sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
190235fbbf241a440a76c815913e8916e9692151768497526b4bdd263b68bd6b | Shell | 2,480 | 65 | #!/bin/bash
# Usage: ./process_batches_gcp.sh <batches_tsv_file> [output_dir] [--per-batch]
if [ $# -lt 1 ]; then
echo "Usage: $0 <batches_tsv_file> [output_dir] [--per-batch]"
echo "Example: $0 batches.tsv config_output"
echo "Example: $0 batches.tsv config_output --per-batch"
echo ""
echo "Options:"
ech... |
b5dd7d9b5938da739bfe15e38978ec427e6957c6907091d20bcf0de70870ca36 | Shell | 2,482 | 81 | #!/bin/bash
input_mdapath=$1
ouput_dir=$2
samplerate=$3
geom_file=$4
# Run bandpass filter stage of Mountainsort
ml-run-process ephys.bandpass_filter \
--inputs timeseries:$input_mdapath \
--outputs timeseries_out:$ouput_dir/filt.mda \
--parameters samplerate:$samplerate freq_min:250 freq_max:5000
ml-run-process e... |
627aba3efe95aee2a8874f90ec71f17646521de5b594e05142215c5af4ab437a | Shell | 2,505 | 77 | #! /bin/bash
# execute this script from within the main project directory, i.e. ./bash/run_velocyto.sh
# run the R script to generate the filtered barcode files
Rscript R/velocyto_helper.R
# activate environment
source /opt/conda/etc/profile.d/conda.sh
conda activate /opt/conda/envs/velocyto
# parse config paramete... |
ab2530ad3a5ddbe2e84aeb27b398a4ddde8282b0eac19d7359c1bfdc7c728907 | Shell | 2,519 | 61 | #!/bin/bash
set -Eeuxo pipefail
#Usage: bash atac-post-process_wrapper.sh
# On gcp , make sure that the bucket containing the inputs is mounted before running the script
##############################################
#Change the paths to USER DEFINED VARIABLES IN THIS SECTION ONLY BEFORE RUNNING THE SCRIPT
download_dir... |
c14074090fda65e44f191ea94c23633105ebca7cb2900b1610f3f570eace892e | Shell | 2,519 | 68 | #!/bin/bash
NAME_PROJECT=$1
if [ $HOSTNAME == 'cleps' ]
then
SCRIPT_DIR='/scratch/gvignoud'
DIRECTORY_PROJECT=/scratch/gvignoud/results_DMS
elif [ $HOSTNAME == 'rioc' ]
then
SCRIPT_DIR='/home/rioc/gvignoud'
DIRECTORY_PROJECT=/scratch/gvignoud/results_DMS
elif [[ $HOSTNAME =~ ^jean-zay[0-9]$ ]]
then
... |
578ea5f7a33627ced6544ccb57c88b5ec823af2beeda47241a752f52d1174844 | Shell | 2,531 | 60 | #!/usr/bin/env bash
# Build an optimal bivariate (T1w and T2w) brain midspace using ANTS.
# This will take from several hours to several days depending on the number of
# individual images, image dimensions and computing resources.
#
# SETUP:
#
# 1. Place all T1w and T2w .nii.gz images in a single directory.
# - the... |
371f870fa60e09b5b59416f707d58b1426f8e0f3d3b2275d0c464c995bc3ac2f | Shell | 2,542 | 43 | # perl -p -i -e "s/from six import StringIO/import io.StringIO as StringIO/" CGATPipelines/*.py
# perl -p -i -e "s/import io.StringIO as StringIO/from io import StringIO/" CGATPipelines/*.py
# perl -p -i -e "s/cachedmethod/cached_method/" CGATPipelines/*.py
# perl -p -i -e "s/openFile/open_file/" CGATPipelines/*.py
# p... |
b95be7d3a20afbf9fdfefcf185318373126dbb089b076ba6aeb3fba23383f2e5 | Shell | 2,597 | 66 | #!/bin/bash
if [ $# -lt 1 ];then
echo ""
echo "Runs GRE with FatNavs recon on the CUBRIC cluster - but this version skips the actual MoCo step"
echo "to try to get the ASPIRE recon (without MoCo) done much faster."
