sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ceb0b8e0e5a82a24c6be5b57b0045d09acfab33329dc61cfab19a062db4b90b7 | Shell | 2,379 | 60 | #----------------------------------------------------------------------
#!/bin/sh
#$ -q single15.q
#$ -S /bin/bash
#$ -e /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -o /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -m eas
#$ -M Barbara.Molz@mpi.n... |
4fc9fdc7fa42fcb321e946dc9945ff7346a3b230aca0b71edbb31fedc8874138 | Shell | 2,394 | 35 | #!/bin/sh
set -ex
# Run this script from where the metadata is saved.
# Mouse cells
s3_mouse_bucket=s3://aibs.test.ani/Musmusculus/
aws s3 ls $s3_mouse_bucket --profile wasabi > aws_log
for line in $(<aws_log);
do
if [ $line != "PRE" ]; then
CELL_ID=$line
echo $CELL_ID
... |
4968651a2eab6aa16d302c9c79c90eac06fc265663d2661c975b6e624d73529b | Shell | 2,397 | 84 | #-----Run Partitioned Heritability-----
# Estimating heritability, genetic correlation and the LD Score Regression Intercept
# ldsc function is from github.com/bulik/ldsc
# For interpreting results, check the tutorial at github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
# This script takes 2 parameters: ... |
ca44cf2ef849380cccab80bdb34909137031ea7ccb6b76f80d30d9d2df003e4b | Shell | 2,434 | 84 | #-----Run Partitioned Heritability-----
# Estimating heritability, genetic correlation and the LD Score Regression Intercept
# ldsc function is from github.com/bulik/ldsc
# For interpreting results, check the tutorial at github.com/bulik/ldsc/wiki/Heritability-and-Genetic-Correlation
# This script takes 2 parameters: ... |
d2408498d19c514b999c2888c4fd543c855e7e6fbe312f7f3d67ea9e37d274f5 | Shell | 2,447 | 80 | #! /bin/bash
# Copyright [2021] Rafael Morales Gamboa, Noé S. Hernández Sánchez,
# Carlos Ricardo Cruz Mendoza, Victor D. Cruz González, and
# Luis Alberto Pineda Cortés.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
b825efeafd80065f46e539c8096e172963fc9de2334ace3987c5970b11e03352 | Shell | 2,470 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot lister_anno.1.annot.gz --out lister_anno.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot lister_anno.2.annot.gz --out lister_anno.2
python ldsc.py --l2 --bfile 1000G.mac5eur.3 --ld-wind-cm 1 --annot lister_anno.3.annot.g... |
4e4e2593aeadeae028f1bebacc57d7eb6621ca9034a5fd60225d0597dc82f339 | Shell | 2,495 | 104 | #!/bin/sh
# this test is also in test_resample.py (though much smaller and neater) ...
# keep this test to exercise the cli interface
# set -x
. ./variables.sh
test_rotate() {
im=$1
inter=$2
printf "testing $inter ... "
# 90 degree clockwise rotate
trn="0 1 1 0"
$vips affine $im $tmp/t1.v "$trn" --interpol... |
ef4ef9e456fea1c871cad4622e396bd2f3649932d3d94d98590b7cc851c947c2 | Shell | 2,501 | 23 | #!/bin/bash
python make_annot.py --bed-file age_neuron.bed --bimfile 1000G.mac5eur.1.bim --annot-file age_neuron.1.annot.gz
python make_annot.py --bed-file age_neuron.bed --bimfile 1000G.mac5eur.2.bim --annot-file age_neuron.2.annot.gz
python make_annot.py --bed-file age_neuron.bed --bimfile 1000G.mac5eur.3.bim --annot... |
19a7152b7f4f422aac352d2b8d4131ed679c530290f1909777d9014f5f83bcd5 | Shell | 2,515 | 37 | # resnet20 on diufpc (4 GPUS, 16 CPUS)
nohup python plot_surface.py --name test_plot --model resnet20 --x=-1:1:51 --y=-1:1:51 \
--cuda --ngpu 4 --threads 8 --batch_size 4096 \
--model_file datasets/cifar10/trained_nets/resnet20_sgd_lr=0.1_bs=128_wd=0.0005_mom=0.9_save_epoch=10/model_300.t7 \
--dir_type weights --xnorm ... |
a1f170aef052daee49b58e15ce0da43ae2f14ce426cfeb5a4e5513e22bc254a3 | Shell | 2,610 | 92 | #!/bin/bash
# Define variables required to run the scripts
atlas_name=200-Schaefer17Networks
class_name=Schaefer2018_200Parcels_17Networks.gcs
subject=MNI
num_par=200
dilution=3
# Create the volumetric atlas in FreeSurfer coordinates
echo ""
echo "Create annotation files for subject $subject"
mris_ca_label $subject ... |
841c989093a28eb4d27d3da7374c9995452ec9f29ae9a396b189b88c1e027d8b | Shell | 2,614 | 54 | #!/bin/bash
