b8f824f5245fa7c26948a8120b06a5499b9e196fb4f53f4935998753c53 | Shell | 3,707 | 142 | #!/usr/bin/env bash
set -euo pipefail
# Default dataset for holdout (allen_scope_neuropixel_area only)
DEFAULT_DATASET="allen_scope_neuropixel_area_subset"
# --- Hard defaults (can be overridden via env or CLI) ---
SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
PROJECT_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
DEFAULT_DAT... |
0ae38ef61c378a342a035fca177d076f49a0dd7f650183827b8e4f6e69737ae3 | Shell | 3,709 | 99 | #!/usr/bin/env bash
#
# Regenerate every paper figure from the cached predictions in results/.
# No GPU, no S3, no cluster needed; everything reads from the local repo.
#
# Usage:
# conda activate hippie
# bash scripts/run_all_figures.sh
#
# Outputs land in figures/<script-name>/ next to the pre-generated reference... |
a292c815e4a90268f1a9c7200011f7eb11f77d42b2cd12248e999ce2314bb5c4 | Shell | 3,724 | 136 | #!/bin/bash
# Adapted from https://github.com/facebookresearch/MIXER/blob/master/prepareData.sh
echo 'Cloning Moses github repository (for tokenization scripts)...'
git clone https://github.com/moses-smt/mosesdecoder.git
echo 'Cloning Subword NMT repository (for BPE pre-processing)...'
git clone https://github.com/rs... |
9715741c06748efe71999f37ce48906d4af6e2139782189295aefa91a6c2954a | Shell | 3,775 | 94 | #!/bin/bash
# Exp C ablation (revised): constrained vs unconstrained at 2k/5k/10k, 3 seeds
# RC: hardest task = random_rand (Simu16, 0% PWM)
# Markov: markov_1_0_5000 / markov_1_0_10000
# 2 jobs in parallel on 192.168.3.17
# Usage: nohup bash run_expC_ablation.sh > /tmp/expC_ablation.log 2>&1 &
PYTHON=/rd1/liut/minico... |
4dd0dd8d936a51275f27ac873531dc51c101b0c84a664280c7425b7d3c0093af | Shell | 3,780 | 104 | #!/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: $0 -d <docs> -t <setting> -k <no_topics>... |
d54b0b700622def4e6aa256852f9b1de417238920c70b4a8eec7b45960ac2bc2 | Shell | 3,802 | 98 | #!/bin/bash
# Stop on error
set -e
CONDA_ENV=encode-atac-seq-pipeline
CONDA_ENV_PY3=encode-atac-seq-pipeline-python3
SH_SCRIPT_DIR=$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)
REQ_TXT=${SH_SCRIPT_DIR}/requirements.txt
REQ_TXT_PY3=${SH_SCRIPT_DIR}/requirements_py3.txt
if which conda; then
echo "=== Found Conda ... |
c0eb84ebfcdc7ce67f9f3cc204e9761685d6d0e963cb7ec055431c4a9d144109 | Shell | 3,805 | 112 | #!/bin/bash
case ${SIMULATION_TYPE} in
AWS)
# Set input and output file paths
INPUT_FILE_PATH="${BATCH_WORKING_URL}inputs/"
OUTPUT_FILE_PATH="${BATCH_WORKING_URL}outputs/"
INIT_FILE_PATH="${BATCH_WORKING_URL}inits/"
# Get copy of the input file
INPUT_FILE_NAME="${FI... |
86a0499d367ce1ee4d2bb3a506af77c45911c6bf539d30d3f560ecbab96e2fc0 | Shell | 3,807 | 129 | #!/usr/bin/env bash
out_root=/tmp
out_name=train_${RANDOM}
num_nonsil_states=1
valid="dev_other"
train="train"
mono_size="-1" # 2000
tri1_size="-1" # 5000
tri2b_size="-1" # 10000
tri3b_size="-1" # 10000
# Acoustic model parameters
numLeavesTri1=2000
numGaussTri1=10000
numLeavesMLLT=2500
numGaussMLLT=15000
numLea... |
2acad4c9abd31a069ed3d258ff178f8e534fac905167aef860d2a703625f9ec6 | Shell | 3,816 | 93 | #!/bin/bash
