sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0c8a0fcccaf0e95b031ed4276277a94758e5906069d4d5259970b846eb83db08 | Shell | 22,607 | 633 | #!/bin/bash
VERSION="0.0"
# Check dependencies
PROGRAM_DEPENDENCIES=( 'ImageMath' 'SmoothImage' 'ThresholdImage' 'antsRegistration' 'antsApplyTransforms' 'N4BiasFieldCorrection' 'Atropos' 'KellyKapowski' )
SCRIPTS_DEPENDENCIES=( 'antsCorticalThickness.sh' 'antsBrainExtraction.sh' 'antsAtroposN4.sh' 'antsJointLabelFu... |
ff27167eab1168fbf7e99a9671649abbe01d5fa7db6e7771658cb8769229dafd | Shell | 25,593 | 448 | #!/bin/bash
#
# Parcellation of the corpus callosum :
# - Upsampled corpus callosum midsagittal section
# - Average unilateral connectivity
#
#
# Initial author: Gabrielle CONVERT (2021, 2022)
# Contributor: Yann LEPRINCE (2022, 2023)
#
# CC-parcellation-from-tractography © 2023 by Gabrielle Convert, Clara Fischer,
# J... |
18cba9e0fcf5e05e21a871a533c0840a2ad47fc63ea6813d96aaa4eab9dbba3e | Shell | 25,809 | 532 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow 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 2 of the License, or
# (at your... |
4aab380ac0630599d2cbd681c6b6ca8965ddd2d9bf92d39bae932c9fee759a79 | Shell | 26,216 | 714 | #!/bin/bash
VERSION="0.0.8 dev"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
if ! command -v ANTS &> /dev/null
then
echo "ANTS program can't be found. Please (re)define \$PATH in your environment."
exit
fi
function Usage {
cat <<USAGE
Usage:
`basename $0` -d ImageDimension -r fixed.ext -i m... |
e423afc327fecb00a11d6c0ccbdcb6ead8e42b006aac12a6398ad49749c87ce3 | Shell | 27,020 | 717 | #!/bin/bash
VERSION="0.0"
if ! command -v N4BiasFieldCorrection &> /dev/null
then
echo we cant find the N4 program -- does not seem to exist. please \(re\)define \$PATH in your environment.
exit
fi
if ! command -v Atropos &> /dev/null
then
echo we cant find the Atropos program -- does not seem to exist. pleas... |
6a4ec0743021752aa6d881a517a08c03ffc833b03407b5c1df878c5daf75ec25 | Shell | 29,836 | 727 | #!/bin/bash
VERSION="0.0"
if ! command -v N4BiasFieldCorrection &> /dev/null
then
echo we cant find the N4 program -- does not seem to exist. please \(re\)define \$PATH in your environment.
exit
fi
if ! command -v Atropos &> /dev/null
then
echo we cant find the Atropos program -- does not seem to exist. pleas... |
09dd64bc1fa5a35651bdb2aa4bd47e62a9763ff7d1e8084fa6c575dd86774b2b | Shell | 35,525 | 645 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow 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 2 of the License, or
# (at you... |
400a85b72b2580728eb86b1faa298c4705c991bec9d6695bb765cf5caab184ac | Shell | 36,905 | 170 | #!/bin/bash
export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=//Users/nagehan/Documents/Github/curveball/curveball_scripts/curveball/Yale_vtk
input="/Users/nagehan/Documents/Github/curveball/curveball_scripts/curveball/subjects_yale_TD.txt"
while IFS= read... |
b70e1ed25645d91c37cd8ee90af56aa84f0d1a9e9d28052c00ffc739926c139d | Shell | 38,088 | 914 | #!/bin/bash
# for i in `cat ./cond1`; \
# do qsub -N des_${i} -l h_vmem=8G,mem_requested=8G,tmpfree=1024G,tmp_requested=1024G \
# -P ParkinsonsDiseaseandNeurodegeneration \
# -cwd -pe smp 6 -V -b y \
# bash ./scripts/complete.sh ${i} 6 ; done
echo "$tmp_requested $TMPDIR"
module load borgue/star/2.5.1a
module load ... |
dd2fb1efb0cde22513ccd030226a688f7c7717bfb6e86d093dc0f7078c077164 | Shell | 44,682 | 1,250 | #!/bin/bash
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=antsRegistration
WARP=antsApplyTransforms
JLF=antsJointFusion
PEXEC=ANTSpexec.sh
SGE=waitForSGEQJobs.pl
PBS=w... |
35e3b73415694d8ac174c286435d84431b106b7f9059ebe441146186623d40b6 | Shell | 45,018 | 1,122 | #!/bin/bash
VERSION="0.0"
# Check dependencies
PROGRAM_DEPENDENCIES=( 'antsRegistration' 'antsApplyTransforms' 'N4BiasFieldCorrection' 'Atropos' 'KellyKapowski' )
SCRIPTS_DEPENDENCIES=( 'antsBrainExtraction.sh' 'antsAtroposN4.sh' 'antsMultivariateTemplateConstruction2.sh' 'antsJointLabelFusion.sh' )
for D in "${PRO... |
3e175720adae4eab993af7525d4874fdaadf04a2514a6883d1a3302569d8d2aa | Shell | 48,895 | 1,360 | #!/bin/bash
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=antsRegistration
WARP=antsApplyTransforms
JLF=antsJointFusion
PEXEC=ANTSpexec.sh
SGE=waitForSGEQJobs.pl
PBS=w... |
8878f02aa40d342a070d233eafd808909da05d6d862f1bdf1dd0b70ffce872dd | Shell | 49,077 | 1,357 | #!/bin/bash
VERSION="0.0.14 test"
afftype=".txt"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
if ! command -v ANTS &> /dev/null
then
echo "ANTS program can't be found. Please (re)define \$PATH in your environment."