echo ""
echo "Usage: cluster_submitGRErecon_skipMoCo.sh <full_path_to_input_raw_twix_file> <full... |
522be63a2ed4fbf9c0dce13512f0a2610f05891bb76b27e09f28ac3598c85fa6 | Shell | 2,616 | 42 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
c1a8146236f77356cdaa6a6a98294096c0e63eb373f200d27137380c6c97b16d | Shell | 2,616 | 41 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0056_vis1_s... |
7cd63170d97e0d2f59b6de046d2016d1d6b025cdb1b701f056eec49ba14fdd36 | Shell | 2,617 | 75 | #!/bin/bash
NAME_PROJECT=$1
RERUN=$2
if [ $HOSTNAME == 'cleps' ]
then
SCRIPT_DIR='/scratch/gvignoud'
DIRECTORY_PROJECT=/scratch/gvignoud/pattern
elif [ $HOSTNAME == 'rioc' ]
then
SCRIPT_DIR='/home/rioc/gvignoud'
DIRECTORY_PROJECT=/scratch/gvignoud/pattern
elif [[ $HOSTNAME =~ ^jean-zay[0-9]$ ]]
then
... |
410113d1ebfa16fd57ebe0ac4c18b8fbc94555987ea7de2a7b7567924db5c518 | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00010000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=1
transposed_5=0
re... |
4ae21c63405ab86f0113606d2a07983433735b7b1be422f953118663aab94df9 | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_01000000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=1
transposed_3=0
transposed_4=0
transposed_5=0
re... |
72a49b5b4976873e88e0b6c5a5f949c11063b3b27cb2cab29182dbef84a1901e | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00000001_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
re... |
966b1a140d7de78934e8b24ad954568a6c1664dea1cbf4cf8ea4fcd00c051052 | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00000100_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
re... |
b86d89d83b211721d380bbb647920e281d9cc1112ec2d522eeead1ca6c4f2e0d | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00000000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
re... |
c024cafafec6e15f4b0c8aeb7f24f2392e18236219bccf9260dec648fde94c3d | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00000010_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
re... |
d490e754f910887d1cb36b3ff8595e00295ae42df597e756c5ac6e93438428ca | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_10000000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=1
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
re... |
dff24f91fe3e80790a4176141de57f28d2971684c77e22e38b0018c8d90959a8 | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00100000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=1
transposed_4=0
transposed_5=0
re... |
f34fd8705a578cd4be1e894be8c2d121a2b8f028479bf80eda0b457dfc60e27a | Shell | 2,636 | 95 | #!/bin/bash
seed=2
run_dir="transformerb_00001000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=1
re... |
36566218add1d1453dc14c814312add5d349beb1b88bb61ad8df5865a9209533 | Shell | 2,658 | 95 | #!/bin/bash
seed=2
run_dir="transformer_00000000_abcd"
training_ids="/project/data/train_participants_ABCD.tsv"
validation_ids="/project/data/valid_participants_ABCD.tsv"
input_height=24
input_width=28
input_depth=24
order_type="raster_scan"
transposed_1=0
transposed_2=0
transposed_3=0
transposed_4=0
transposed_5=0
ref... |
3c51788cca6758cc30fb8536e3ca7b1f4de5a5d0c86985bda81e981da3746216 | Shell | 2,660 | 54 | #!/bin/sh
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
python3 ${root_path}/data_preprocessing_TCGA/3.data_gene_embedding/1.1.DNA_methylation_promoterid.py \
--reference_path ${root_path}/reference/ \
--rawdata_path ${root_path}/data_TCGA/1.raw_data/ \
--save_path ${root_path}/data_TCGA/3... |
630e1276f9eb44fa6afe8d68ea34b88b58c9d451f72929021ea16a339afa42f5 | Shell | 2,680 | 86 | #!/bin/bash
input_dir=$1
ouput_dir=$2
samplerate=$3
geom_file=$4
# Run bandpass filter stage of Mountainsort
ml-run-process ephys.bandpass_filter \
--inputs timeseries:$input_dir/converted_data.mda \
--outputs timeseries_out:$ouput_dir/filt.mda \
--parameters samplerate:$samplerate freq_min:250 freq_max:50... |
00e93fc9184ba96e6a61813acc7753bf27a097464da3bebcf287032a8fdf5de5 | Shell | 2,682 | 84 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
while getopts "h" opt; do
case $opt in
h)
echo "No help available!"
exit 0
;;
\?)
exit 1
;;
esac
done
shift $((OPTIND - 1)... |
e60bcbd534b360c947338085903479a82c71927d553c9f1486d985ee06b91a1f | Shell | 2,682 | 36 | #sldsc
#prepare annotation file
for i in Ast End Ex In Mic Oli Opc Per union sc_Ast sc_End sc_Ex sc_In sc_Mic sc_Oli sc_Opc sc_Per sc_union Bulk
do
ldfile=/zs32/data-analysis/liucy_group/jiangyi/database/ld.haploreg/LD_EUR.gt0.2.gz
#snp 的chr,pos path:/vg_sklmgdata_hw_01/data/tychu/eqtl/sldsc_eqtl/new
eqtl=/vg_sklmgdata... |
1267d8bbe5f186f8147e42c3e339a0f0151da8e528a4b64df033c3975000a85f | Shell | 2,692 | 36 | #!/usr/bin/env bash
# PreProcess:
# Usage:
# ./Generate_ROIs.sh <CellType>
# $1 = cell code name as listed in rnaseq.csv and in the data folder
[[ "$1" == "" ]] && { echo "Two arguments required: <Hi-C window size Bases: default 10000> <CellType: as appears under folder src/data>"; exit 0 ; }
cell_type=$1 # Has... |
380cdf66161f2050ecb752e87f4dc1244da2432883c35cc02145a2a9ecf343c6 | Shell | 2,695 | 64 | #!/bin/sh
# title: script for single-cell data analysis
# author: Tingting Zhao
# email: tzhao7@bwh.harvard.edu
# date: "02/05/2022"
# usage: source scRNA_seq.sh
# platform: BHW ERISone
# folder structure: project folder (data, output, result, scr)
# bash setting
index_file="/data/bioinformatics/projects/hassan2022/s... |
865a374a37398507be15ce0e29ba967cf8d547aedd585055649dd2852e97431b | Shell | 2,697 | 62 | #!/bin/bash
if [[ ( $@ == "--help") || $@ == "-h" || $# == 0 ]]
then
echo " "
echo "Usage: $0 <projectDirectory> <subjectNumber>"
echo " "
echo "projectDirectory...BIDS directory containing /sub-xxx/ses-yyy/anat/sub-xxx_anat.nii"
echo "subjectNumber......value of xxx above. For example 001,002 etc."