####################################################################
# Merge Fetal Human Gained Enhancers #
# This script concatenates bed files, sorts rows based on chr. number
# and start pos., and merges overlapping ranges/rows.
#############################################################... |
efa1af92214bd71ea388aa41f9eaed12674685942af016771a9fd0edd33a6da2 | Shell | 2,690 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot hm_anno_baseline.1.annot.gz --out hm_anno_baseline.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot hm_anno_baseline.2.annot.gz --out hm_anno_baseline.2
python ldsc.py --l2 --bfile 1000G.mac5eur.3 --ld-wind-cm 1 --annot h... |
1062372cd4be9ccc6276b6cb1ca7d1471a1a5269ac7ef869ee4ac483ae128da4 | Shell | 2,712 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot age_neuron.1.annot.gz --thin-annot --out age_neuron.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot age_neuron.2.annot.gz --thin-annot --out age_neuron.2
python ldsc.py --l2 --bfile 1000G.mac5eur.3 --ld-wind-cm 1 --annot... |
3f52bd01c614ca4eafbbfe5625eac9a1fdd1cfa0dc7d71af2f44342e13f05b3b | Shell | 2,781 | 48 | #!/bin/bash
########################################## D E S C R I P T I O N ###################################################
#
# Evaluation process:
# -------------------
# The input consists of a single temperature signal and relative humidity signal from the same site.
# Therefore, the input must come in pairs... |
df2ee3cb5483ae8dfe84d02c3ec8ec5697f1fbb8992cd8e67d57b41135e6f73d | Shell | 2,806 | 58 |
#!/bin/sh
#----------------------------------------------------
#This script runs genetic correlations between all surface based sumstats to create a genetic correlation matrix needed for Pheno SPD
# Created by Barbara Molz, May 2022
#---------------------------------------------------------
#set up the python... |
ca94736a0570f8050332778d5a78d14d91dd582c188b84e9bdcb88376f54bbea | Shell | 2,829 | 56 | #!/bin/sh
#----------------------------------------------------------------# This scrip runs LDSC genetic correlations between derived DIT summary statistics to create correlation matrix for PhenoSPD
#Info about LDSC: https://github.com/bulik/ldsc
# by Barbara Molz, Nov 2021
#---------------------------------------... |
4843bb37913b11b3509df31ca5cddb41c375a3fee18dda347827702c8a073342 | Shell | 2,920 | 61 | #!/bin/sh
#----------------------------------------------------------------
# This scrip runs LDSC genetic correlations between derived summary statistics and UKBB derived summary statistics
#Info about LDSC: https://github.com/bulik/ldsc
#Info about summary stats from UKBB: https://open.win.ox.ac.uk/ukbiobank/big40/
#... |
60bdc5944b7e18ee3eb3a3d415347f61b213f0951470f64455db34d2d1e3e0c7 | Shell | 3,036 | 43 | python munge_sumstats.py --sumstats GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.txt --merge-alleles w_hm3.snplist --out BMI --a1-inc
python munge_sumstats.py --sumstats pgc.cross.BIP11.2013-05.txt --N 11810 --merge-alleles w_hm3.snplist --out bipoplar
python munge_sumstats.py --sumstats Pubertal_growth_10F_12M... |
b61d0c58b200483de58de6eb1cbfe0a8192244300ef9d65a247e24cf79ec325c | Shell | 3,042 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot hm_anno_may2021_baseline.1.annot.gz --out hm_anno_may2021_baseline.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot hm_anno_may2021_baseline.2.annot.gz --out hm_anno_may2021_baseline.2
python ldsc.py --l2 --bfile 1000G.ma... |
370a5fab0b308a075f99f30ad445e121347305cae2436f427edfb715d937e70c | Shell | 3,090 | 93 | #!/bin/sh
# Prepare:
# 0. Check test-suite/images/sample.jpg includes XMP and ICC profile
# 1. Read image with XMP and ICC profile
# 2. Save it with no options to keep_all.{jpg,png,webp,avif}
# 3. Save it with --keep=none to keep_none.{jpg,png,webp,avif}
# 4. Save it with --keep=icc to keep_icc.{jpg,png,webp,avi... |
70b335102789896f00eac15f62006bea129a73708295cf5eb6d16a4166800df7 | Shell | 3,229 | 76 |
#----------------------------------------------------------------
#This scrip runs LDSC genetic correlations between derived summary statistics and Enigma 3 summary statistics
#Info about LDSC: https://github.com/bulik/ldsc
#Info about summary stats from E3: https://www.science.org/doi/10.1126/science.aay6690
# by Ba... |
00c9029ab670dfe59404e937bc5b57362f45c6e51a2266081ebb19f4920691e6 | Shell | 3,240 | 23 | #!/bin/bash
python ldsc.py --l2 --bfile 1000G.mac5eur.1 --ld-wind-cm 1 --annot all_dmrs_hg19_age_glia.1.annot.gz --thin-annot --out all_dmrs_hg19_age_glia.1