exit
fi
# Test availability of helper scripts.
# No need to test this more than onc... |
417a482589540f7e736dc514d8a7549ab89483c3597229d11e03cb163a31c62f | Shell | 63,182 | 1,641 | #!/bin/bash
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
JLF=antsJointFusion
ANTS=antsRegistration
WARP=antsApplyTransforms
SMOOTH=SmoothDisplacementField
PEXEC=ANTSpexec.... |
cd539f04343981b0d21a7d15b31364b26c374ced4bbe9feae4695feabdf8674c | Shell | 66,159 | 1,514 | #!/bin/bash
VERSION="0.0"
# Check dependencies
PROGRAM_DEPENDENCIES=( 'antsRegistration' 'antsApplyTransforms' 'N4BiasFieldCorrection' 'Atropos' 'KellyKapowski' )
SCRIPTS_DEPENDENCIES=( 'antsBrainExtraction.sh' 'antsAtroposN4.sh' )
for D in "${PROGRAM_DEPENDENCIES[@]}";
do
if ! command -v ${D} &> /dev/null
... |
a5013919df812c4c1cd5c518525b2af1a043b7570c8c34951996982d3f56899f | Shell | 70,519 | 1,737 | #!/bin/bash
set -euo pipefail
# Use extended globbing to allow for more flexible pattern matching
shopt -s extglob
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=ANTS... |
0f4f33513fdf35b0048b003d68ab22f6ef44027d41a35ac9b4727c7056d2af18 | Shell | 71,028 | 1,261 | #!/bin/bash
# This program 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.
# This program is distributed in the hope tha... |
35c8d6b9a63ada529e83173b8a2d2193bca3d6b08375314a08cbff105f37cbcd | Shell | 76,592 | 1,943 | #!/bin/bash
set -euo pipefail
# Use extended globbing to allow for more flexible pattern matching
shopt -s extglob
VERSION="0.0.0"
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=antsRegistration
WARP=antsApplyTransforms
N4=N4BiasFieldCorrectio... |
fae6054e5622af29c41b1f936f1032a15f801deb98defd557d390bd0797db0e8 | Shell | 99,432 | 1,138 | #!/usr/bin/env bash