echo... |
53f05d50060a87536d7f23c067fd50b7293c14a105c08ed3af5ce8179558991a | Shell | 2,709 | 49 | expected="expected/"
myDiffs=""
if [ $# -eq 1 ]
then
expected="$expected$1"
./samTest 2> results/samTest.log && \
diff $expected/testEqWithBases.sam results/outSamEqBases.sam && \
diff $expected/testEqWithEq.sam results/outSamEqEquals.sam && \
diff $expected/testEqWithOrig.sam results/outSamEqOrig.sam && \
diff $ex... |
20981e960f79bba8918f1f4d351c5e1872074971977efe19f7df7e9eaf2f497c | Shell | 2,712 | 45 | STEP_DIR="$ROOT_DIR/6-synthesize"
# Reset folder
rm -rf "$STEP_DIR"
mkdir -p "$STEP_DIR"
# activate environment
source "$ROOT_DIR/.venv/bin/activate"
# Copy checkpoint from training (or download it from Zenodo)
cp "$ROOT_DIR/4-start-training/checkpoints/103500.pt" \
"$STEP_DIR/checkpoint.pt"
# Download pre-traine... |
1b6ffe445907b7cdd6f52127ead48d4ef56efd4b4a5f87cee3a80f8ddeb62ddc | Shell | 2,713 | 98 | #!/bin/bash
#These are optional flags but you probably want them in all jobs
#$ -S /bin/bash
#$ -j y
#
# Submit chainsaw job array to SGE cluster
#
# usage:
# qsub -t 1-16933 chainsaw_submit.ucl_cs.sh
#
# Assumes index file has been split into chunks e.g. "zipindex.00000001":
# split -a 8 -d 1 -l 1000 data/zipi... |
b89c8c53a27b7c5bc07b9323d24b33e7c84f8b407ebe064c8e1aa54bceeb66af | Shell | 2,721 | 46 | #!/bin/sh
## Preprocessing data of Darbandi et al., bioRxiv (2023)
## https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE248876
Rscript Darbandi_2023_to_bed.R
## Common promoter & enhancer of five ASD TF (TableS3_5TRa_Peaks_May23.xlsx)
# merge bed files
cat ASD5TF_proximal.bed ASD5TF_distal.bed | sort -k1,1V -k2,... |
fda3b0ecb768373780da0553e0254f7cdcfd46a922b908a2a098cad32fbab802 | Shell | 2,728 | 83 | #!/bin/bash
# This is Step 0: Generate Input Data and setup file folder structures.
# Run this before CBIG Parc Step 1.
# Additionally, the preproc data was formatted sub-0#. Adjust the script as necessary to fit your naming conventions.
##########################
# Specify output directory
##########################... |
6815f2158abc3a6956629a242086c4546abf7625ff64de80ae2842d471c25482 | Shell | 2,735 | 39 | #!/bin/bash
# This script will perform Level 3 stats across social
# and nonsocial conditions in the ISTART Social Doors task
# for models containing covariates
MAINDIR=/data/projects/istart-socdoors/derivatives/fsl
robust="no"
task="socialdoors"
for modelnum in 10; do
#for type in "act"; do
for type in "act" "... |
c740be962bdb9f180aff60a184536ecf9ff61c493d4e37200944a305623195e8 | Shell | 2,753 | 79 | #!/bin/bash
ARG_LST=("thin" "full") # "thin" "full")
SERVER_TYPE=("cpsign-cp-reg-server" "cpsign-vap-clf-server" "cpsign-cp-clf-server")
for arg in "${ARG_LST[@]}"; do
for st in "${SERVER_TYPE[@]}"; do
echo " now running with argument=$arg and st=$st"
# Build the image
docker build --ta... |
3798f79f585525b61d90c97249d0b256a57c13e5453a40862213181dea82fc6b | Shell | 2,779 | 57 | #!/bin/bash
# Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in... |
35731b58125f2930dc0bf53b7a9b5094458b918e6ad1429dd0dc466d07dc7520 | Shell | 2,810 | 88 | # List with all .nii files to be VBM processed. The file paths must be relative to the spm12 docker container.
ALLFILES=all_nii_files.txt
# Number of lines to split file list in multiple jobs (PART 1 only)
NSPLIT=1123
# template filenames to replace strings
JOBTEMPLATE1=spm12_template_part1.m
JOBTEMPLATE2=spm12_templat... |
b47fc7767e90b6080c253e32552952398da42606945e18e61f096866e3cfbcd7 | Shell | 2,830 | 79 | #!/usr/bin/env bash
# DeepMapper verification datasets — downloader for VERIFIED public scRNA-seq sources.
# All URLs returned HTTP 200 on 2026-06-20. See docs/data-sources.md for provenance & ground-truth notes.
#
# Usage:
# ./download_data.sh [target_dir] # default: ./data
# GROUP=cd4 ./download_data.sh ... |
78ac3360f0a0ee44134ffcd46e757adaa7ff23c52cba597b789f7952c6240550 | Shell | 2,836 | 84 | #!/bin/bash
# Slurm Parameters
#SBATCH -p gpu
#SBATCH --time 00:30:00
#SBATCH --job-name=plot_circos
#SBATCH -o plot_circos_%A.log
#SBATCH -e plot_circos_%A.err
#SBATCH -c 1
#SBATCH --mem 20G
#SBATCH -C scratch
#SBATCH --array=10-14
#SBATCH --gpus 1
#######################THIS SCRIPT CAN PRODUCE CIRCOS PLOT AS WELL A... |
195126cec36c5b1d9970b62d474f280f9b780ccbb891772672b62b2180620af8 | Shell | 2,840 | 114 | #!/bin/bash
#
# Submit chainsaw job array to SGE cluster
#
# usage:
# qsub -t 1-16933 chainsaw_submit.ucl_cs.sh
#
# Each job will expect to find an equivalent file containing a list of zipfiles,
# created by:
#
# split --suffix-length=8 --numeric-suffixes=1 --lines=1000 ../all_proteome_zipfiles.txt zipfiles.
#
lo... |
fc36da6c7a618ec18c4687f5e3564b49c435491250e315fb089c05663b406d09 | Shell | 2,879 | 77 | ################################################################################
# Copyright (c) 2016, 2025 Genome Research Ltd.
#
# Author: George Hall <gh10@sanger.ac.uk>
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "... |
d9d39af2eaf10ca8b671b23b355c4357055b3f01faa78c1f006fb2bc1f75e621 | Shell | 2,911 | 102 | STEP_DIR="$ROOT_DIR/5-convert-chinese-to-ipa"
# Reset folder
rm -rf "$STEP_DIR"
mkdir -p "$STEP_DIR"
# activate environment
source "$ROOT_DIR/.venv/bin/activate"
# Download universal narrow pronunciation dictionary
wget https://zenodo.org/record/7528596/files/pronunciations-narrow.dict \
-O "$STEP_DIR/pronunciatio... |
2e63e3389eec3ab2ed1d8875ca81037e800473541da15832588ae0f69ff05f35 | Shell | 2,917 | 71 | #!/bin/bash
# the _fixUpsideDown.sh script is a modified version of the original to handle
# the upside-down issue with some subjects where the slice orientation was prescribed
# incorrectly in the scanner.
if [ $# -lt 1 ];then
echo ""
echo "Runs GRE with FatNavs recon on the CUBRIC cluster."
