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5221a09088c0d6340eb2e7adc9f4603d6f797da030d3e2563e6d95e4326c366e | Text | 845 | 16 | # Mouse Brain eccDNA
This repository contains code from "Hong, X. et al. The extrachromosomal circular DNA atlas of aged and young mouse brains".
## Code
### eccDNA Analysis pipeline
eccDNA-p... |
e8546cf2c149c34e49edc1c6f50361ac3893538ccaa8a32d32a478b0b0376ec4 | Text | 850 | 12 | # Bruker_PrairieLink
Stream data from PrairieView into MATLAB to allow online analysis
To increase speed of data analysis immediately prior to an experiment raw acquisition samples are streamed from the microscope to custom software (via PrairieLink, Bruker). This raw stream is used to process pixel samples, construct... |
c3791ffc66d5fc2ec790c76e6e9ff7ad9830ab2f168490306af42aa827b3297e | Text | 855 | 37 | ========
tractify
========
.. image:: https://img.shields.io/pypi/v/tractify.svg
:target: https://pypi.python.org/pypi/tractify
.. image:: https://img.shields.io/travis/salimansourc/tractify.svg
:target: https://travis-ci.org/salimansourc/tractify
.. image:: https://readthedocs.org/projects/tractify... |
5dc8d3bd0b42187fc5ce7427dc0c93cc2ac32bef1f78e9521163e61084572d2e | Text | 856 | 11 |
This work is a result of a collaboration at UCLA between the Golshani Lab, Silva Lab, and Khakh Lab. Contact Daniel Aharoni, DBAharoni@gmail.com, with questions or comments.
msRun.m will walk you through the order one would generally run the processing and analysis functions on a single recording session. We highly ... |
fefd42f1176bf44c6c344e180d7e7a5706dc26f319bab8c71554bde73168d4cf | Text | 857 | 14 | # Diet and Microbiome in PD
This repository hosts the code and methodology used for filtering high-resolution sequencing data, conducting statistical analyses, and generating figures as presented in our research paper, published in npj Parkinson's Disease, 2024.
## Overview
The purpose of this repository is to provide... |
3a5cad616d76cc1394c9c37c85fc9b92dc8f282ff6bca82b4d9401855c6e13ba | Text | 864 | 13 | # iCSD
Python-implementation of the inverse current source density (iCSD) methods from http://software.incf.org/software/csdplotter
The methods were originally developed by Klas H. Pettersen, as described in:
Klas H. Pettersen, Anna Devor, Istvan Ulbert, Anders M. Dale, Gaute T. Einevoll,
Current-source density estim... |
7c2f71620103aac52145b8ce919925d5109e7b216fbd89fadb16c11c30663344 | Text | 864 | 23 | ---
Orthogonal Stochastic Linear Mixing Model
---
This is the python implementation of the paper [Bayesian Inference in High-Dimensional Time-Series with the Orthogonal Stochastic Linear Mixing Model].
We propose a new regression framework to model multivariate output response data, which not only capture the com... |
d223f78df3375b84e42eebb6974f3dc0e9eea404cea95b17e80509c42b29813b | Text | 865 | 29 | # NeuronBridge image aligners
These containerized aligners are used by NeuronBridge to align user-uploaded imagery in preparation for ad-hoc searching. They run using Docker on AWS Batch.
## Build Containers
### Prepare container build environment
Copy 'env.template' to '.env' and set the container namespace or if... |
34bfee127dee6f68ed242b173db4d69a3c455509c1409aa16b13baca406b538f | Text | 871 | 17 | # tetxglu
Codes used for RNA-seq analysis in the "Tet Controls Axon Guidance in Early Brain Development through Glutamatergic Signaling" manuscript.
DOI: https://doi.org/10.1101/2023.05.02.539069
Authors: Hiep Tran<sup>1</sup>, Le Le<sup>1</sup>, Badri Nath Singh<sup>1</sup>, Joseph Kramer<sup>3</sup>, Ruth Steward<s... |
55c9e770d88f12bb54b892c66908bc05e48a1bad44757601d3b0df3bb5f173bf | Text | 894 | 45 | # dataknead
**Fluent conversion between data formats like JSON, XML and CSV**
[Read the docs](https://hay.github.io/dataknead/)
Ever sighed when you wrote code to convert CSV to JSON for the thousandth time?