# Copyright (C) 2019 Christoph Gorgulla
#
# This file is part of VirtualFlow.
#
# VirtualFlow 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 2 of the License, or
# (at your... |
b7587c8ae487e1d107593381f62b977f0a56e0f67f8e8252ffdc4cbdf65d263c | Stan | 1,092 | 40 | data {
int<lower=0> N; // number of samples
int<lower=0> D; // number of dimensions
real slog[N]; // log normalization constants
int M[N]; // binary group membership vector
int y[N]; // observed microbe abundances
real control_loc;
real control_scale;
}
... |
114e04cd5417f5c5c13345ed335ace91444af80c1ab484b03ac486478ec964ae | Stan | 1,130 | 42 | data {
int<lower=0> N; // number of samples
int<lower=0> D; // number of dimensions
real slog[N]; // log normalization constants
int M[N]; // binary group membership vector
int y[N, D]; // observed microbe abundances
real control_loc;
real control_scale;
... |
355d91a1b5b2f90c97a99b8f79c9330b3c52f29d2ae2e97850d1436cecf2ca4b | Stan | 1,555 | 56 | data {
int<lower=0> N; // number of samples
int<lower=0> D; // number of dimensions
real slog[N]; // log normalization constants
int M[N]; // binary group membership vector
int y[N, D]; // observed microbe abundances
real control_loc;
real control_scale;
... |
cbf5c4e4d44abd916735e259721c07ef16d1a3929814a06d99a4269dc208ddef | Stan | 1,650 | 54 | functions{
vector alr_inv_lg(vector x){
int d = size(x);
vector[d + 1] y = to_vector(append_col(0., to_row_vector(x)));
return y;
}
}
data {
int<lower=0> C; // number of controls
int<lower=0> N; // number of samples (2 * C)
int<lower=0> D; // number of s... |
8c044d5d1c442f4440a0a63e6056839098302c5c8a3d9a88fc19f7f3ea12be56 | Stan | 2,021 | 67 | data {
int<lower=0> C; // number of controls
int<lower=0> N; // number of samples (2 * C)
int<lower=0> B; // number of batches
real depth[N]; // log sequencing depths of microbes
int y[N]; // observed microbe abundances
int cc_bool[N]; ... |
9fd282399a24d246b5713e4f0e288dc46da82d63d1901b20f56d5bdf21b7feec | Text | 10 | 1 | # BRAINBOX |
ac8e1eab11ee77d0083dc1394898e818966ebb489c7087d36a1728afdbad0e7a | Text | 10 | 1 | # DIAM-CNN |
0f6b0a960ef585cb70cd6bceb3662a2e63fbea19dc406b53d33804ce3bd53111 | Text | 11 | 1 | # MAToM-SNN |
b53ddc7693e269f4792ed74a835e5c152f78213f6c483d64902da19c85ac7ffa | Text | 27 | 1 | # Rat_Hypothalamus_scRNAseq |
085b198caa1d1bfb58572f040ef2c13e7391d5cf4690fbb56154980ea113d2b8 | Text | 41 | 1 | # Functional imaging processing pipeline
|
ec014cd1b5e3681db7cd39f59f1e75a7d64664b9c4b02ec9ef79afc27e6b4370 | Text | 69 | 2 | # Shawn Lyv
The dataset generated during the study is attached here.
|
f9b1992984439c0bcff67cb66733c588c921051068dd6091f26c5e2012d0dd78 | Text | 75 | 2 | # q2-differential
A collection of common differential abundance techniques
|
8033054288bb21b20cb35139e2f64fd03be5aa16831d20dcdeeb0088eb29d040 | Text | 76 | 2 | # BPC_NRISdata
Code and data will be uploaded after the paper is published.
|
42af15fcc2d14a5c36b74eaa7f483f5aa260c458345395c502065e2b9018ad27 | Text | 79 | 2 | # pub_file_share
code written for data analysis to be included in publications
|
c619a6e7b30b871da3fb1114bc5b9566a31da060c1deaab09ba31014883c3929 | Text | 80 | 2 | # KPE
Github repository associated with the Ketamine reconsolidation manuscript
|
cf99d16f3fc51d6cfb0096b54b3520bb604238caba4b6ea7decaf2651f1fa9b3 | Text | 80 | 2 | # QC_2P
Small repository to share some code to check data quality of 2p movies
|
c1ecf159672574463b66700bd76dc5203e8a53bafe38e0bd6154b0100a6b3130 | Text | 84 | 2 | # continuousfeedback
Analysis scripts for the continuous feedback processing paper.
|
89e9aaea40ed45b4431657a1312db85c69381b81db142fe3b11d6f7dbf0cd99e | Text | 87 | 2 | # HGS_exome_paper
Computational codes for UK Biobank hand grip strength exome analysis
|
7a0ae0d37f7e7578ac5cc84169d9aa4260193dc55640636290a5a8d1569421c7 | Text | 96 | 2 | # PET-Phantom-Generators
These files generate 2 and 3 dimensional test phantoms for PET testing
|
62a54663eba40fbf59ab5a525a128dd0536ca652209ebfa3b056ce82ba2f64f5 | Text | 99 | 2 | # friedman_etal_2023
Code used for analysis presented in Friedman et. al (2023), Animal Cognition.
|
0c953526c48c4e8f923d688e5b52230bfeb79f70041bf860e318cc2876114888 | Text | 100 | 2 | # Automated_QuPath_TIL_-Classifier_for-TNBC
H&E image based-QuPath TIL classifier for TNBC WTIs
|
809570433487eb879c690bcb58c80ddeee38936d220043c29b7ae9ec99f5b7f6 | Text | 104 | 2 | # DiabetesAging
A global landscape of expression patterns of genes related to comorbidites of diabetes.