echo ""
echo "Usage:... |
8227702d40ee81502a66a73caf2015f172aa7249e66d810226f3828cbef4d69e | Shell | 2,943 | 90 | #!/bin/bash
# Slurm Parameters
#SBATCH -p medium
#SBATCH --time 2-00:00:00
#SBATCH --job-name=STAR_index
#SBATCH -c 10
#SBATCH --mem 40G
#SBATCH -e STAR_index_%A.err
#SBATCH -o STAR_index_%A.log
#SBATCH -C scratch2
module load star/2.6.0c
module load rsem/1.3.0
rnadir='/scratch/users/txie/RNA-seq'
... |
c9e81269c9960c9eee6c3a39c5e78a2c99b45d4ccfb4b150cd64cf7c1c6c3d28 | Shell | 2,956 | 56 |
# ------------------------------- training arguments -------------------------------
# models
# --model: "twostage_RCAN3D" or "twostage_Unet3D"
# --upsample_flag: 0 or 1, whether the network upsamples the image
# training settings
# --load_all_data: 1 for load all training set into memory before training for faster ... |
dc81c5cd6d91b2a44a6bc7410d80020ad3a6a4b7a6f0e3d9738bd150bd759943 | Shell | 2,956 | 104 | #!/usr/bin/env bash
# References
# http://kvz.io/blog/2013/11/21/bash-best-practices/
# http://jvns.ca/blog/2017/03/26/bash-quirks/
# exit when a command fails
set -o errexit
# exit if any pipe commands fail
set -o pipefail
# exit when your script tries to use undeclared variables
set -o nounset
# trace what gets ... |
a0924380bef6355026024827164efc3974113daedf3a22e89b17c0183a4c1901 | Shell | 2,979 | 30 | ###########################################################################
## 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 ... |
eab289320c08b1a4837f895b05253f272b99928e47f045a6b9a1ba5b29bf988b | Shell | 2,995 | 102 | #!/bin/bash
set -x -e
function usage()
{
echo "pybatch : Paul's SGE/SLURM/LSF launcher"
echo "Usage:"
echo " pybatch.sh [options] <command> [args]"
echo "Options:"
echo " -m <value> : Set memory requirement for job (e.g., 8G)"
echo " -n <number> : Set CPU core requirement for job (e.g... |
83b21227749b919d1f01534a2c6de3d7188e8b229f6feee1773a5a6c50bca042 | Shell | 2,997 | 114 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
source ${FSL_LOCAL}/etc/fslconf/fsl.sh
# Copy nii files to topup directory
echo "Copy nii files to topup directory"
cp ${NII_RAW_DIR}/*X${TOPUP_LR_RUN}P1.nii.gz ${TOPUP_DIR}/data_LR.nii.gz
if [ $FLAG_TOPUP_RETRO_RECON == "NO" ]; then
cp ${NII_RAW_DIR... |
de0aa70eede25b6cf68b8e2e8194b519afc0615e9fabe9f67c6497429600a304 | Shell | 3,008 | 59 |
# ------------------------------- training arguments -------------------------------
# # models
# --conv_block_num: number of upsampling or downsampling block in U-Net
# --conv_num: number of convolution layer in each conv_block
# --upsample_flag: 0 or 1, whether the network upsamples the image
# # training settings... |
3471727c50bed55a5e537f81f186f4bfe588be56b5dae31868a5c66537dd857d | Shell | 3,015 | 81 | # Download THCHS-30 dataset from OpenSLR: https://www.openslr.org/18/
wget https://openslr.elda.org/resources/18/data_thchs30.tgz \
-O "$ROOT_DIR/data_thchs30.tgz"
# Unpack dataset
rm -rf "$ROOT_DIR/THCHS-30"
mkdir -p "$ROOT_DIR/THCHS-30"
tar zxf "$ROOT_DIR/data_thchs30.tgz" \
-C "$ROOT_DIR/THCHS-30"
# Convert da... |
57a430889394cd30e62a824bf81919c2b7d074e7e9bbc5ee2c4370055d214c97 | Shell | 3,015 | 58 | #! /bin/bash
## This bash script is for quick pre-processing
## Path settings
train_pos_dir=data/XU_train/positive
train_neg_dir=data/XU_train/negative
test_pos_dir=data/XU_test/positive
test_neg_dir=data/XU_test/negative
train_pos=$train_pos_dir/XU_pretrain_train_positive_example.fasta
train_neg=$train_neg_dir/XU_pr... |
76ebbfc9157c238e9ca7158e3c57a9e2d42415d16a455b069e62d2b1878891de | Shell | 3,035 | 38 | #!/bin/bash
set -eu
# Initialize a variable to keep track of errors
errors=0
# Check the conditions
git grep '^from langchain import' langchain_classic | grep -vE 'from langchain import (__version__|hub)' && errors=$((errors+1))
git grep '^from langchain\.' langchain_classic/load | grep -vE 'from langchain.(load|_ap... |
1b761cbdcbda114aa758f878128017228706f566b6f9794f4aa97ec03377a98e | Shell | 3,041 | 87 | #!/bin/bash
# Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is licensed under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with the
# License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... |
7610d502940548deab255ede9a04acbebe86408338654a23dfcb504b441fb6dd | Shell | 3,058 | 61 |
# ------------------------------- training arguments -------------------------------
# # models
# --conv_block_num: number of upsampling or downsampling block in U-Net
# --conv_num: number of convolution layer in each conv_block
# --upsample_flag: 0 or 1, whether the network upsamples the image
# # training settings... |
b6cd6d3f9838a33ca6f9dd009c539dfede1b0b4c8f35373da2e11065d95cbd50 | Shell | 3,093 | 86 | #!/bin/bash
# Copyright 2026 DeepMind Technologies Limited
#
# AlphaFold 3 source code is licensed under the Apache License, Version 2.0
# (the "License"); you may not use this file except in compliance with the
# License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... |
baab98b0892aec89dfb47f068a302dfe89118a9e21d515a18a59bdafc3719305 | Shell | 3,100 | 50 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