# this function runs replication of all results in our paper
#
# Written by Kong Xiaolu and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
root_dir=`dirname "$(readlink -f "$0")"`
cd root_dir/part2_pMFM_main/Constant_I/scripts
bash CBIG_pMFM_step1_training_conI_wrapper... |
bf0799a12c3085a0f0fca23ff4064aa473deade0e95ec36818f0bbe7815f193d | Shell | 3,822 | 88 | #!/usr/bin/env bash
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# Prepare librispeech dataset
base_url=www.openslr.org/resources/12
train_dir=train_960
if [ "$#" -ne 2 ]; then
echo "... |
d3ed9171b90825fcb05fae49854e7ce6780bfb6ea8d7ef699de4cc2338564bb7 | Shell | 3,857 | 49 | #!/bin/bash
#$ -cwd
#$ -N magma_gsa
#$ -o ./logs/magma_gsa.o
#$ -e ./logs/magma_gsa.e
#$ -l mem_free=8G,h_vmem=8G
echo "**** Job starts ****"
date
model="snp-wise"
ANNO=/dcs04/lieber/lcolladotor/with10x_LIBD001/HumanPilot/Analysis/Layer_Guesses/MAGMA/GRCh37_ensembl_GENES_SpatialExprs.gene.loc
MAGMA=/dcs04/lieber/lcol... |
fbcf84ae59456f36dfb8001b4f1c940a0368d66fc3d582d9d4073e0b482a53d4 | Shell | 3,884 | 110 | #!/bin/bash
# Exp C small-sample ablation: constrained vs unconstrained (same nk and param-matched nk=5)
# RC: abs-ran_fix2, n=1k,2k,5k; Markov: markov_1_0_5000 (n=2k,5k)
# 2 jobs in parallel on 192.168.3.17
# Run from: Kattn-sim-dev/src/simulation/
# Usage: nohup bash run_expC_small.sh > /tmp/expC_small.log 2>&1 &
PY... |
b3798aa4d145dc1a26cb1f8996d58bddb657a6712b958e6b48d2f258c2085e9b | Shell | 3,885 | 52 | # rely on ms msms Seq-Gen genomics_general twisst
Scripts=./Scripts
ERICAPath=./ERICA
ERICAtrioPath=./ERICATrio
# 0. Data simulation of dataset with outgroup introgression
python ${Scripts}/FourTaxonSimulationOutgroup.py -o Outgroup_intro --RepNum 100 --Demography OutIntro
mkdir Outgroup_intro_weights
cd Outgroup_in... |
bd5fab1a33e17e789a7e48f9cb5d2c9fa2d047eb2e24c2d7e3e6c1ae8a9a36ea | Shell | 3,888 | 103 | #!/bin/bash
# Resume Exp B: transformer RC runs (sequential, batch=128) + all Markov runs
# Run from: Kattn-sim-dev/src/simulation/
source env_setup.sh
SEEDS=(0 1 2)
MAX_EPOCHS=500
PATIENCE=20
AUROC_THRESHOLD=0.99
RC_DST="abs-ran_fix2"
RC_SIZES=(5000 10000 20000 50000 100000)
MARKOV_MODELS=("KNET" "cnn" "transformer_... |
dbea5128be7627553797941247d723e6b6f34e6a966dd062f55fa23be84ac0e5 | Shell | 3,891 | 104 | #!/bin/bash
# Written by Xiuming Zhang and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
###########################################
# Usage and Reading in Parameters
###########################################
# Usage
usage() { echo "
Usage: $0 -b <brainList> [-t <brainList_tmp... |
1ae14603476d291faa2d411a15200fb139af085fa9d483ecb69020d4956e3bcd | Shell | 3,931 | 48 | #!/bin/bash
set -e
# version
VER=$(cat atac.wdl | grep "#CAPER docker" | awk 'BEGIN{FS=":"} {print $2}')
DOCKER=quay.io/encode-dcc/atac-seq-pipeline:$VER
# general
java -jar ~/dxWDL-0.79.1.jar compile atac.wdl -project "ENCODE Uniform Processing Pipelines" -extras <(echo "{\"default_runtime_attributes\":{\"docker\":\... |
dee2df8f718f810d8ebca0499e9b3468a951d4245f741fb9a59c8b2d3e133aec | Shell | 3,934 | 114 | #!/bin/bash