|
4a4ec84c11043eb7699d1255db2d8b7471968db72fb467f7637c983f2212392f | Text | 106 | 2 | # Publication-Code
This repository contains code that accompanies publications from the FIL Physics Group
|
0fcfa32c4a1aa59281532c9b4415799e9439fb45d4096bd7a7b5120bdbda7612 | Text | 114 | 8 | # FL
Codes for Functional Learning
Please refer to our new site:
https://github.com/eehyc/Functional-Learning
|
badd65410fc69a5ad08a75642713132548883e641ad158bb224ee737d2be59fd | Text | 114 | 2 | # PACNet
Core code of "Phase-amplitude coupling-based adaptive filters for neural signal decoding" (ID: 1153568)
|
aeb4bd634e0820eec542fd24737bbd4d85c8bb9ee791f5f8f39bb55fa24cca2c | Text | 123 | 5 | # Code for the paper Intrathymic AAV delivery
Code for Calabria et al, Intrathymic AAV delivery
Currently under revision
|
85f6e2629f233d471d7476b62f6bec7c9993f45e7cb6bc14c05599fbc150bad7 | Text | 126 | 4 | # CognitiveSubtypes
Cognitive Subtypes and Associations with Brain Structure in the UK Biobank: A Machine Learning Approach
|
c2d9ea36875a1bcde6dfc6b9d707d8909e7b1b7768a813a5be43c7a0a4354f0d | Text | 128 | 2 | # jcni_2018
Recurrent gains in RET and HER2 signaling represent clinically actionable targets in breast cancer brain metastases
|
a4605a70897cc055e5237c6c0033799403e28d2a806c5597543d7b271da19ccb | Text | 136 | 2 | # Shroff-Lowet-Nature-Communication-2023
[](https://zenodo.org/badge/latestdoi/623008776)
|
4fe98c1f5c4a33a8595729fa15a44398086e176de3d9f76c99d1a7294cbe78ef | Text | 140 | 2 | # gnn_gda
Availability of data and materials related to the paper Identifying candidate Gene-Disease Associations via Graph Neural Networks
|
5c8f975be0713f5fc8a44f98315d94bb57ea90e8a5fa7de104da50798c8efe5c | Text | 151 | 1 | This is a placeholder repository for code used in https://doi.org/10.7554/eLife.82598. Code and data can be obtained through email to mmender@umich.edu |
35f329a3f4423d9f0bc3e8730c4eacdde80483c3dd9d61766257e7893b8284a9 | Text | 161 | 3 | # Hydra_Somersaulting
Codes used for the paper for somersaulting.
[](https://zenodo.org/badge/latestdoi/530252253)
|
04d1c115460c6b62d680a70480d1164c7d56636a5f713ccae470a81fc9c29acc | Text | 167 | 5 | # q2-longitudinal
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org. |
7b1b5d845af838701e4731c4cd6d05e26a4669e5dedcb1aefdbdd7e64b32efb1 | Text | 172 | 7 | # inhomogeneous-rf-nmr
NMR simulations with RF inhomogeneity
Pulse sequences:
1. R-PDLF with R18^7_1 and rINEPT
for questions, contact tiago.ferreira@physik.uni-halle.de
|
925a052a4ee432cebadc05951c33dd46d365dea8db60a7f3772d6dd1aadbc9eb | Text | 183 | 3 | # AD_RNA-Seq
Supplementary material towards the manuscript: Modelling early changes in Alzheimer’s disease by RNA Sequencing of brain regions differentially affected by pathology.
|
9ab0ac22a78a8f97f7e69b47e4117a37009a96d0861e44d3922ace7d6f0c303a | Text | 184 | 2 | # AD-project
## Detection of Alzheimer´s Disease Phenotype using Machine Learning Classifiers and early Electrophysiological Aberrations in the Hippocampus of the TgF344-AD Rat Model
|
f8e888a45f09b73ac42f81c0069421804b1fb2184a3a5171bb3ef268f474f05d | Text | 192 | 1 | This repository contains the code to reproduce the main results of the article "Stasenko S.V., Kazantsev V.B. Information encoding in bursting spiking neural network modulated by astrocytes".
|
7a3dea2ed7a572ed0987b84bc1a835ba9365b125cf6a1be41280977efc8da4e8 | Text | 203 | 3 | # Citation
- Vladimir Kosonogov, Danila Shelepenkov and Nikita Rudenkiy. “EEG and peripheral markers of viewer ratings: a study of short
films”. Frontiers in Neuroscience 17 (2023). issn: 1662-453X.