```python
import csv
import json
data = []
with open("cities.csv") as f:
reader = csv.DictReader(f)
... |
705b0e2383bb4524121b11564110f91f0cb343d5a4aedd11527add975c8c9f64 | Text | 901 | 30 | # Development of Pericardial Fat Count Images Using a Combination of Three Different Deep-Learning Models: Image Translation Model From Chest Radiograph Image to Projection Image of Three-Dimensional Computed Tomography
This repository includes source code of our paper. The detail of the model is described in our ... |
57722ddfbd3de99cb40f854a54fe63fe859ebce383c5812d6af582c8bbe7bcf1 | Text | 904 | 18 |
## Functional Connectivity Development along the Sensorimotor-Association Axis Enhances the Cortical Hierarchy
**Article**: [https://www.nature.com/articles/s41467-024-47748-w](https://www.nature.com/articles/s41467-024-47748-w)
**Study preregistration**: [https://osf.io/vf8ew](https://osf.io/vf8ew)
**Preprint**:... |
d58f13dd51428cc98d61d27bca9a37da71408509ab04faca7cf3a32bb93c305e | Text | 921 | 29 | # Z2F
Z2F: Heterogeneous Graph-Based Android Malware Detection
# Floder:decompile
Step1:using apktoo.jar and apktool.bat to install apktool to decompile Android packages;
Step2:using decompile.py to batch decompile Android packages.
# Floder:filter_samples
using check_empty.py,check_smali.py,delete_empty.py and filte... |
452531ced09bd5b630f8740da644aa81b82829654f4668904ba9eeb8d7922fc3 | Text | 926 | 19 | # PD_beta_bursts2
This repository contains scripts for characterization of beta bursts in Parkinson's patients and healthy controls presented in the manuscript:
Vinding, M. C., Eriksson, A., Low, C. M. T., Waldthaler, J., Ferreira, D., Ingvar, M., Svenningsson, P., & Lundqvist, D. (2021). Different features of the cor... |
85096741ea1a769986ae31c57f3c4b8326b0351b21e53508c7398147477d6126 | Text | 926 | 9 | # Opto-microprobe-implantation
This is a demonstration of opto-microprobe implantation surgery for D1/D2 tagging experiment with freely moving mice. <br>
<br>
A. Front and side view of the opto-microprobe holder. <br>
B. Demonstration of post-surgery setup. The whole recording system was protected with headstage cap, o... |
423f1ccd3f236115383dc807411901e1d391e89dd5c6ba8d5b3a8808d4010c34 | Text | 938 | 10 | # CANDELA
Code for the publication "Cancer Drug Sensitivity Estimation using Modular Deep Graph Neural Networks"
`run_experiments.sh` contains the driver code for running the both pretraining tasks and the proposed models:
- `data_preprocessing.py` contains the code for the data preprocessing for the pretraining and d... |
57025f053c68b5cfb63574ce803a4fc433ee1c0bc85b918867100247b1a3941e | Text | 943 | 24 | # PLISM-registration
`smartphone_wsi_registration.py` is a Python script for image registration between Whole Slide Images (WSI) and smartphone captured images.
## Installation
The code requires Python 3.8.5.
To install the necessary dependencies, run the following command:
`pip install -r requirements.txt`
## Usage... |
3b62816d97f8220c3f671f327e08f8d8fb08b29480fb98fc1f7a4689c571a0e4 | Text | 947 | 16 | Expertly segmented structures on high resolution T1 and T2 human brain scans
----------------------------------------------------------------------------------
This repository holds the offical release of the CoBrALab manual segmenations of
5 high resolution T1 weighted and T2 weighted brains.
The brains themselves ... |
4a4f76125cac5a0521939a67497cb4588df040bbfd202eadb7bc17f41e81f1ca | Text | 956 | 42 | # iEEG scripts for "Temporal organized..."