SRC=$RECODIR/21_recos_rt/vol0082_vis1_s... |
c56299f1ed964dee1dc5f50385ffba5126a60eb630777ef4f9a2e45aed5ea1f0 | Shell | 3,105 | 100 | # Install SpeedSeq on blank Amazon Linux machine
# running on Amazon Linux AMI 2014.09.2 (HVM) - ami-146e2a7c
# m3.large, 2 vCPUs, 7.5 GB memory
# ---------------------------------
# 1. Install prerequisites
# ---------------------------------
# SpeedSeq prerequisites
sudo yum -y update
sudo yum -y install make autom... |
e440fa28b79b15739d0f7a58011f78a8420d2a9d7188c8ecea37f6553d0da039 | Shell | 3,128 | 126 | ## installing ldsc
# python -m virtualenv venvldsc
source venvldsc/bin/activate
#follow ldsc page https://github.com/bulik/ldsc
conda activate ldsc
module load bio/ldsc
sed -i -e "s/LogOR/beta/g" ./rg_META/previous_studies/PGC_UKB_depression_genome-wide.txt
./ldsc/munge_sumstats.py \
--out ./rg_META/previous_studies/d... |
e744830258f0ffa1b08dbd0dd1738d78e14f7d85d6a4c66bb8e9ca4b137105a7 | Shell | 3,209 | 58 |
# ------------------------------- training arguments -------------------------------
# models
# --model: "twostage_RCAN3D", "twostage_RCAN3D_compact" or "twostage_RCAN3D_compact2"
# --upsample_flag: 0 or 1, whether the network upsamples the image
# training settings
# --load_all_data: 1 for load all training set int... |
453d66e8049f8e6351baab37a7038d3ba0cfb27576269fd4d133f2c671a8fc70 | Shell | 3,240 | 93 | # To Start a GPU-interactive job:
# srun --nodes=1 --ntasks=1 --cpus-per-task=8 --gpus=1 --mem=100g --time=04:00:00 --pty bash -i
name=activ72h_B
rep=rep1
peak_name=${name}_${rep}
g2a_input=/mnt/bioadhoc-temp/Groups/RaoLab/Edahi/ForFerhatGit/ghmc_to_abc/ABC_input
g2a_output=/mnt/bioadhoc-temp/Groups/RaoLab/Edahi/ForFe... |
870c6462bdac3811c36031ea5fcf8b5778b6dd71e93607c33a783d5f1ffca7f0 | Shell | 3,309 | 124 | #!/bin/bash
# Copyright (c) 2008-2026 the MRtrix3 contributors.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Covered Software is provided under this License on... |
84aac9b1ae28fec7085db7d0d8a22b890d9b4c4a6a7e8eb62e30c0c00faf4a6c | Shell | 3,321 | 127 | #!/bin/bash
# This file needs to be copied in the preprocessing folder of each respective subject. Potential changes in processing should be made in this folder.
# Folder of Bruker Data in Bruker Format
BRUKER_RAW_DIR=
#########################################
# Select Scans for Processing
# Reorientation Check
CHE... |
5bce0a3f79317a260c57ff6f0491964f38d38635d21ca8905171ac91fb4ec348 | Shell | 3,326 | 74 | #!/bin/bash
# The script creates 2 .mcool files with merged data for neurons
# and non-neurons separately. The final Hi-C matrices are sampled to the
# same size.
#
# Run this script from the directory with .mcool files to be merged.
# Modify "PLUS_FILES" and "MINUS_FILES" with correct names of mcool files
# for neuro... |
637625f47fffbd6125d018c14c414ac1097267308cf5e7945ef10337141bfcf7 | Shell | 3,331 | 92 | #!/bin/bash
set -e
# preprocess_single_subject.sh <SubID> <SesID> <TR> <TASK>
# INPUTS:
# All paths assume BIDS structure
# SubID : BIDS format SubjectID (including sub-, e.g. sub-A00001234)
# SesID : BIDS format Session ID (including ses-, e.g. ses-BAS1)
# TR : TR in ms
# TASK ... |
1a7dbf783507f072849a5c3dc00ab1a01fac149cb159a07de9f60f847d5bde5f | Shell | 3,353 | 104 | #!/bin/bash
# Slurm Parameters
#SBATCH -p medium
#SBATCH --time 8:00:00
#SBATCH --job-name=neoloop
#SBATCH -o Neoloop_%A.log
#SBATCH -e Neoloop_%A.err
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --mem 50G
#SBATCH -C scratch
#SBATCH --array=2
#THIS SCRIPT CAN PRODUCE ALL CNV/CNV-bw/SV/filtedSV/NEO-LOOP/NEOTADS/deleted or dupl... |
eb2d79a7f3eee775233c517bf191a5a6a2e13b0210754a8e811e606045af425b | Shell | 3,354 | 86 | #!/bin/bash
# Nicole Gay
# 13 May 2020
# ATAC-seq alignment stats
# usage: bash align_stats.sh [NUM_CORES] [indir] [bamdir]
# make sure the vm has bc and samtools istalled
# sudo apt install bc
set -e
cores=$1
indir=$2
bamdir=$3
if [ -z "$4" ]; then
type="glob"
else
type=$4
fi
#indir=/projects/motrpac/PASS1A/ATA... |
52fafe53216fb149f0b1d1b9bc27b446955e5f8d9594ebcfd97cfc5186730330 | Shell | 3,355 | 66 | #!/bin/sh
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
for d in plasma platelet
do
python3 ${root_path}/data_preprocessing_cfRNA/1.data_gene_embedding/1.data_expression_TPM.py \
--input_path ${root_path}/data_cfRNA/1.raw_data/${d}/ \
--reference_path ${root_path}/reference/ \
--save_path ... |
753b21c0898098c9c8dbdb255aef5be5ba0f70b55ece2b697f8c130b38e6b638 | Shell | 3,367 | 113 | #!/bin/bash
# Function to reverse complement a DNA sequence
revcomp() {
echo "$1" | tr "ACGTMRWSYKVHDBNacgtmrwsykvhdbn" "TGCAKYWSRMBDHVNtgcakysrwmbdhvn" | rev
}
# Function to display usage
usage() {
echo "Usage: [-h] -i <input_file> -o <output_prefix> -s <start> -e <end> -t <tmp_dir>"
echo " -i Input FA... |
171f751fe6e1c0676d4d06bb7baf7136aaec880dea6ad5128ad53b04af7fb2ee | Shell | 3,377 | 112 | DATA_ROOT=${1}
Cell_Type=${2:-GM12878}
if [ -z "$DATA_ROOT" ]; then
echo "Error: DATA_ROOT is not provided."