python ldsc.py --l2 --bfile 1000G.mac5eur.2 --ld-wind-cm 1 --annot all_dmrs_hg19_age_glia.2.annot.gz --thin-annot --out all_dmrs_hg19_age_glia.2
python ldsc.py --l... |
94307884c5d6543eb23d665a156c78e6f591064195eb72d8173c3a03cff1ed01 | Shell | 3,240 | 109 | ### Assumes prediction_subs have been projected onto fsaverage and stored in
### $PREDICTION_DIR/projected_labels/$LABEL
SUBJECT_LIST=/home/weiner/HCP/subject_lists/HCP_processed_subs_all.txt
SUBJECTS=$(cat $SUBJECT_LIST)
SUBJECTS_DIR=/home/weiner/HCP/subjects/
PROJECT_DIR=/home/weiner/HCP/projects/ifrms_HCP/
PROJ... |
5b3cf18911270ff019a919fb2e6f8531cbb900bc744e4140a09b345df889c6c6 | Shell | 3,574 | 110 | #! /bin/bash
# Copyright [2021] Rafael Morales Gamboa, Noé S. Hernández Sánchez,
# Carlos Ricardo Cruz Mendoza, Victor D. Cruz González, and
# Luis Alberto Pineda Cortés.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
818a397b1879f1651563423c422420695129e886f0ef4db7197c8bb89d49506c | Shell | 3,675 | 84 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
# log in to JGI
COOKIES="cookies.txt"
function jgi_login() {
if [ ! -f "$COOKIES" ]; then
read -p "JGI Phytozome Username: " JGI_USER
read -s -p "JGI Phytozome Password: " JGI_PASSWORD
echo
curl 'https://signon.jgi.doe.gov/signon/... |
18ecef67723733bd40b8f13187eac1be8b42c257324ec5306dc6db28c3b2a1e6 | Shell | 3,682 | 33 | #!/bin/bash
python ldsc.py --h2 bip.sumstats.gz --ref-ld-chr baseline. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5eur. --out bip_baseline
python ldsc.py --h2 pubertal_growth.sumstats.gz --ref-ld-chr baseline. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5eur. --out pu... |
bdd5ef21896bb6f71d24908dddd3ff83f086f15488b9f1633f95bb7d0e940ca4 | Shell | 3,707 | 26 | #findMotifsGenome.pl 'hyper_dmrs - autosomes - refined_age_common_glia.bed' mm10 hyper_dmrs_autosomes_refined_age_common_glia/ -size given -cpg -p 3 -nomotif
#findMotifsGenome.pl 'hyper_dmrs - autosomes - refined_age_f_unique_glia.bed' mm10 hyper_dmrs_autosomes_refined_age_f_unique_glia/ -size given -cpg -p 3 -nomotif
... |
73d42741eee8b74b06462eb01a0204990fa80ea89c8d8d895a0915296e85e82a | Shell | 3,723 | 157 | #!/bin/bash
#
#SBATCH --job-name=CpG_Me_SE
#SBATCH --ntasks=1 # Number of cores/threads
#SBATCH --mem-per-cpu=1000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_SE_%A_%a.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_SE_%A_%a.err # File to which STDERR will be written
#SBATCH --... |
1aaef24dae78057caa179a3f6d0ba2ae8c882dd0232af9dc75563042422066ec | Shell | 4,012 | 33 | #!/bin/bash
python ldsc.py --h2 bip.sumstats.gz --ref-ld-chr hm_anno. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5eur. --print-coefficients --out bip_hm
python ldsc.py --h2 pubertal_growth.sumstats.gz --ref-ld-chr hm_anno. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5... |
e824820a4d5844d6092771d31650f1c46da63041140889a8b4b94bd34e93cc43 | Shell | 4,031 | 118 | #!/usr/bin/env bash
## build.sh: compile manuscript outputs from content using Manubot and Pandoc
set -o errexit \
-o nounset \
-o pipefail
# Set timezone used by Python for setting the manuscript's date
export TZ=America/New_York
# Default Python to read/write text files using UTF-8 encoding
export LC_ALL=e... |
ef27b33ecf5eeddbc3bfb3d347a19539303e9693320b4596b7a0b2dc8a99f004 | Shell | 4,071 | 69 | ####################################################################
##################### Haplotype Block Finder #######################
####################################################################
module load plink/1.9b6
module load bedtools/2.29.2
# Identify haplotype blocks using default max block length ... |
c7d6e3d7fa76135b6c593a555220a5a7ef4da9b0959ffdede8b6617bd2c73d95 | Shell | 4,099 | 174 | #!/bin/bash
#
#SBATCH --job-name=CpG_Me_PE
#SBATCH --ntasks=1 # Number of cores/threads
#SBATCH --mem-per-cpu=1000 # Ram in Mb
#SBATCH --partition=production
#SBATCH --output=CpG_Me_PE_%A_%a.out # File to which STDOUT will be written
#SBATCH --error=CpG_Me_PE_%A_%a.err # File to which STDERR will be written
#SBATCH -... |
fa43eb130ba1e53f9d7d81fe966405a80210f02e983deb4cc7019b9e003c809d | Shell | 4,152 | 106 | #!/bin/bash
NAME='OTUsamples2krona'
VER='v0.2.2' # version for Github
AUTHOR='Bruno Gomez-Gil' # Laboratorio de Genomica Microbiana, CIAD. https://github.com/GenomicaMicrob
REV='May 21, 2018'
DEP='KronaTools v2.5'
LINK='https://github.com/GenomicaMicrob/OTUsamples2krona'
display_version(){
echo "
_____________________... |
cc43ccd694f0970e4a4b1ec20c93db252996f002ae68e534a3d9cc6495103717 | Shell | 4,325 | 135 | # Copyright 2025 The Magenta Authors.