# Dependencies
MNE-python
scikit-learn
nilearn
numpy, pandas, matplotlib
# Task code
Code to run the risk task are all in ./TaskCode
(requires Matlab and PTB3)
# Behavioural analysis
parseBehav.py # convert .mat to .csv
behaviour.py
riskModel.py
# Neural ... |
50c9a83f78a15f9951266539d4c191d61ce217d7cb331e10e52e4548b15e5e1e | Text | 968 | 37 | # Transformers_for_Remote_Sensing_A_Systematic_Review_and_Analysis
#### 介绍
data of the paper
#### 软件架构
软件架构说明
#### 安装教程
1. xxxx
2. xxxx
3. xxxx
#### 使用说明
1. xxxx
2. xxxx
3. xxxx
#### 参与贡献
1. Fork 本仓库
2. 新建 Feat_xxx 分支
3. 提交代码
4. 新建 Pull Request
#### 特技
1. 使用 Readme\_XXX.md 来支持不同的语言，例如 Readme\_en.... |
ad8600f48ba61ef957e279ee3a64cbd0abcd21defab9a40b226429320a97beb5 | Text | 977 | 9 | # imbalance-gain-causality
This repository contains the supporting codes for the article **Robust inference of causality in high-dimensional dynamical processes from the Information Imbalance of distance ranks** ([arXiv](https://doi.org/10.48550/arXiv.2305.10817), [PNAS](https://doi.org/10.1073/pnas.2317256121)).
The... |
ec487a0ca1e3f84ef486477e297d584c8160e986f61c6dfb8603221d97b55e1e | Text | 980 | 11 | ## Code repository for "Iterative convergent computation may not be a useful inductive bias for residual neural networks"
This repository contains the code required to reproduce the analysis in the paper "Iterative convergent computation may not be a useful inductive bias for residual neural networks."
'Environment.y... |
6987deecc6de0b4c1318a14c5615d690496f23a93c71f64845503ec4394e6905 | Text | 988 | 18 | # beamforming-based_artifact_removal
These Matlab codes allow you to design spatial filter for artifact removal from EEG or MEG
List of functions
BF_type_cleaningFilt.m - the basic function for using beamforming- based EEG cleaning, when you know the topographies of the artifact subspace
SOUND_veryfast.m - SOUND cle... |
52d3da4711831c912a4065b9c02f10f8f7da7782c344eb33655c52275d9eba95 | Text | 994 | 9 | # Nutil-To-Usable
Please read the N2U protocol if it is your first time using the app as it will guide you step by step in how to use the app. It will also provide descriptions on the more specific/confusing elements so please refer to it if you get lost.
This app is also hosted as a Shiny application at the followin... |
faf1643c959bff47ec64f6f72226a7c5858ffecf2c57b262d1c6fb2aa16bc16e | Text | 1,000 | 31 |
# edgeCounter
<!-- badges: start -->
[](https://github.com/yeyuan98/edgeCounter/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
`edgeCounter` is a R-package for counting edges (5'/3') of BAM alignment reads. ... |
99fc4df20c4c7ca688ff3660f8e12c90827f6ff1faf0d0b56de78c35e063151f | Text | 1,008 | 13 | # Mesoscale simulations of classical eyeblink conditioning
Code for model, simulations and analysis of classical eyeblink conditioning with a spiking neural network, E-GLIF neurons and spike-driven plasticity, as described in Geminiani et al., Plos Comp Bio, 2024 - doi: [https://doi.org/10.1101/2023.06.20.545667](https... |
921e1d3f4695c7e2c53aad5e8b17cf36e4c4edca01513e656004ef09836a3028 | Text | 1,016 | 24 | # rtDCCA
rtDCCA ("Real-time Detrended Cross Correlation Analysis") is an open-source MATLAB class that allows for
fast linear (pairwise) or parallel (matrix-wise) DCC analysis of multiple time series. The class also
allows for the easy calculation of the DCC Coefficient.
For a detailed explanation, see:
Z. K... |
dd4462ebd0bd496bc0472d6a183934b8f0eb10d26ed8f07cf305cc9af668b0ce | Text | 1,037 | 34 | chromosome-network-modeling
===========================
This repository contains the scripts needed to reproduce the analysis published
in *Parental and stochastic skewing of X-chromosome inactivation predicts
phenotypic penetrance of fragile X syndrome* (citation link to come)
To reproduce this work:
1. Clone this... |
1cad3ba05da345da2e1e4bbfc54b3a25ded7f858f739ec5857b55188627b986a | Text | 1,050 | 12 | ## Zinc_NNPs
Modeling the potential energy surface of Zinc complexes. The repository is based on [the Open Catalyst 2020 (OC20) Project](https://github.com/Open-Catalyst-Project/ocp) and [EwaldMP](https://github.com/arthurkosmala/EwaldMP?tab=readme-ov-file). Please consider to cite their original work if you find this ... |
3ca4f47d10287e080f8027ebc2a4bfe587bc1c04d150e9d2a390a1c47b123312 | Text | 1,052 | 4 | # Visual_Tracking_BCI
The GitHub repository contains the online system code derived from the 'visual tracking brain-computer interface' research. This code encompasses fixed visual tracking tasks, random visual tracking tasks, painting application, and snake game.