|
16f50e896ea746b2e43a78cab18922dd6e9b175048d483176d69e3d0a0c363ab | Text | 216 | 1 | # streamlit_demo [](https://share.streamlit.io/miketrizna/streamlit_fish_masking/main/fish_masking_classification_streamlit.py)
|
c920dee912326a6c70886606349e01b40fdfee576f2febd29b82501040c09a64 | Text | 227 | 4 | # brain_ms
This repository is intended to accompany the following manuscript:
M. Grabowski, B.T. Kopperud, M. Tsuboi, and T.F. Hansen (2023) Both diet and sociality affected primate brain size evolution. _Systematic Biology_.
|
d90cd0c48619ba2ff87aa3bcf32990c3eaf56d52366baaab90d49870a6b2cfd0 | Text | 229 | 5 | # MPD-DNN
Monkeypox detection using deep neural networks: https://doi.org/10.1186/s12879-023-08408-4
In the implementation of this paper, the dataset with the address https://github.com/mahsan2/Monkeypox-dataset-2022 was used.
|
fadab2c350dab28253462e696000d7a3659228e2d951129f8e645f5e126aa386 | Text | 234 | 7 | # emwave_pulse_PC_App
Source code are only for research purpose, not for commercial usage.
It is a c# Window Form Project for Pilot study on HRV.
The study includes Emotion and Cognition Lab and SAIL Lab at USC and other parties.
|
b78caf130769ad6583f83f889112f747bb70ac54ed7dc9f0fdab8a5b462b83cb | Text | 242 | 3 | Code to reproduce figures of Demirci, Hoffman, and Holland (2023).
All the data generated from this study are available on [Zenodo](https://doi.org/10.5281/zenodo.6638528). This data is required the run the codes and reproduce the results.
|
fe462db3b9975b556015f579a5fd892972d74ff566178a478729227a6d979e24 | Text | 243 | 4 | # ottenheimer-et-al-2022
Code and pointers to data associated with Ottenheimer, Hjort, Bowen, et al. 2022.
Code to analyze data is uploaded in this repository. Data files are available on figshare: https://doi.org/10.6084/m9.figshare.21365598 |
9e8270ede4a26c4824a32844688310f651545598d0562293f9bfe98333193c9d | Text | 270 | 6 | # FBXO7
In this repository, the marcos and pipelines used in the manuscript can be found.
"PARK15/FBXO7 is dispensable for PINK1/Parkin-dependent mitophagy in iNeuron and HeLa cell systems"
Link to preprint: https://www.biorxiv.org/content/10.1101/2022.11.02.514817v1
|
1ef4c91dce062a9c250758b5f4ec25e7f1557d991e1cf3964d913e2394e69d3b | Text | 280 | 4 | This Git contains all necessary files for generating the images and animations shown in the manuscript:
"iMPI - iMPI – portable human-sized Magnetic Particle Imaging Scanner for real-time endovascular Interventions" by P. Vogel et al.
Patrick.Vogel@physik.uni-wuerzburg.de
|
0a19485570be087e9e8277fb7000fcae1e3d3d6d9086fb587623f1f085c79b13 | Text | 286 | 3 | Computational Models used in:
Purohit, P., Dutta, P., & Roy, P. K. (2023). Empirically validated theoretical analysis of visual-spatial perception under change of nervous system arousal. Frontiers in Computational Neuroscience, 17, 1136985. https://doi.org/10.3389/fncom.2023.1136985
|
e0da7b41a2dc7cedbac1c3fa1b4c2aad59d21e34d4dd64bc657d244e050c26ec | Text | 286 | 2 | # Stimulation-Evoked_Perception_Behavioral_Software
This package includes the MATLAB 2022b scripts to run the behavioral software application GUI described in the research paper "Behavioral Paradigm for the Evaluation of Stimulation-Evoked Somatosensory Perception Thresholds in Rats".
|
494a47b26e4817859f2a4c6aa28336bcd3818b400400da547ebfca7a45a4a9bb | Text | 293 | 9 | Filename convention is <cell number>-<TA/HipTA>-Pattern.dat
.dat files contain 400 ms pretrigger and 600 ms posttrigger neuronal activity.
Each line is a trial.
Resolution is 1 ms.
Delimiter is ",".
Example to load with python:
import numpy as np
trials = np.loadtxt(filename, delimiter=",")
|
c580cfe45834083477911f079d394573fbe219432c7525d6cce281f5ee627833 | Text | 312 | 9 | # Perseus
Event-driven simulator of spiking neuron networks
Version: 2.1.3i (June 24th, 2013) by Maurizio Mattia
Citation:
Mattia M, Del Giudice P. 2000.