#
# 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 ... |
8126c159b3ef1248e2c76b0f9cdb6cbdccf86e4427974b0c0ffd89f30d33e3f8 | Shell | 4,404 | 26 | #!/bin/bash
# Script for running HOMER on all the age_neuron modules
findMotifsGenome.pl 'control clusters - 111 to 000 in male neurons - 10.bed' mm10 control_clusters_111_to_000_in_male_neurons_10/ -size given -bg 'background clusters - 111 to 000 in male neurons.bed'
findMotifsGenome.pl 'control clusters - 111 to 00... |
fbdccdbca04ed28c7d5e461333171c8c38c30dd082c816c8b399d89d6d1eb631 | Shell | 4,431 | 33 | #!/bin/bash
python ldsc.py --h2 bip.sumstats.gz --ref-ld-chr hm_anno_baseline. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5eur. --print-coefficients --out bip_hm_baseline
python ldsc.py --h2 pubertal_growth.sumstats.gz --ref-ld-chr hm_anno_baseline. --w-ld-chr weights.hm3_noMHC. --overlap-an... |
7b3f2db0d330d194363e27b40f74607d625e60ec7039b4e8433e3b350f2b05fc | Shell | 4,588 | 205 | #!/bin/sh
# this has now been mostly superseded by test_foreign.py ... keep this around
# as a test of the command-line interface
# set -x
set -e
. ./variables.sh
# poppler / pdfload reference image
poppler=$test_images/blankpage.pdf
poppler_ref=$test_images/blankpage.pdf.png
# giflib / gifload reference image
gif... |
1fc429797cda33699b7437165adf311250883fdc9d8a8dfd3ea3a40a0d7aa94b | Shell | 4,783 | 33 | #!/bin/bash
python ldsc.py --h2 bip.sumstats.gz --ref-ld-chr hm_anno_may2021_baseline. --w-ld-chr weights.hm3_noMHC. --overlap-annot --frqfile-chr 1000G.mac5eur. --print-coefficients --out bip_hm_baseline_may2021
python ldsc.py --h2 pubertal_growth.sumstats.gz --ref-ld-chr hm_anno_may2021_baseline. --w-ld-chr weights... |
a9c264e81455d824c9627d1884534ee72a08d93d1634ed6222d218dd9655b275 | Shell | 5,064 | 117 | #!/usr/bin/env bash
set -euo pipefail
method_mid () {
local WINDOW_SIZE=$1
local PROXIMAL_CUTOFF=$2
echo "Using midpoint method to generate windows" >&2
if (( (WINDOW_SIZE % 2) != 0 )) || (( WINDOW_SIZE <= 1 )); then
echo "Window size needs to be even and 2bp or more" >&2
return 1
else
echo "U... |
e3f5b335212b1b981518303d704b0ea77f01be67649118c76e02001b43da3f54 | Shell | 5,268 | 152 | #!/bin/bash
# Gokberk Alagoz
# 29.04.2021
################
# This script extracts 1000G phase 3 SNPs which
# fall within the evolutionary annotations from
# VCF files.
################
# paths:
vcf="/data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/enigma_evo/evolution/resources/1000G_phase3"
bed="... |
39caa4512cee7c2ef75bc9f355e83b968e03abbc1d455036740d89dadd95617d | Shell | 5,458 | 126 | #!/bin/bash
#PBS -S /bin/bash
#PBS -N all_in_one
##PBS -q yossarian
#PBS -l nodes=1:ppn=1
#PBS -l walltime=11:59:59
#PBS -l mem=1500MB
#PBS -V
#PBS -e PBSout/one_err_av
#PBS -o PBSout/one_out_av
##PBS -t 1-3
# module load HDF5-1.10.0 # add this (and other modules you may need) to your shell config!
set -x
cd "$PBS_O_... |
cd16e595286a247f0f56dca7714d7d9c9ee3484c2c9c4b1594026a2f77d9e816 | Shell | 5,561 | 132 | #!/bin/bash
#PBS -S /bin/bash
#PBS -N GC_all_in_one
#PBS -q yossarian
#PBS -l nodes=1:ppn=2
#PBS -l walltime=14:59:59
#PBS -l mem=50GB
##PBS -M gche4213@uni.sydney.edu.au
##PBS -m e
#PBS -V
#PBS -e PBSout/
#PBS -o PBSout/
#PBS -t 1-1
# module load HDF5-1.10.0 # add this (and other modules you may need) to your shell c... |
8d4e3d8b45bde2a95fc7de7ace458b785974d6f2263e8a94deeadd11c9e83d50 | Shell | 5,600 | 103 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
# log in to JGI
COOKIES="cookies.txt"
function jgi_login() {
if [ ! -f "$COOKIES" ]; then
read -p "JGI Phytozome Username: " JGI_USER
read -s -p "JGI Phytozome Password: " JGI_PASSWORD
echo
curl 'https://signon.jgi.doe.gov/signon... |
1b13dd7a66c5dcef37983d58f07f3ea8348e2bc1db375272ba8b23fca52db2b8 | Shell | 6,009 | 243 | #!/bin/bash
##########################################################################################
# Author: Ben Laufer
# Email: blaufer@ucdavis.edu
##########################################################################################
##############
# Initialize #
##############
# Manually set mainPath
ex... |
cf74e40caaff31b8b3aa7489fc094055dd550be7bc7b6dfd26fe2ee779e2bed3 | Shell | 6,011 | 243 | #!/bin/bash
##########################################################################################
# Author: Ben Laufer
# Email: blaufer@ucdavis.edu
##########################################################################################
##############
# Initialize #
##############
# Manually set mainPath
ex... |
0dd5150c948d0277a8e0e17b1d4b7db525e3750fee70d07aa048d80cd9e6279b | Shell | 6,626 | 172 | #!/bin/bash