# ================================================
# Script: get_loftee_resources.sh
# Author: Florian Bénitière
# Date: 11/05/2026
#
# Description:
# Downloads and sets up the necessary LOFTEE resources for VEP pipelines.
# Supports genome versions GRCh37 (hg19) and GRCh38 (hg38).
# Downloads the LOF... |
429ace6c52cd3ccc4d4bd26e49bd91176b0aa2dba876470e1998e40c05eaebcc | Shell | 3,961 | 37 | #!/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.
#
SRC=si_LK
TGT=en_XX
MODEL=criss_checkpoints/criss.3rd.pt
MULTIBLEU=mosesdecoder/scripts/generic/multi-bleu.pe... |
d34382e7986f6fdaede569edc7a5c15670ed4583867fb847436f423bb3865a41 | Shell | 3,962 | 142 | #!/bin/bash
# Adapted from https://github.com/facebookresearch/MIXER/blob/master/prepareData.sh
echo 'Cloning Moses github repository (for tokenization scripts)...'
git clone https://github.com/moses-smt/mosesdecoder.git
echo 'Cloning Subword NMT repository (for BPE pre-processing)...'
git clone https://github.com/rs... |
611ac77a37194c5c001d5a6f90e234c591c4dc8c90cdfd6942d721429edcc333 | Shell | 4,009 | 107 | #!/bin/bash
# Demo script of Group Independent Component Analysis (gift) BIDS-App,
# using BIDS-App data (16 subjects) and fMRIPrep
# Version 1.000
# Cyrus Eierud, TReNDS
# Please note that before running this demo the following is needed:
#
# 1) Install Docker (https://www.docker.com/products/personal).
#
# 2) Open ... |
e9e0a2657e7e649ba18db61d304aeb1f10051d653fd0cbc837763848e89d03ce | Shell | 4,061 | 120 | #!/usr/bin/env bash
set -xe
env | sort
echo "***** Start: Building Miniforge installer(s) *****"
CONSTRUCT_ROOT="${CONSTRUCT_ROOT:-${PWD}}"
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
cd "${CONSTRUCT_ROOT}"
echo "***** Install constructor *****"
MINIFORGE_CHANNEL_NAME="${MINIFO... |
dcbf07c7ed7605ffa0dce6029733f2fca1ed74281a49c2de7f4e911e361c87e0 | Shell | 4,085 | 101 | #!/bin/sh