exit 1
fi
# Enformer
python -m train \
experiment=hg38/gene_express \
wandb.mode=online \
wandb.group="Enformer_CAGE_${Cell_Type}" \
wandb.name=pretrainFalse \
hydra.run.dir="./out... |
11ad70cf87d52640939d86153fb1d59aa181b68bf0e04d9378136d9c295b600a | Shell | 3,394 | 47 |
# ------------------------------- inference arguments -------------------------------
# --bs: batch size, a tuple of length n for n input images. e.g. 3 7 for 2 input images
# --num_seg_window_x: number of segmented patch along x axis for each input image, a tuple of length n for n input images. e.g. 3 7 for 2 input ... |
bbaf16df1ed37345d8ca39ceb1629d2dd5b0136bbc1ef7e7f89cc54e9c7c89a6 | Shell | 3,396 | 105 | !#bin/bash
# declare relevant env variables
FSLDIR='/opt/fsl/6.0.0'
template='/opt/fsl/6.0.0/data/standard/MNI152_T1_2mm.nii.gz'
template_mask='/opt/fsl/6.0.0/data/standard/MNI152_T1_2mm_brain_mask.nii.gz'
root_dir='/project/4180000.19/human'
roi_folder=$root_dir'/ROI'
#location of the S1200 HCP dataset
data_dir='/pr... |
b7de3a13279167b566a28f4698d06577f405389299b49d5d72bd1162f20369fb | Shell | 3,402 | 76 | #!/bin/bash -l
# Set SCC project
#$ -P ivc-ml
# Request 4 CPUs
#$ -pe omp 2
#$ -m ea
# Request 1 GPU
#$ -l gpus=1
#$ -l gpu_memory=48G
#$ -l h_rt=1:00:00
module load python3/3.8.10
module load pytorch/1.13.1
# # conda info -e
conda activate py3.8
export LD_LIBRARY_PATH=/share/pkg.7/miniconda/4.9.2/install/lib/
c... |
7a3300fedee5636752ba622c0faae6bd4ab53c87f162fb7e33474041d26e6f4b | Shell | 3,451 | 89 | #!/bin/bash
set -Eeuxo pipefail
# Author: Nicole Gay, Anna Scherbina
# Updated: 7 May 2020
# Script : encode_to_count_matrix.sh ${in_dir} ${src_dir} ${cores} ${final_results_dir}
# Purpose: generate peak x sample read counts matrix from tagAlign and hammock files
# Run pass_extract_from_gcp.sh before this
#get a merge... |
9a1f9b0e261d9f84e99565e28312ee71439025d965e2c43482999e547139e0f4 | Shell | 3,493 | 114 | #!/bin/bash
## Preprocessing data of Roadmap Epigenomics Project
## Among these, we only used fetal stage samples
chain=/data1/Resources/liftOver_chain/hg19ToHg38.over.chain.gz
echo $(date)
for m in $(seq 1 1 9)
do
echo "liftover E00${m}"
liftOver regions_prom_E00${m}.bed.gz $chain regions_prom_E00${m}.hg38... |
17fa8b76f5f524d1ae9ab14a55befb5c1fc8e2f29039553350e6cb5811662722 | Shell | 3,535 | 148 | #!/bin/bash
set -x -e
ROOT=/project/hippogang_3/sravikumar/atlasPHG2019
source $ROOT/scripts/common.sh
# Relies on list of subjects manually entered in manifest
function copy_hires_mri()
{
while IFS=$'\t' read -r ID_SR ID FWPATH args; do
echo $ID_SR
# Create the input directory
IDIR=$ROOT/pmatlas_raw/... |
a975c4754b12b0286a433a84e31de786c7b25dc4a47f44411ec5894f59d56693 | Shell | 3,538 | 101 | #!/usr/bin/env bash
###############################################################################
#
# Download and extract genome resources from
# ENSEMBL server (annotation in GTF and sequences in FASTA).
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinform... |
0ae8c76c8c5fb2d71255e5530bc7f69d02c1549a5415133de7da731ddb79022a | Shell | 3,579 | 97 | #!/bin/bash
#Purpose: Determine which subjects have which number of runs available and create lists accordingly for MSHBM Step3.
#Inputs: Generate_data_step_2.5 sess_lists output.
#Outputs: Text lists with corresponding subjects for each number of sessions.