These systems operate in conjunction with stimulus pro... |
a901c37847aa682ef40a98501fee144faf6da3e2fb54757e4002256d7dbac58b | Text | 1,061 | 27 | # SLMPhaseMaskMaker3D
Generates phase masks for display on an SLM using a weighted GS algorithm (Martin Persson's [HOTlab](https://github.com/MartinPersson/HOTlab))
To calibrate the generation of SLM phase masks that target ROIs in an imaging stack see [SLMTransformMaker](https://github.com/llerussell/SLMTransformMake... |
f1f71e495cfb6f8dd18f2255a6a59bdda06186386e9df144fb8959405fa41d0b | Text | 1,061 | 33 | ## BitterGNN
[](https://doi.org/10.5281/zenodo.10018600)
We created a new GNN (HGNN, combined four modules including edge attention, GAT, MPNN and Weave-GNN), and trained the predictors BitterGNN can distinguish bitter/non-bitter and bitter/sweet taste of... |
0daf38ff01b7804c5f8f89520b7bda6c244a9071907097b6b53fb3f25ac2371b | Text | 1,073 | 17 | # SBVS-PARP1
You will find herein the code and files related to our paper:
**Caba, K., Tran-Nguyen, V. K., Rahman, T. & Ballester, P. J. Comprehensive machine learning boosts structure-based virtual screening for PARP1 inhibitors. ... |
1a31de515af545cefa71c99d488d72f26b8a1a5a1b7d432fc62d4e7aa8810172 | Text | 1,092 | 18 | # Unbiased quantification of the spatial distribution of murine cells using Point pattern analysis (PPA)
This repository contains the material associated with the **StarProtocol** for Point pattern analysis (PPA).
## Files
`Atlas_Regions.csv` is a dictionary containing brain area names and acronyms. It is useful to ... |
6e2ace05e37cbfe5391bd86ecf086d494896b85e7abae1cf23fc7a949d6704f5 | Text | 1,105 | 24 | vegas
-----
This package is for evaluating multidimensional integrals using
an improved version of the adaptive Monte Carlo vegas algorithm.
The central package is :mod:`vegas`. A tutorial on its use
is in doc/html/index.html (or doc/vegas.pdf if you prefer pdf).
The vegas algorithm has been widely used for decades to... |
16108e104147b9236b575337642ebb5f940b04a3bade5ad3daa53499817f2fe1 | Text | 1,106 | 24 | <h1>Quantitative T2 mapping-based longitudinal assessment of brain injury and therapeutic rescue in the rat following acute organophosphate intoxication.<h1>
<h3>Code for T2 mapping using 2 functions:<h3>
<h4>1. Voxel-wise (curvefitting21.m)<h4>
<h4>2. Regional (curvefitting31.m)- averaging all voxels within a regio... |
dd044a10b9b87851ba1f053750b7d6a69859af351bf7b836671869bdfc347330 | Text | 1,114 | 19 | # Code for "Global spatiotemporal synchronizing structures of spontaneous neural activities in different cell types"
## Dependencies
* Python.
* Python packages in "requirements.txt".
## How to run it
* Install Python.