# CBIG_IndCBM_compute_profile.sh <surf_mesh> <proj_dir>
# This function calls CBIG_MSHBM_generate_profiles.m and CBIG_MSHBM_avg_profiles.m to compute profiles based on a MSHBM
# folder structure. See CBIG_CODE_DIR/brain_parcellation/Kong2019_MSHBM for details.
# Input:
# surf_mesh: mesh name for your surf... |
e7b7d4afb23ff20c4c9a9bb9a76baf99c394285ac2aa935f1cdadaf55583b7f5 | Shell | 4,102 | 104 | #!/bin/bash
# Written by Nanbo Sun and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
doc_dir=$1
visualize_dir=$2
out_dir=$3
unit_test_path=${CBIG_REPDATA_DIR}/stable_projects/disorder_subtypes/Sun2019_ADJointFactors
if [ -z "$1" ]; then
doc_dir=${unit_test_path}/step2_MMLDA/r... |
b718ea38edafffc7017791d44e00f78630dfba4c035a78e0f5f625bb4f12b6c4 | Shell | 4,247 | 115 | #!/usr/bin/env bash
# MIT License
#
# Copyright 2025 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, c... |
8bcaec780ef9183423c9e79216b5f9c97f06509930e6d008431b42a49ac7f29e | Shell | 4,294 | 88 | #!/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
# Setup freesurfer and directories
export FREESURFER_HOME=/tools/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfe... |
7d5166abcd21b8b045ab94ba16a7d27d01d6076e57dbe8b6beac7626cfd7a671 | Shell | 4,316 | 80 | #!/usr/bin/env bash
##
# @file test_pc.bash
# @author Simon Yu
# @date 10/04/2025
# @brief Script for testing PC models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
# Independently trained with data-driven PC
./test_pc.py -p "42.awa2.pc.cccp.2024.12.12.19.5... |
21dc31e4ea310d62aba65d8579a725ce1b5e5c2f1da6a2e210a7d3cac1094015 | Shell | 4,327 | 122 | #########=================depth===================###########
mripy_create_hd_mesh.ipy -f pial smoothwm -i ../whole_SUMA -o ../whole_SUMAhd -p 3 -j 6
mripy_compute_depth_fhguoEdited.ipy -b bigbrain_SurfVol.nii -s /Users/guofanhua/Desktop/gfh/work/StandardBrainTemplateAndAtlas/BigBrain_LaminarProfile/whole_SUMA -l L1... |
28336c3b729dd393344b7392ba0170eafc8934b00a2f6409000f5f5b26e03baf | Shell | 4,331 | 117 | #!/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 -i <inDir> -d <idList> -s <scriptDir>... |
fe002037e2ae4bc1e79ff81d424fe4a15fb3405e9563044c6eea80547eaaee62 | Shell | 4,367 | 93 | #!/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
# Set up freesurfer for bbregister command
export FREESURFER_HOME=/tools/freesurfer
export SUBJECTS_DIR=/data/elev... |
bffaf5322c97cd2e6e8d7cdbe69ad4389bdfbf9c7f84ce58ba703ef85d2ae4fd | Shell | 4,370 | 164 | #!/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.
# set -x -e
if [ -z $WORKDIR_ROOT ] ;
then
echo "please specify your working directory root in environ... |
b153b415a281941839d79ab1f7da9910e730549e6d1971980a8dc57645db3874 | Shell | 4,386 | 133 | #!/bin/bash
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
SRCS=(
"de"
"fr"
)
TGT=en
ROOT=$(dirname "$0")
SCRIPTS=$ROOT/../../scripts
SPM_TRAIN=$SCRIPTS/spm_trai... |
0f1ca8e8282df39387c17eec437a27c52c469a928c796198c078f0da6a61b0df | Shell | 4,411 | 113 | #! /bin/bash
# Written by Wei Hou Tan and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
echo "Executing this script will install Python packages used by CBIG."