#Written by M. Peterson, Nielsen Brain and Behavior Lab und... |
6a038e2332cef73377a6bd8ef0494470f3b7ecd852fb9f55ca28a1a0b40974dc | Shell | 3,625 | 33 | GRPHOME=/path/to/grphome
PROJHOME=${GRPHOME}/path/to/projhome
WORKHOME=/path/to/processed_data
IDS=$(id -u):$(id -g)
#rm -rf ${WORKHOME} #uncomment if restarting from scratch
#mkdir -p ${WORKHOME} #uncomment if first time
docker run --name "${USER}_cellranger2" -it --rm --user ${IDS} -v ${WORKHOME}:/work -v ${GRPHOME... |
0d22129a84d2bfd9d34949509a980fd432877d9aa396116263533aa4f50a1164 | Shell | 3,737 | 114 | #!/bin/bash
# Runs colocquial.R on a set of lead SNPs in series
# This version is intended for user who do not have cluster computing resourcesa
# Input files needed in directory: qtl_config.sh (modified)
module load plink/1.90Beta4.5
module load R/3.6.3
module load bedtools2
module load htslib #or module load tabix
m... |
651dce4a32601499bf0ade0050c9988cab6ef444908f1471cccf6c2cb5f13961 | Shell | 3,741 | 124 | #!/bin/bash
# Slurm Parameters
#SBATCH -p medium
#SBATCH --time 8:00:00
#SBATCH --job-name=neoloop
#SBATCH -o Neoloop_%A.log
#SBATCH -e Neoloop_%A.err
#SBATCH -n 1
#SBATCH -c 8
#SBATCH --mem 80G
#SBATCH -C scratch
#SBATCH --array=13
#THIS SCRIPT CAN PRODUCE ALL CNV/CNV-bw/SV/filtedSV/NEO-LOOP/NEOTADS/deleted or dup... |
791f3835bb6e8d8307fc35219c1d46d197ad1067b5a3e8b815b4cc204eb03aff | Shell | 3,754 | 88 | #!/bin/sh
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
echo "feature_filter"
feature_path=${root_path}/reference/feature_type.txt
for i in `cat ${feature_path}`
do
echo ${i}
python3 ${root_path}/comparison_methods/data_feature_filter/1.1.feature_filter_of_ratio_0.py \
--feature_path ${roo... |
be84ab4848d266cc47afb0e713e68d895b37fcc8bdba081744b539f7e1cdcd1f | Shell | 3,788 | 134 | #!/bin/bash
# parse config parameters:
source parse_yaml.sh
eval $(parse_yaml ../config.yaml CONF_)
PARSE_PIPE_CFG="$1"
if [ $# -eq 0 ] ; then
echo "usage: ./run_parse_pipe.sh PIPE_CONFIG.yaml"
exit 1
fi
eval $(parse_yaml $PARSE_PIPE_CFG CONF_)
OUT_ROOT=${CONF_out_root_host}/parse/parse_pipe
DATA_ROOT=${CONF_... |
3b7e4ff4773b3c67d30d480e883debaf8764a2fe5319963020b9552ad97df965 | Shell | 3,907 | 32 | GRPHOME=~/path/to/grphome
PROJHOME=${GRPHOME}/path/to/prjhome
WORKHOME=/path/to/processed_data_new
IDS=$(id -u):$(id -g)
docker run --name "${USER}_cellranger3" -it --rm --user ${IDS} -v ${WORKHOME}:/work -v ${GRPHOME}:/grphome -v ${PROJHOME}:/prjhome cancerbits/cellranger-7.1.0 multi --id=day3rep1 --csv=/prjhome/metad... |
fda16a03abb1a753e3b62f81f82ec92ba622f78d38bd33eef16846a307407074 | Shell | 3,913 | 111 | #!/bin/bash
# Runs colocquial.R
#This version is designed to use an LSF job submission to parallelize the coloc jobs
# Input files needed in directory: qtl_config.sh (modified)
module load plink/1.90Beta4.5
module load R/3.6.3
module load bedtools2
echo "modules loaded"
#source the config file for this run (parame... |
aa2aaf6cacb7fbcdc7a559e6197e754edf4198c409a325ea18e6c2fc16aa380d | Shell | 3,921 | 80 | #!/usr/bin/env bash
# ensure paths are correct irrespective from where user runs the script
scriptdir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
maindir="$(dirname "$scriptdir")"
# base paths
#for TASK in social+doors social-doors; do
#for TASK in socialdoors; do
#MAINOUTPUT=${maindir}/deriv... |
09fa26280bebcc55a3e90c5509f474b92f49e4126492ae42d565eaef7d64afcc | Shell | 4,026 | 118 | #!/bin/bash
# Nicole Gay, modified by Archana to work on copying outputs to GCP and locally
# 6 May 2020
#
# description: copy necessary outputs from GCP to final destination on GCP or local cluster
#
# Usage: bash pass_extract_atac_from_gcp.sh ${NUM_CORES} ${CROO_OUTPUT_PATH} ${DOWNLOAD_DIR}
#
### Expected numbers of ... |
a3a62bcf336968d527b81055cd0aa6715b8061e73ab7c713331a2d72868bfdad | Shell | 4,125 | 121 | #!/bin/bash
# Don't forget to copy over 40 sub HCP priors to /generate_individual_parcellations/priors or generate your own priors in Step 2
# This is Step 2.5, which will generate the profile lists for Step 3
##########################
# Specify output directory
##########################
HOME=/fslgroup/fslg_spec_... |
a4e7d543a61b559f793ca285ee3ad76507c2cabfe675eaae45b5084b5154e1bc | Shell | 4,160 | 136 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
# Copy nii files to topup directory
echo "Copy nii files to respective directories"
#FA 5 deg
cp ${NII_RAW_DIR}/*X${FLASH_FA_05}P1.nii.gz ${FLASH_DIR_FA05}/data.nii.gz
#FA 12.5 deg
cp ${NII_RAW_DIR}/*X${FLASH_FA_12p5}P1.nii.gz ${FLASH_DIR_FA12p5}/data.nii... |
17caa4ecb15882c947da669ff2d1cd13bcf8e1d43089dc7196baeeb4ee8cdf51 | Shell | 4,162 | 152 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
# Check Segmentations
mrview ${TISSUE_SEGMENTATION_DIR}/*fuzzy*.nii.gz
# Average input classes for WM Mask
# e.g.,
# INPUT_CLASSES_WM_MASK=\
# ${TISSUE_SEGMENTATION_DIR}/'noFA_fuzzy_label_4class_idx_1.nii.gz '\
# ${TISSUE_SEGMENTATION_DIR}/'noFA_fuzzy_la... |
2701ba6f4d84811bc79ad44f8b53813529354241229824519b759f87e476164f | Shell | 4,235 | 111 | #!/bin/bash
#This script uses pre-processed brain fMRI data and and creates a general linear model using AFNI.