Efficient event-driven simulation of large networks of spiking neurons and dynamical synapses.
Neural Comput 12:2305–29. doi:10.1162/089976600300014953
|
61ead1b741d6fe868fdbd34a97bb498b56ad51a8b293ac13f844ccfca2de2fe6 | Text | 316 | 6 | # q2-picrust2
QIIME 2 plugin for PICRUSt2
For descriptions of how to install and run this plugin, see [here](https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial/).
Please first check our [FAQ](https://github.com/picrust/picrust2/wiki/Frequently-Asked-Questions) if you have any questions about PICRUSt2.
|
5d3f162f37ab7203e1716f304ba159114c5a3ca5a6e13e74bee8b927866f9447 | Text | 325 | 5 | # gromacs_scripts
assorted scripts for working with gromacs, mostly system building with some mdp files for membrane simulations.
TODO. Add automation for detection of ligands to genrestr_sequence.sh so you don't need seperate scripts for each ligand/molecule class.
TODO. Change top2psf.pl to detect segname from top ... |
c519a70627376994252f00cc64d81a9c67e6cbd0a5e93716e0b92dd2c1853c69 | Text | 346 | 4 | # onlinequantumtimeseries
Codes for generating the figures of the paper "Online quantum time series processing with random oscillator networks": one .nb file for each figure.
It's strongly recommended to download the files as they are not properly displayed here. Opening the files requires a working recent installatio... |
dc196416a28caf0ddeaefc710ad4f99c4ab1b8a591171a833619c56ce89fa4c9 | Text | 352 | 6 | # Latent Complex Normal Model
This repository contains estimation and inference code for a latent complex normal model given in the following paper:
Urban, K. N., Bong, H., Orellana, J., and Kass, R. E. (2023). "Oscillating Neural Circuits: Phase, Amplitude, and the Complex Normal Distribution." *To Appear in the Ca... |
64ab2d1f4edbf9346aaf2722890a08e9d721ff9b109f5c2439b20c7c30480d94 | Text | 372 | 3 | # Robust pancreatic cancer classification in CT images with an annotation-efficient deep learning approach: Clinical implementation
This code is an official implementation of 'Robust pancreatic cancer classification in CT images with an annotation-efficient deep learning approach: Clinical implementation' base on the ... |
7235ebf39c01bca45b078b3cf5993cab6642954aa0e2cf6cc89381db8543bfec | Text | 420 | 3 | # JSIT
This is the codebase for the Joint Sparse method for Imaging Transcriptomics, as described in our publication _Optimization-Based Decoding of Imaging Spatial Transcriptomics Data_, published in _Bioinformatics_.
JSIT accurately "decodes" raw data from imaging-based spatial transcriptomics methods like MERFISH an... |
edbbddf9a36debbdcb0ea8003da8825f2e0c66870be8cf5408092be3f8fb5790 | Text | 425 | 8 | # dnnbrain (db)
Use DNN to study the brain and use brain measurement to evaluate DNN.
DNNBrain includes both tools to explore internal representation of DNN and tools to examine the correspondences between DNN and brain.
Installation, Tutorials, Examples, etc. are available in [DNNBrain Documentation](https://dnnbrai... |
4fc61bbada32551c419191403227babb1583246008ea0c2663ad310ed1747476 | Text | 430 | 8 | # 2processmodel
Little scripts to make a 2-process model plot.
Running "ExamplePlot.m" will recreate [the classic figure](https://www.researchgate.net/publication/275524207_Vulnerability_to_Sleep_Deprivation_A_Drift_Diffusion_Model_Perspective).
But you can make your own figure however you want.
The function `plo... |
6231f91fa2996abb914ca2d4c201c603b25dfeacc1b57a011af1bb858756e39b | Text | 435 | 4 | # Computing the effects of switch dimensions on brain and behaviour
Here is the code used for analyses of the results contained in the manuscript titled "Planning ahead: Predictable task switching recruits task-active and resting-state networks."