read -p "Are you sure? (y/n) " answer
if echo "$answer" | grep -iq "^y"; then
# store current directory
WORKDIR... |
2da4ba310a7ab8e143cb8044f59d0a425fbc8d50917cd7af96b6da073b213cd9 | Shell | 4,427 | 168 | #!/usr/bin/env bash
# add 'x' for command tracing
set -eu
#-------------------------------------------------------------------------------
#
# Utilities
#
# For builds not triggered by a pull request TRAVIS_BRANCH is the name of the
# branch currently being built; whereas for builds triggered by a pull request
# it ... |
dcae6fe3aef9c87462a2d495f8714e68cbcc333d7c0c88d911fa7e74b77867a4 | Shell | 4,440 | 43 | # Copyright 2023 BioMap (Beijing) Intelligence Technology Limited
# Enhancement
python get_embedding.py --task_name Baron --input_type singlecell --output_type cell --pool_type all --tgthighres a5 --data_path ./examples/enhancement/Baron_enhancement.csv --save_path ./examples/enhancement/ --pre_normalized F --version ... |
1ca973827bcd10aacd3bc3fab6e706c0aa2c45234ba6b8a24568e74657ea5620 | Shell | 4,474 | 130 | #!/bin/bash
# Script to compare the variable and dependent prior across six population size scenarios:
# 1. Medium
# 2. Large
# 3. Decline
# 4. Expansion
# 5. Bottleneck
# 6. Zigzag
# Navigate to the experiments directory (scripts are now here)
# cd /Users/yuxinning/Projects/popgensbi_snakemake/experiments/dependent-p... |
591cbb28c102c08c12e7dfff2b581407e6ff06261551e0a2c91b69ec3761d24e | Shell | 4,540 | 144 | #!/usr/bin/env bash
# Written by Wu Jianxiao and CBIG under MIT license: https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
# This function registers a moving volume to a fixed volume using ANTs
###########################################
# Main commands
###########################################
main(){
#... |
b1a8339962e1fff96655231aa34b1caf99d3873014e1bc51e0330a8d7e2605cd | Shell | 4,549 | 93 | #!/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
# Setup freesurfer and directories
export FREESURFER_HOME=/tools/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfe... |
0f539c1b8cb208d32d3b29d9ccb0d93b26b40841632ff75f7c8c1770f13079fe | Shell | 4,605 | 148 | SCRIPT=$(dirname $(readlink -f "$0"))
contig='chr1-22'
PARALLEL='parallel'
WHATSHAP='whatshap'
SAMTOOLS='samtools'
THREADS=24
RETRIES=3
phase=1
GEN_PY='generate_hap_both_onehot_refalt.py'
help_message="
Usage: $(basename "$0") [-o <out_path>] [-b <bam_file>] [-v <vcf>] [-m <model>] [-r <ref_path>] [-p <phase>] [-h <he... |
93958086c894dca8b69527134bfd2081c708c265fb45f72956112aef6596e349 | Shell | 4,617 | 109 | #!/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: $0 -i <imgList> -d <idList> -s <step> -t... |
e6d7f0031893a55a434c43c6bbb9059f2fdc8503f9a2db74782e4c3dbe0e406a | Shell | 4,628 | 135 | #!/bin/bash
# Define paths
results_dir="/egor2/egor/MovieProject2/bids_data/derivatives"
output_dir="${results_dir}/group_analysis/somatotopy/group_stats"
mkdir -p "$output_dir"
log_file="${output_dir}/group_ttests_log.txt"
> "$log_file"
nifti_out_dir="${output_dir}/niftis"
mkdir -p "$nifti_out_dir"
# get subjects
s... |
a6252420a7db596cb9e9a58f7e06c0c38beaa193079a683ab6431153dece6017 | Shell | 4,668 | 124 | #!/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 -a <docs1> -b <docs2> -t <setting> -k... |
ec823baee8b916a0d48ce5e18e9874a3ac2f00ac613ef710afe031c4f854a001 | Shell | 4,668 | 83 | #!/usr/bin/env zsh