# This script trains a Multimodal DBN using deepnet.
# Before running this script download and extract data from
# http://www.cs.toronto.edu/~nitish/multimodal
# Location of deepnet. EDIT this for your setup.
deepnet=$HOME/deepnet/deepnet
# Location of the downloaded data. This is also the place where lea... |
3a329053e0c7e48f43fd5ac386c32d8ebbfeab69ed42b609965af15b5cc35756 | Shell | 6,660 | 150 | #!/usr/bin/env bash
set \
-o errexit \
-o nounset \
-o pipefail
# log in to JGI
COOKIES="cookies.txt"
function jgi_login() {
if [ ! -f "$COOKIES" ]; then
read -p "JGI Phytozome Username: " JGI_USER
read -s -p "JGI Phytozome Password: " JGI_PASSWORD
echo
curl 'https://signon.jgi.doe.gov/signon/... |
66e51ad1180db2a3b8e10124a120074abf5cb010ab813461e10630e2869ced87 | Shell | 6,742 | 204 | #!/bin/bash
# MICA T1w/T2
#
# This script will register a Quantitative Image to T1nativepro space and then to Hippunfold surfaces
#
# Outputs will be store under anat/surfaces/morphology
#
help() {
echo -e "
\033[38;5;141mCOMMAND:\033[0m
$(basename $0)
\033[38;5;141mARGUMENTS:\033[0m
\t\033[38;5;197m-sub\033[0m ... |
7e02181f51c74552e230aa66a2c48948ea48b90b0eb59ba49905b4231dbccbbe | Shell | 7,194 | 284 | #!/bin/bash
##########################################################################################
# Author: Ben Laufer
# Email: blaufer@ucdavis.edu
##########################################################################################
##############
# Initialize #
##############
# Manually set mainPath
ex... |
ea56205210caf177406dc2927fe55922613f0294bab078f4be7c03f9b0034476 | Shell | 7,196 | 284 | #!/bin/bash
##########################################################################################
# Author: Ben Laufer
# Email: blaufer@ucdavis.edu
##########################################################################################
##############
# Initialize #
##############
# Manually set mainPath
ex... |
56b1222885ea2782958bade0f327dc306f949a2dce48a3be4297ff89ee842ac3 | Shell | 7,309 | 201 | #!/bin/sh
#$ -S /bin/bash
#$ -cwd
#$ -m eas
#$ -N subset_snpstats_DTI
#$ -q single15.q
#$ -e /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -o /data/workspaces/lag/workspaces/lg-ukbiobank/projects/enigma_evol/final/log
#$ -M Barbara.Molz@mpi.nl
#script written by Dick Schijven... |
f7862fd0c3acafe352bdac52bb968cf0e7690b81f7e236f38195030dd5f666ff | Shell | 7,325 | 223 | #!/bin/bash
# Copyright 2017 Google Inc. All Rights Reserved.
#
# 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 applica... |
5cfd73b397f91d1fe048d8b8be6b307b534c2cc4b0b33c5ef3fd6f39be351ca9 | Shell | 7,479 | 30 | findMotifsGenome.pl 'select clusters - 101 in female p12 neurons - random subset - 1.bed' mm10 select_clusters_101_in_female_p12_neurons_random_subset_1/ -size given -bg 'background clusters - 101 in female p12 neurons.bed' -p 3 -nomotif
findMotifsGenome.pl 'select clusters - 101 in female p12 neurons - random subset -... |
10642e45c4b668c36196486fbfaa32cf34b2f73d32807f4c587ec3fdc4b1c5a9 | Shell | 7,544 | 107 | #!/usr/bin/env bash
# Reproduction driver for scfc v1.0.0. Every Makefile target calls this script; see docs/REPRODUCE.md.
# ./reproduce.sh <target> targets: env test fetch-exploration sa-axis exploration benchmark-smoke
# benchmark-v1 fetch-confirmatory confirmatory decide figures... |
f7d47232feff52bdf18823925aca8678bdfd73cf0013658d6e789740d602de2e | Shell | 7,868 | 235 | #!/bin/bash
# MICA T1w/T2
#
# This script will create a T1w/T2 using two files from the rawdata directory
#
#
#
#
#
help() {
echo -e "
\033[38;5;141mCOMMAND:\033[0m
$(basename $0)
\033[38;5;141mARGUMENTS:\033[0m
\t\033[38;5;197m-sub\033[0m : Subject identification (no 'sub-')
\t\033[38;5;197m-out\033[0m ... |
a3c61d7a04f59b2904cc12f928bf11446fe4db5f258a8fc78a374aaf28be0404 | Shell | 8,201 | 296 | #!/bin/bash -eu
export PKG_CONFIG="pkg-config --static"
export PKG_CONFIG_PATH="$WORK/lib/pkgconfig"
export CPPFLAGS="-I$WORK/include"
export LDFLAGS="-L$WORK/lib"