The code is organised into folders according to different analyses. If y... |
032b44519fc4d9435c3f486842ac394e757fde796f0cc4bc67020694a2268620 | Text | 455 | 6 | # NRXN1_effects
The script of single-cell analysis of NRXN1_del effects in human brain organoids. For more details, please refer to
>
> <cite>[Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia](http... |
91abed2d4377106e190b301c13ac890a5dd732a7126425eb8f06b64e55bcd921 | Text | 458 | 13 | # HRV-ER-dataset_release
scripts for Heart rate variability biofeedback training and emotion regulation (HRV-ER) dataset in openneuro
doi:10.18112/openneuro.ds003823.v1.2.1
For questions, contact hyunjooy@usc.edu
Description
• freesurferQC/: a folder including scripts for T1-weighted MRI data quality control
This... |
d0218468ccba4beef4d8b1a5560c27257eede1b1c64bc1bbff9608b85149a6a5 | Text | 466 | 9 | ### Code Release for [Pipeline PSRO: A Scalable Approach for Finding Approximate Nash Equilibria in Large Games](https://arxiv.org/abs/2006.08555)
1. [Installation](docs/install.md)
2. [Running Poker Experiments](docs/running_experiments.md)
3. [Interfacing with the trained Barrage Agent](docs/barrage_agent.md)
An up... |
c7aa7393b202ae43db061f1f1930f713fa929872d3c8fb7d8297e692d82d7fb3 | Text | 469 | 13 | readme file for codes and data for
Metzen & Chacron (2023) Descending pathways promote neural heterogeneity: implications for decoding and behavior
% -----------------
Asumes using Matlab version 2021a or higher.
Keep all files in the same folder. Each main Matlab code has a small description at the beginni... |
0d8f65f358b2ab59a4b38f1be92617495f1ade857d58c19b0dbaa9335616d371 | Text | 477 | 10 | # biophysical_ppglm
This is the code repository for paper:
A biophysical and statistical modeling paradigm for connecting neural physiology and function
Nathan G. Glasgow, Yu Chen, Alon Korngreen, Robert E. Kass & Nathan N. Urban
Journal of Computational Neuroscience (2023)
https://link.springer.com/article/10.1007/s... |
015fc5cbb95f8d3f96d6546f01880418deb8cdc5ef7256ec060ad6e7d2f2c750 | Text | 482 | 13 | # Osmo Publications
This repository contains related code and data for publications released by [Osmo](https://osmo.ai/).
All datasets in this repository are released under the CC BY 4.0 International
license, which can be found here:
https://creativecommons.org/licenses/by/4.0/legalcode. All source files in this
re... |
8e1f5507e2c53b19084a0d5325d3d4dc2594a6eb372a8505ce38258cbdadf156 | Text | 489 | 13 | # Entropic associative memory using a single register
This repository contains the procedures to replicate the experiments presented in the paper
Pineda, Luis A. & Rafael Morales (under review). _Imagery in the Entropic Associative Memory_.
The code was written in Python 3, using the Anaconda Distribution, and was r... |
55797d8b839a6e60de45ba717e7b41229b9f0557e9803a8bc626040ac92bcd13 | Text | 510 | 13 | # Shoeibi-COVID19-Dataset
Details of the dataset are given in our paper, and if you think this is helpful in your research, cite our paper:
```
@article{ghassemi2021automatic,
title={Automatic Diagnosis of COVID-19 from CT Images using CycleGAN and Transfer Learning},
author={Ghassemi, Navid and Shoeibi, Afshin a... |
8226de0ffa4032cb294536b3eb3cc1a56e74c048553da21443d701fe967c2006 | Text | 516 | 8 | # data_bee_decision_making
This repository contains the data for the paper "H. MaBouDi, J. Marshall, N. Dearden, A. Barron. (2023), How honey bees make fast and accurate decisions", published in eLife, 2023.
The paper can be accessed through the following link: https://doi.org/10.7554/eLife.86176.
For any questions ... |
62b4ab01e5a054d971f8c56e59a455aad027ea4bed6e603a7370b5e7ce11db4b | Text | 521 | 14 | # BRAINBOX
The **BRAINBOX toolbox** is an implementation of the brain topography mapping methods.
AUTHOR: Ing. Vaclava Piorecka, Ph.D.
CONTACT: vaclava.piorecka@nudz.cz, vaclava.piorecka@fbmi.cvut.cz
[](https://zenodo.org/badge/latestdoi/115143863)
This toolbox is t... |
62cffb460d6fe386c1fbc01f76dfd87a9f21aa89f82d07ca734d9a0b414501ff | Text | 528 | 21 | # Spatial-temporal-EEG-fusion-framework-for-MDD-detection
successfully using RNN and CNN to detect MDD using spatial temporal EEG fusion
#### *by: Dr Zhang\*,
## Data
We used three public datasets in this study:
-MODMA Dataset(http://modma.lzu.edu.cn/data/index/)
## Reproducibility
If you want to update the train... |
70696898db5dd614f64d752c8a27827143efea6c0b028ce5f424c6eb8658becc | Text | 551 | 16 | NOTE: change path in config to data path (uploaded via Dryad)
processed data (histograms generated under different conditions) are provided in figureDataSources.