* Install all required Python packages using something like ```pip install -r requirements.txt``... |
66bd3745fc911d472447e3d41ec35632dd251d1dda78edcb9830af44473c38e1 | Text | 1,118 | 38 | ===============
Qbiome
===============
.. figure:: https://img.shields.io/pypi/dm/qbiome.svg
:alt: qbiome PyPI Downloads
.. figure:: https://img.shields.io/pypi/v/qbiome.svg
:alt: qbiome curent version
.. image:: http://zed.uchicago.edu/logo/qbiome.png
:height: 300px
:scale: 30 %
:alt: qbiome logo
:... |
9009f54e97a0cc12f58f3b01792e43b2e242f30a023ed09492e9668a06e11ecb | Text | 1,120 | 3 | This repository provides the non-identifiable data published in article: de Souza WM, Fumagalli MJ, de Lima STS, Parise PL, Carvalho DCM, Hernandez C, de Jesus R, Delafiori J, Candido DS, Carregari VC, Muraro SP, Souza GF, Simões Mello LM, Claro IM, Díaz Y, Kato RB, Trentin LN, Costa CHS, Maximo ACBM, Cavalcante KF, Fi... |
a22dc66e492840f0bc8548ec78cb3d62a1dea1aa218879d1bc65d0e8ff756dfe | Text | 1,122 | 6 | To demonstrate how to obtain the structural/velocity/flow direction maps using the localization data, a small script (i.e., MainFunc_static_TNTutrack.m) along with a sample dataset which was generated using the open-source TrackNTrace toolbox, which was originally developed for single-molecule localization microscopy (... |
6f1e0e57f44e45f66e2bfe9d1eae1621f3a6f9843d0e67b8ae76fd55bbd88019 | Text | 1,127 | 17 | # Dataset for BodySize\_Affordance manuscript
---
The dataset contains all behaviour data, fMRI data and stimuli used in the experiment.
## Description of the data and file structure
The folder "27objectimages" contains the stimuli used in behaviour experiment.
In the "behaviour data" folder, "AllBehviourData.xlsx... |
eeb0ffe0df42b92445009932d6457ee16c1c3862c76e76b428043eae348bc9c0 | Text | 1,147 | 50 | # Wilmot-et-al.-2023-Data-and-Code
Repository containing data and code to reproduce figures in:
"Phasic locus coeruleus activity enhances trace fear conditioning by increasing dopamine release in the hippocampus" (Wilmot et al., 2024, eLife)
Please note that code was written for the analysis of this specific data and... |
309ea681f328dd023b8546c71d62b8488db83483fc2ceb09dac06bff17faf09a | Text | 1,154 | 22 | # dPFT (DDR-based Pulmonary Function Test)
dPFT ([Santibanez, V., Pisano, T.J., et al. 2024](https:....)) are generated using an automated lung analysis pipeline that takes raw dynamic digital radiography (DDR) videos and outputs DDR-based Pulmonary Function Test (dPFT) data. This ... |
6918294ba0b7ad540ada26d56667c5ad260f8de9394cb213de6b7f08e70c6256 | Text | 1,163 | 22 | Code and data for
Wurm F, Ernst B, Steinhauser M (2023) Surprise-minimization as a solution to the structural credit assignment task (PsyArXiv, https://doi.org/10.31234/osf.io/kmqp7)
The study consists of two separate experiments. Behavioral data for experiment1 and experiment2 is available in this repository (BEHdat... |
e8527c09641d348db2ff1d7f85d47e288421a8bca270d3ab7f53fb4058a919c7 | Text | 1,167 | 32 | This the Princeton multi-voxel pattern analysis toolbox for
Matlab.
http://code.google.com/p/princeton-mvpa-toolbox/
See the website for more information, or for the latest version.
Please contact mvpa-toolbox@googlegroups.com with any suggestions, bug reports
or feedback.
Copyright Greg J Detre, Sean M Polyn, C... |
3ac2ca37313454fc985db09d6109883125a3fb7b85df05df502d9e0733a3f40c | Text | 1,197 | 17 | When using this code, please cite:
Van Hilten, N.; Verwei, N.; Methorst, J.; Nase, C.; Bernatavicius, A.; Risselada, H.J., Bioinformatics, 2024, 40(2) DOI: 10.1093/bioinformatics/btae069
This repo contains:
- data/training_set.txt sequence and MD-calculated ddF for 53,940 sequences in the training set
- data/valida... |
c4c149142a73f4b92e36b2b78a93c59cfd64e7897c0deb6b3fc52acf75b24932 | Text | 1,197 | 27 | <h1 align="center">ELD – Effortless Landmark Detection</h1>
<p align="center">
<img src="https://i.postimg.cc/6pmrDxB6/ELD.png" alt="ELD logo"/>
</p>
This repository contains notebooks and code for the ELD software from *"Spatial landmark detection and tissue registration with deep learning"*.