# `-fuse-ld=gold` can't be passed via `CFLAGS` and `CXXFLAGS` as Meson
# injects `-Werror=ignored-optimization-argument` during compile tests.
# https://g... |
08eb5074704d0a07918ff6643d92f61d71c6518a0c9bba121b95c5b283133211 | Shell | 8,646 | 118 | #!/bin/bash
# NOTE: O P T I O N S & I N S T R U C T I O N S
#-----------------------------------------------------------------------------------------------------------------------------#
# data_file_id: unique identifier for the file containing the tfrecord data
#--------------------------... |
2f142c439022ee372a22e9f40dd65ea6915dfbe147ef21f8b01a33e26a811395 | Shell | 10,538 | 233 | #!/bin/bash
#
# DWI structural processing with bash:
#
# Preprocessing workflow for diffusion MRI.
#
# This workflow makes use of freesurfer, FSL workbench and MRtrix3
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 : pa... |
1fe46a22ac7bd2e3960a24b2ddde4b9ed98c020934c0486c0a5ba59da0932611 | Shell | 13,959 | 401 | #!/usr/bin/env bash
PROG_NAME=$0
BASEDIR=$(dirname "$0")
function red(){ # From https://stackoverflow.com/a/57096493
echo -e "\x1B[31m $1 \x1B[0m"
if [ -n "${2}" ]; then
echo -e "\x1B[31m $($2) \x1B[0m"
fi
}
function green(){
echo -e "\x1B[32m $1 \x1B[0m"
if [ -n "${2}" ]; then
... |
6e23692ec15860e27fd1cd5f6d8df24e63db8d9d0df9abbf110b789e34c38a7d | Shell | 14,249 | 284 | #!/bin/bash
#
# DWI POST structural TRACTOGRAPHY processing with bash:
#
# POST processing workflow for diffusion MRI TRACTOGRAPHY.
#
# This workflow makes use of MRtrix3
#
# Atlas an templates are avaliable from:
#
# https://github.com/MICA-MNI/micaopen/templates
#
# ARGUMENTS order:
# $1 : BIDS directory
# $2 :... |
fb53a8630a3d4a1cd83ec3e8f475ec5576d466c11f103df40efc5555be5b9be3 | Stan | 634 | 14 | /*
GIST is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
GIST is distributed in the hope that it will be useful,
but ... |
068d5834afe1cd6e9f85e387e0e505d7c3bd66025fa2e1eb194d4069d0649cdd | Stan | 1,469 | 56 | //
// Learn more about model development with Stan at:
//
// http://mc-stan.org/users/interfaces/rstan.html
// https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
//
// The input data
data
{
int<lower=0> numGenes; // The number of "genes"
int<lower=0> numCellTypes; // number of cell types
vector[n... |
1fb4ae841b613f3a8fd5b26d8274889354f83b9090e2d936331c7d1c26e47240 | Stan | 1,724 | 66 | //
// Learn more about model development with Stan at:
//
// http://mc-stan.org/users/interfaces/rstan.html
// https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
//
// The input data
data
{
int<lower=0> numGenes; // The number of "genes" (1000)
int<lower=0> numCellTypes; // number of cell types (2)... |
abb2c1bc42ab0e05315b0e69e12408bc123482e09b5a0695e3de8e62353bb803 | Text | 14 | 1 | # MD-reservoir |
0eb35d8b00d48d07ce1c3a13853905ba3f7b46cd42552de19334dacd92215c02 | Text | 17 | 2 | # Zazio-FHN2022
|
41bf24d0fad213e05fb616d6c11805b9a492a3d04f0982fb81dfa80c2146b817 | Text | 24 | 1 | # reverberating_habenula |
2507916a0426b5e4ddeb71b1fa0753f70458c023a948d403ff059652f9743fb0 | Text | 38 | 1 | # Tarietal-2022-SubclonalInteractions
|
97502f2ad66281a01e02106367e6983638feecc24086052704304edf7da13c38 | Text | 55 | 2 | # TDP_LOF
RNA-Seq of TDP-43 loss-of-function datasets
|
e525485fe804a4bc8fd88d23e60ee5ef7c28a93b257b4be2d5a35ef6f150d9b6 | Text | 57 | 2 | # BipolarClustering
Clustering Analysis of Bipolar Cells
|
8fe20e0a2d5982ea751ae1209e928c1f209a51358eeba1d78911fc005469ae4f | Text | 62 | 2 | # nf-metavir
Nexflow pipeline for viral metagenomics analyses
|
27002e94653cdaa96d8bfc2e40777c07b5af357da2d2209080114e42c051e806 | Text | 68 | 2 | # Research
Custom-made scripts for data analysis in research papers
|
63932fba610a3dd5965cbb04c53e7b1f0781dca10e64646b090fb3fc438756b4 | Text | 76 | 2 | # viewworm
Neuron segmentation and fluorescence quantification in c.elegans
|
faa0b3616325d2f4a71792b87179796e79b46d33dedaddb67dbe97b425f7b6d3 | Text | 83 | 2 | # SorbentsScreening0D
Equilibrium model for VTSA simulation and sorbents screening
|
80f0206fba2e96bf92a50b63dccf114d8c7b9897656c2315ab14a37db37ab49a | Text | 92 | 1 | Datos extraídos del mapa de ATU (Lima, Perú) en https://sistemas.atu.gob.pe/paraderosCOVID |
ada5b79871fe4311780f238057dfa85b52772f3118c08db7ce560376f9bba5e0 | Text | 97 | 3 | # CSDH-cytokine
Inflammatory profile in chronic subdural haematoma and response to dexamethasone |
708cfa7b1c6b616bc8b42e97fff7b6292abfc1174ec095a1fad33041fab678ed | Text | 151 | 2 | # Flow Cytometric Analysis Frame
This project is for our article named "Treatment of marmoset intracerebral hemorrhage with humanized anti-HMGB1 mAb".