# 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.
lg=$1
text_path=$2
target_dir=$3
min_phones=$4
phonemizer=$5
lid_path=$6
sil_prob=$7
if [ -z "$lid_path" ]; then
lid_pat... |
f9297fbc40932f0c39fb0788aead54ca78a9db72a74c58789cdf11dfd14e753a | Shell | 4,723 | 82 | #!/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/... |
658e4398b9d723b863696d52f7e4fb060e28d37055b033eb0e0af21b0deb6f65 | Shell | 4,802 | 153 | #!/usr/bin/env bash
set -ex
echo "***** Start: Testing Miniforge installer *****"
CONSTRUCT_ROOT="${CONSTRUCT_ROOT:-${PWD}}"
cd "${CONSTRUCT_ROOT}"
export CONDA_PATH="${HOME}/miniforge"
MAMBA_VERSION=$(grep "set mamba_version" Miniforge3/construct.yaml | cut -d '=' -f 2 | cut -d '"' -f 2)
export MAMBA_VERSION
echo... |
88403e3688a4226013d124ee15e2137f037eb2406beb3f95c11b18a887799fad | Shell | 4,911 | 121 | #!/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 -a <docs1> -b <docs2> -t <setting> -k... |
f7772ead97e2efbda861e5d3c4fe60ed4349d10bf4c5c9a59ed4b7bb10fe918e | Shell | 4,971 | 136 | #!/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: $0 -i <id_list> -d <deform_dir> -s <scri... |
88c26740e9471fd537a834005cd569e097e78de0d9b808992072bea27735c2e6 | Shell | 4,984 | 114 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
288e36645520d48b04dc048a7774a1ec51ca5445bf534efd20aed8c4c22357a7 | Shell | 5,001 | 186 | #!/usr/bin/env bash
set -euo pipefail
# =========================
# 0) Common settings
# =========================
export HYDRA_FULL_ERROR=1
DATA_DIR="${DATA_DIR:-data/GeneOntology}"
ESM_PATH="${ESM_PATH:-/cta/share/users/esm/ESM-1b}"
RESULTS_DIR="${RESULTS_DIR:-results}"
TEST_LIST="${DATA_DIR}/nrPDB-GO_test.txt"
IN... |
4bddd24748f69835dad5099311d9b6e0720f375d92d5792eb439adcdcf4bb09a | Shell | 5,034 | 134 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
932c8923be310b2fd2136e0f91895239963ac69b172f26187fee4fcad60809c9 | Shell | 5,081 | 143 | #!/bin/bash
function usage {
echo -e "usage : stats2multiqc.sh -s SAMPLE_PLAN -d DESIGN -a ALIGNER [-p][-h]"
echo -e "Use option -h|--help for more information"
}
function help {
usage;
echo
echo "stat2multiqc.sh"
echo "---------------"
echo "OPTIONS"
echo
echo " -s SAMPLE_PLAN"... |
c858a3507198f905f50878e71a20fb05df3afdad3be50f11748e204a0b58b7aa | Shell | 5,188 | 173 | HYDRA_FULL_ERROR=1 CUDA_VISIBLE_DEVICES=0 python src/train.py \
name=puffin_K64_v2 \
callbacks.model_checkpoint.dirpath=ismb26/models/puffin_K64_v2 \
encoder=puffin \
encoder.gnn_type=GAT \
encoder.hidden_dim=512 \
encoder.num_clusters=64 \
encoder.num_res_gnn_layers=2 \
encoder.num_seg_gnn_layers=2 \
... |
9d8dab9b1e45caa6d8690264ec75434bd7b53c67064a5fdd2b6eed18551c8e98 | Shell | 5,239 | 125 | #!/bin/sh
# CBIG_IndCBM_create_template.sh <surf_mesh> <binary_mask> <output_dir> -m(optional) <midline> \
# -l(optional) <lh_vertex> -r(optional) <rh_vertex>
# This function creates a cifti template combining the cerebral cortical surface and the cerebellum in the volume.
# Input:
# surf_mesh: Mesh neame for ... |
9efed8c9d077da172e1f08bc0586e8e673091477d207278cb62ca3fc31e92d3b | Shell | 5,269 | 173 | #!/bin/bash
# Output config file
CONFIG_FILE="generated_path_config.yml"
# Function to write the YAML structure comment block to a file
cat <<'EOF' > "$CONFIG_FILE"
# The yaml file follows the following structure
# * categories (datasets/methods/metrics)
# - {name}
# - env: path/to/conda/env/.yaml
# ... |
8379432432e7c816cca039067fe4f12c4d8bb6411d4661c9b3b65e7145b95330 | Shell | 5,278 | 203 | #!/bin/bash
CONDA_PATH=$(which conda)
# Activate the fastsam Conda environment
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate fastsam
# Enable nullglob so *.tiff expands to nothing if no match
shopt -s nullglob
# Define project root
proj_dir="/home/matt/HDD_exp/C2.1 gloid live imaging"
# Functi... |
0097cffaf372346a4ba5fd37b864db4394790114bdac04b8d9d77e9c8f42988c | Shell | 5,308 | 80 | #!/usr/bin/env bash