#It takes 2 runs of the same task as input and uses ME-ICA rejected components
#Check if the inputs are correct
if [ $# -ne 13 ]
then
echo "Insufficient inputs"
echo "Input 1 should be the fMRI data you w... |
cd5af15b88beb05292cf5d8e6b114786ab07a186b9dce48fb2467dfef6d32d87 | Shell | 4,256 | 140 | #!/usr/bin/env bash
[[ ! -d .git ]] && echo "You need to be in the root directory of the repo" && exit
echo "Note that it's discouraged to switch between using compile.sh and VSCode calling CMake"
echo "Combining both might lead to an illegal state."
echo "In this case you need to remove the build folder once."
echo
... |
44775d997abc59be5c0fc9aca5bac8cee2ba3621ea9b5aeb28648ab96337c3ef | Shell | 4,263 | 124 | #!/bin/bash
# Load Local Variables
source ./SET_VARIABLES.sh
python3 ${SCRIPTS}/round_bvals.py \
--in ${DIFF_DATA_NORM_RELEASE_DIR}/data_norm.bval \
--out ${DIFF_DATA_NORM_RELEASE_DIR}/data_norm_rounded.bval
echo 'Fit CSA odf'
python3 ${SCRIPTS}/fit_csa.py \
${DIFF_DATA_NORM_RELEASE_DIR}/data_norm.nii.gz... |
9bf3b0bff190bd87a775e5c00bd813fe44f6ab1373b9d15a66d07d10f842f248 | Shell | 4,283 | 122 | #!/bin/bash
# Nicole Gay, modified by Archana to work on copying outputs to GCP and locally
# 6 May 2020
#
# description: copy necessary outputs from GCP to final destination on GCP or local cluster
#
# Usage: bash pass_extract_atac_from_gcp.sh ${NUM_CORES} ${DOWNLOAD_DIR_without_trailing_slash} ${gcp_path_to_atac_cro... |
24ea62da57d5ed443b801cc5735d2cdcbe38d10d2f45f50422f6b129c30f5fd0 | Shell | 4,296 | 107 | #!/usr/bin/env bash
###############################################################################
#
# Example MAPP workflow run:
# * download test data
# * set up the environment
# * prepare configuration files
# * initiate local run in conda envs
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Bas... |
e4dcebed0fb8d0a6e0ddbc4720de91a2e8d27cf4401215294a6d1683b5768965 | Shell | 4,406 | 66 | #!/bin/bash
#Copyright 2023. TU Graz. Institute of Biomedical Imaging.
#Author: Moritz Blumenthal
set -eu
SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )
cd $SCRIPT_DIR
if [ -z "${RECODIR:-}" ]; then
RECODIR="$(readlink -e $SCRIPT_DIR/../)"
fi
WDIR=$(mktemp -d 2>/dev/null || mktemp ... |
d5442e3ca3d9066fc8dd75793653d87132e52b67ccc28dc66935332c09e210d0 | Shell | 4,461 | 76 | # # NOTES:
# top 10 interaction has 20 thousand edges
# Create another network from fithic interactions that has at most 20 thousand edges.
# - Filter to nodes having genes
# - Active B cells
# - What is the longest interaction that we have in our dataset, or the 99th percentile
# - Make a histogram of those distances... |
34d04e8019580dfbfd64a5dc43acb6936602d4c339f7f6e00fae966690bce54c | Shell | 4,481 | 116 | #!/bin/bash
# This script implements the baseline methods for the final test.
# rrnDB & CopyRighter (Python)
python
import pandas as pd
import numpy as np
from math import sqrt
from sklearn.metrics import mean_squared_error
from statistics import mean, stdev
from utils import CopyRighterSimulator, rrnDBSimulator
def... |
199f12152ea2b57e06971b3c9ebd882466bd82953e65cb7baabd8660e8515dca | Shell | 4,493 | 114 | #!/bin/bash
set -Eeuxo pipefail
trap "echo ERR trap fired!" ERR
# Author: Nicole Gay, Anna Scherbina
# Updated: 7 May 2020
# Script : encode_to_count_matrix.sh ${indir} ${srcdir} ${batch_file} ${cores} ${final_results_dir}
# Purpose: generate peak x sample read counts matrix from tagAlign and hammock files
# Run pa... |
aca18a1ccdb89c07916d4cbc97e54afe164a1421068936a22f4d58a0bf28cd02 | Shell | 4,493 | 94 | #!/bin/sh
root_path=$"/apps/home/lulab_liuxiaofan/qhsky/project/multi_omics_paper/"
cd ${root_path}/Pathformer_code
echo 'attention_map'
python3 ${root_path}/code/Interpretability/1.attention_map.py \
--modal_all_path ${root_path}/Result/BRCA_survival/modal_type_all.txt \
--modal_select_path ${root_path}/Result/BRCA_... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.