|
54da0ae8b8e9f32d6c85abbe0edc9d332750138bf5fe2e063401c6b81324548a | Text | 154 | 3 | # AIC-DLS_Microstructure_Modeling
Drinking microstructure computation and modeling of drinking in the dark experiments in Haggerty et al. 2022 in eLife.
|
c34c3137eb4cca5f56d5e9b4c780f875ddd57603e7ac82ff22871ebb49071ab5 | Text | 173 | 3 | 1) Add main forder and subfolders into the Matlab path
2) Select the script corresponding to the respective figure
3) Within each script select the panel you want to plot
|
c5602d29f513390b82e295951f1b9f425f7fbd878dbd75375c44c5129810b2fe | Text | 183 | 4 | # Documentation
Use the [Wiki](https://github.com/neuropsytox/Documentation/wiki) for documentation on several lab things
+ [Home](https://github.com/neuropsytox/Documentation/wiki)
|
bcc6c2e6dfec3266184632180b371febd8ad50ccb3973302c383f2f523798e9b | Text | 193 | 9 | # iNaturalist Competition Datasets
## Current Competitions
* [2021 Competition](2021)
## Previous Competitions
* [2019 Competition](2019)
* [2018 Competition](2018)
* [2017 Competition](2017) |
9418c2595c5507c0404a6c7af44323524061acb518628453f2fa2a6eea978a50 | Text | 243 | 10 | # GIST
Guiding-Image Spatial Transcriptomics
R package implementing the GIST base-model, GIST enhanced-model and other utilites for processing spatial transcriptomics data.
To install:
```r
devtools::install_github("asifzubair/GIST")
```
|
54e2f5abb85182546d63d614f006b39e1b0598fa8a15ad2742ba9d7b5bf4e8c1 | Text | 264 | 9 | # MD-dynamics
Code accompanying the manuscript:
**A circuit mechanism for independent modulation of excitatory and inhibitory firing rates after sensory deprivation**
Authors: Leonidas M. A. Richter and Julijana Gjorgjieva
Email: leonidas.richter@brain.mpg.de
|
5d6f67ead8d763347ae2b41df0b0e8198da74288b74e058d5c26c40aff82be70 | Text | 268 | 7 | Python 3.6 with packages listed in "requirements.txt"
Push the "requirements.txt" file to anywhere you want to deploy the code, and then type in terminal:
$ virtualenv <env_name>
$ source <env_name>/bin/activate
(<env_name>)$ pip install -r path/to/requirements.txt
|
91497ca4d81c5f702239b3828fea99a7ad8bd4072edab0199a2e4a07202160b3 | Text | 273 | 7 | # Psignifit Custom
Custom configuration of Psignifit 4 toolbox under Matlab needed to calculate temporal order thresholds.
# Adaptive procedure
Python adaptation of UML MATLAB Toolbox used to estimate intervals during TOJ task.
Authors: Jan Nikadon & Mateusz Chojnowski
|
cb9acd42e727c65c2f3e76245b2fb4bab4f71d1912274ef5a96953204b2472e4 | Text | 364 | 11 | Description of files :
fULM.m : matlab script to process fULM data and display activation maps
Visual_stim.mat : visual stimulation fULM experiment data.
To be processed in fULM.m
Whiskers_stim.mat : visual stimulation fULM experiment data.
To be processed in fULM.m
colormap : colormap used in fULM.m ... |
7b8c1c29a8d7198e69111529ac419c8b74d6a6b56d39e73f3690a603cca96191 | Text | 371 | 5 | # cffDNA and Brain Manuscript
This repository contains the scripts to reproduce the analyses from:
Laufer BI et al. Integrative cell-free fetal DNA methylation profiles correlate with infant brain multi-omics and behavior in a rhesus macaque model of maternal obesity. *bioRxiv* preprint. **doi**: [10.1101/2021.08.27.... |
52282092ec16e69737c7af879d967bd2e7fd933a44b0b49092ce8c272410e2b8 | Text | 383 | 15 | # Hyper-Model
Model to investigate gamma hyper-PLV with cross-frequency coupling
## Getting started
```
python run_kuramoto.py
```
## References
D. Laszuk, "Python implementation of Kuramoto systems," 2017-, [Online] Available: http://www.laszukdawid.com/codes
Kuramoto, Y. (1984). Chemical Oscillations, Waves, an... |
4996a6c7743699e55b32216daa19f090c247c474cfb9d2e4eca5537a2fa44e76 | Text | 385 | 5 | # tremordetector
A detector for human tremor using accelerometer signals. If you use this code in your project, please cite the paper:
Sahin, Gürdal, Pär Halje, Sena Uzun, Andreas Jakobsson, and Per Petersson. “Tremor Evaluation Using Smartphone Accelerometry in Standardized Settings.” Frontiers in Neuroscience 16 (Au... |
f9d7b07f9e6cd7f7d8527f8edfb5519bd8985172d18ad79e330858fff939042f | Text | 418 | 9 | # Improve_Imagination
This is a repository for "Improving classification and reconstruction of imagined images from EEG signals".