##
# @file test_neural.bash
# @author Simon Yu
# @date 10/04/2025
# @brief Script for testing neural models.
##
# Go to script directory
cd "$(dirname $0)"
# Go to source directory
cd "../../src/npc-models"
# Independently trained
./test_neural.py -r "42.awa2.neural.resnet34mtl.2024.12.12.2... |
6552cbf01b17bbfee2c2a26091441f7f9f8019b2208176915861f02d6a85cd54 | Shell | 5,337 | 110 | #!/bin/bash
## Edit these settings --------------------------------------------------------
BIDSDir="/home/josephccchen/data/OAgenDIS/OAgenDIS-BIDS"
Level1Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level1"
Level2Dir="/home/josephccchen/data/OAgenDIS3/OAgenDIS-AFNIproc-level2"
VectDir="/home/josephccchen/... |
f09994eb25e1a756b557e37ffcaec5f0e04cf4cd0efe282cce3798fab429b661 | Shell | 5,384 | 138 | #!/bin/sh
datadir="/media/sf_MRI-Data/Projects"
project=${1}
vnum=${2}
hum_num=${3}
datadir=${datadir}/${project}/${vnum}/${hum_num}
bids=${vnum}_${hum_num}
echo ${datadir}
if [ -f ${datadir}/acpc/${bids}-tfl.nii.gz ];then
echo "acpc/tfl file found"
fi
if [ -f ${datadir}/mt/${bids}-t1.nii.gz ];then
echo "mt/t1.ni... |
4acb8f73f89a751fd24492b70f007bfb0231987eb0209d3407cbba4f620f0507 | Shell | 5,426 | 129 | #!/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 -i <imgList> -d <idList> -s <subinfo>... |
0bf7dec1006d4301c99fc210d887088063a74244daf6b1e6f2af09645f52549d | Shell | 5,436 | 132 | #!/bin/bash
# This script will generate example input data for two examples:
# 1) group priors estimation
# 2) indidividual 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... |
ac9b7f0025d7f411d4ac0ff13f37c749868e104ffc84a099c1bcb79872b93f68 | Shell | 5,446 | 105 | #!/bin/env bash
################################################################################################################################
### demo_eigenmode_calculation.sh
###
### Bash script to demonstrate how to calculate the eigenmodes of a cortical surface and a subcortical volume.
###
### NOTE 1: This scr... |
15c5065a7a7df02865b229fec8855517d17f930b2198d23815b5123bdd6ce174 | Shell | 5,454 | 159 | #!/bin/sh
# CBIG_IndCBM_generate_list.sh <MNI_input_dir> <surf_input_dir> <output_dir>
# This function generate file list for replication for a given subject.
# Data will be split into discovery set and replication set by session.
# 3 set of lists will be generated: all, discovery, replication.
# Input:
# MNI_input_... |
47c6cfff237dade43ce4ce5a5b4a10bcab49596cba60ff3c47fbc1222809247a | Shell | 5,484 | 176 | #!/usr/bin/env bash
# scripts/global_prototypes.sh
# ------------------------------------------------------------------------------
# Auto-discover model dirs under segments/ and run global prototypes:
# - fit on train
# - assign valid/test
# - sweep K: 128,256,512,1024,2048,4096
#
# Usage:
# bash scripts/global_prot... |
394101b05e33b9171b41feff933ae2ac7620e10885d320fd9239bbab523c4729 | Shell | 5,570 | 122 | #!/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 -i <imgList> -d <idList> -s <step> -c... |
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