However these can be regenerated with the following scripts:
- quantile_based_eye_dir_effects.m
- recomputeHistAll_mesh_orig_masks.m
- recomputeHistAll_mes... |
7cd207f0d8c63b8509a218c9ea64014e26fb1a1b9735c1ef6956c29f63ad252d | Text | 560 | 8 | # HeviAI_picai
Welcome to our PICAI Challenge submission repository! We've developed an end-to-end solution for prostate segmentation and lesion detection. This repository contains everything you need to understand, implement, and extend our solution.
## Citation
**If you find this project useful, we would be gratefu... |
eff256ec05eb2a9a297e582ce394f751e744f0ab20e8f39ca4296dc0cd2ee066 | Text | 589 | 16 | # Gradient Correction
This code repository contains code and access to data to reproduce the analysis from "Correcting gradient-based interpretations of deep neural networks for genomics" by Majdandzic, Rajesh, and Koo. Code in this repository is shared under the MIT License.
For questions, email: koo@cshl.edu
Dow... |
fa991a92c22f5efbc130635f671d637aa285c449e5d65603271330c9398ea7fd | Text | 590 | 20 | # Short_Decoding_Time
Code for Lenninger, M., Skoglund, M., Herman, P. A., & Kumar, A. (2023). Are single-peaked tuning curves tuned for speed rather than accuracy?. Elife, 12, e84531.
https://doi.org/10.7554/eLife.84531
Code tested on MATLAB 2018 and jupyter notebook.
How to run:
1. Download the folder(s) correspo... |
3a1cb064f162bb9c9a68a6fac3e0dd96963846e6db54abadb88c1ecef09090c6 | Text | 615 | 14 | **ARCHIVE** - this project is no longer actively maintained. If looking for an alternative, I recommend looking at Andrew Senior's version that runs entirely offline:
- https://andrewsenior.com/cuneify/index.html
- https://github.com/asenior/cuneify
---
This is the source code for CuneifyPlus, which is currently hos... |
2a0fb97dd5b34949f1ed6780046dcbf0684bae9d0ac14d583437cb2c79f6f008 | Text | 618 | 11 | # Influence of deafening on gene expression in birdsong vocal motor circuitry
Analysis of the effects of deafening on birdsong and gene expression in birdsong neural circuitry. Companion code for
Colquitt, B. M., Li, K., Green, F., Veline, R. & Brainard, M. S. Neural circuit-wide analysis of gene expression during dea... |
a47b607d79b28e5f75dc151c9d4f54b78a6e2ed12eb491e1b9b621cb237d9561 | Text | 645 | 12 | # pySEAS
python Signal Extraction and Segmentation
See the [ReadTheDocs](https://pyseas.readthedocs.io/en/master/modules.html) page to browse example experiment commands, documentation, and available function help.
**Publication describing functionality**:
Weiser SC, Mullen BR, Ascencio D, Ackman JB (2023) Data-dr... |
d662964b5ca29ec256644309de639928f21e30a1aa4e0ebcf538740652733a8d | Text | 648 | 21 | # McDermott-et-al-Aging
Analysis code for McDermott et al manuscript "Delayed formation of neural representations of space in aged mice"
The analysis code for this paper is based on the pipeline introduced in Frechou at al. and available at https://github.com/GoncalvesLab/Frechou-et-al-Neurogenesis
Pre-processing of... |
00091a880b866874d2398c94ebd270f14a21658cd233fd1e63f4cd4cdd661606 | Text | 663 | 9 | # Drosophila_flexible_recall
This is a repository with the data analysis and plotting programs used for the published, eLife paper: Flexible specificity of memory in Drosophila depends on a comparison between choices (https://elifesciences.org/articles/80923).
All analysis scripts were written in Matlab. In general, t... |
65f2221e9a9d37fd48a84ec281a3f56443282422c7c3564b974293c8b97511da | Text | 677 | 8 | # distributedActivity
This repository provides the source code for training spiking neural networks operating in the balanced state, as investigated in the following paper.
Kim, C. M., Finkelstein, A., Chow, C. C., Svoboda, K., & Darshan, R. (2022). Distributing task-related neural activity across a cortical network ... |
e12ee90870b936240b88604cbd2865eee639f471171ab035cb704602b47bcb70 | Text | 704 | 5 | # TransDecoder
> **PyTransDecoder supersedes this Perl TransDecoder.** [PyTransDecoder](https://github.com/TransDecoder/PyTransDecoder) is the Python implementation of the same method, and new users are encouraged to start there. It runs faster (about 2.7 times on our benchmark) and has more features, including homolo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.