https://doi.org/10.1371/journal.pone.0274847
For EEG data, please visit
https://osf.io/2fgks/
If you use codes or data, please cite my paper:
Shimizu H, Srinivasan R (2022) Improving... |
11ff0b09e9038c2a9721af0938a2369ce332e2579deaf80865f35f0e651466c9 | Text | 428 | 7 | # cffDNA and Brain Manuscript
[](https://zenodo.org/badge/latestdoi/386458928)
This repository contains the scripts to reproduce the analyses from:
Laufer BI et al. Multi-omic brain and behavioral correlates of cell-free fetal DNA methylation in macaque maternal obesity ... |
cfb55a92d3f020c765bf2ee088f53ee4bb09ccef455050f26882adb05d408815 | Text | 429 | 4 | # spls
Sparse Partial Least Squares method using L1 and L2 norm constraints. Please check the paper by [Monteiro _et al._ 2016](http://www.sciencedirect.com/science/article/pii/S0165027016301327) for details.
The computation of the first weight vector pair (u,v) should be done using `spls.m`. Then, matrix deflation sh... |
b9b709b61ec8e02628e33914a55e1405a301312480ae1b2b7b856d4f8dff4333 | Text | 438 | 7 | # PRANet
Pyramid Residual Attention Network for Dermoscopy Segmentation
this is my first demo and paper for skin lesion segentation, I am honor to pubilish my first work, and thanks for the CANet, they provide me with a good training structure.
in this work, we composed three efficent modules to an integertion, and ge... |
2dd6910baa82491cad3ecce340da107835be5f2d6e5167d0a4cab27d040e6c2e | Text | 442 | 17 | deepnet
=======
## Implementation of some deep learning algorithms. ##
GPU-based python implementation of
1. Feed-forward Neural Nets
2. Restricted Boltzmann Machines
3. Deep Belief Nets
4. Autoencoders
5. Deep Boltzmann Machines
6. Convolutional Neural Nets
Built on top of the [cudamat](http://code.google.co... |
6dd444010dfd1f789d62c7fe33af8f4d14ac5debf10497aac6bbbb622ced6633 | Text | 459 | 17 | # Chloride dynamics determine the optimal distribution of inhibitory synapses to minimise dendritic excitability
## Installation
1. (Recommended) Create conda environment
```
conda create -n inhiblevel python=3.9
conda activate inhiblevel
```
2. Install requirements (including NEURON)
> [**WINDOWS ONL... |
31981e060c0d71b5b530ce611c66a4a1627f4b300e2ea7461f023c27ab8414df | Text | 656 | 10 | # pysmFISH [](https://travis-ci.org/linnarsson-lab/pysmFISH)
pysmFISH is a library for the analysis of cyclic single molecule fluorescence hybridization (smFISH) experiments.
pysmFISH ([full documentation](http://linnarssonlab.org/... |
1fd649e9888656a9157d706742f6e38bc9ed81b69561340eb7bbcf0dd24fb495 | Text | 681 | 23 |
===============================================================================
Source code for the paper:
A Deep Neural Netork model of the Superior Colliculus in emotion recognition.
Carlos Andrés Méndez, Alessia Celeghin, Matteo Diano, Marco Tamietto
University of Turin, Italy
Feb 2022
==============... |
79a5643938c416476442d278d4bf12db0d890737418bb05563deaab2afe20374 | Text | 699 | 8 | # Manasig
MANASIG: Python Package to MAnipulate NAnopore SIGnals from sequencing files
Thus we present a Python package designed to manipulate, extract and process nanopore sequencing files and provide a helpful tool to analyze squiggles. It provides a single API to access the reads attributes allowing extraction and ... |
dfafca4ee1ccec399c71ed0eff00184e5c217bc55a91cbe850c4a849db182f4b | Text | 719 | 20 | # sc_ConsensusClustering
Scripts for unbiased clustering and consensus clustering
**NMF-ANLS/**
----------
matlab scripts for doing NMF-ANLS clustering.<br>
Original nmf_bpas code was downloaded from: http://www.cc.gatech.edu/~hpark/software/nmf_bpas.zip
**Graph_Louvain/**
----------
python scripts for doing graph Lo... |
3fc0c31ffc70a9c766b7233d424bc38e15b2559f8d594b901515a4f11642cf94 | Text | 720 | 5 | This folder contains data in support of the preprint titled "Human electromagnetic and haemodynamic networks systematically converge in unimodal cortex and diverge in transmodal cortex", which is also available on bioRxiv: Shafiei et al., 2022, bioRxiv; doi: https://doi.org/10.1101/2021.09.07.458941
Full data and code... |
66d3dd4ac25a027037f81f868e01866978115eaac783792cc8d83566aa660f74 | Text | 739 | 20 | # Small, correlated changes in synaptic connectivity may facilitate rapid motor learning
Corresponding paper: [Feulner et al. 2021](https://www.biorxiv.org/content/10.1101/2021.10.01.462728v1)
## Requirements
Python 3 and PyTorch 1.8
## Usage
1) train a modular recurrent neural network to produce hand trajectories
... |
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