## Installation a... |
dca42c39e4c649cfa12456f7aa736e25ed529d19394d306a127543561a43b54b | Text | 1,230 | 35 | # DeepDDI #
#Project
This project is to develop a framework that systematically predicts drug-drug interactions (DDIs) and drug-food interactions (DFIs).
#Features
- DeepDDI predicts DDIs and DFIs using names of drug-drug or drug-food constituent pairs and their structural information as inputs
- DeepDDI predicts 86 D... |
035905f28b267f74d8e49653dc2a0275fdbcd7f4607679ee9315c538e6f21c7a | Text | 1,236 | 27 | # MCMG [](https://zenodo.org/badge/latestdoi/369146587)
MCMG: multi-constraints molecular generation approach based on conditional transformer and reinforcement learning
## Environment
- python = 3.8.3
- pytroch = 1.6.0
- RDKit
- numpy
- pandas
## How to run？
The defau... |
296182c0681f8d50d3db9d9e554555a5ac09ffdb597f7c37158907cc603c381c | Text | 1,263 | 1 | Erythropoietin (EPO) aids in rectifying hippocampal transcriptional networks and synaptic structures of pyramidal lineages, thereby mitigating mood and cognition-associated disorders. An imminent conundrum is how EPO restores synapses by involving interneurons. By analyzing ∼ 12,000 single-nuclei transcriptomic data, w... |
bf17ce3aa5b8c9bfddb7860d96cfc34680a13adeb6512cf5df2a685650721214 | Text | 1,276 | 18 | This repository contains code to analyze preprocessed data and run figures from the following paper:
Blanpain, L.T., Cole, E.R., Chen, E. et al. Multisensory flicker modulates widespread brain networks and reduces interictal epileptiform discharges. Nat Commun 15, 3156 (2024). https://doi.org/10.1038/s41467-024-47263-... |
6740ba382ee982382fffa63498515456054b445ef42bfb081af07bf129d55f3a | Text | 1,284 | 36 | # Shunt Prediction using LSTM for Subarachnoid Hemorrhage Patients
This project aims to predict the need for shunt in subarachnoid hemorrhage (SAH) patients from intensive care unit (ICU) using a Long Short-Term Memory (LSTM) model.
### Dataset
The dataset used for this project was obtained from the University Medical... |
487348fb008e1bdcc895682411648976335a053efd9dd738c33f8a45171d54d6 | Text | 1,314 | 24 | DoM_Utrecht
===============
<strong>Detection of Molecules</strong> (DoM) plugin for ImageJ, Utrecht University
[](https://zenodo.org/badge/latestdoi/6157101)
<img src="http://katpyxa.info/software/DoM_logox.png" align="right" style="padding:100px"/>This is <a href="http:/... |
ea4a9cc26bd6e83e451b28e572cc4146e4e0ff7e32a880788a375fcdc5719ce3 | Text | 1,319 | 18 | iNeuron_ERphagy
Exploring ER-phagy receptor specificity and redundancy in iNeurons
R Markdown file contains all relevant code for proteomics figure generation related to manuscript below:
Title: Combinatorial selective ER-phagy remodels the ER during neurogenesis
Authors: Melissa J. Hoyer, Cristina Capitanio*, Ian R... |
7503d691ac55e517db6908dddbd7ecc21a17c4b6c006161d900de14218a4369c | Text | 1,324 | 25 | # Towards a more robust non-invasive assessment of functional connectivity
Britta U. Westner, Jan Kujala, Joachim Gross, Jan-Mathijs Schoffelen
## Repository
This repository contains the simulation code and data for the project _Towards a more robust non-invasive assessment of functional connectivity_.
This paper wi... |
32cfbc16429c34db56820fa3216998cada726d3dad53b0263808af4a4fa7e533 | Text | 1,342 | 25 | # 3DMorph
3DMorph is a MATLAB-based script that analyzes microglia morphology from 3D data. Outputs include cell and territorial volume, branch length, and number of branch and end points.
------------------------------------------------------------
Written by Elisa M York
Packaged May 2018
This package comes with n... |
1e79ba9e3981e16f687e03f265d5e61dea975c9901e83eed7a26c10245fb3140 | Text | 1,345 | 27 | # hadge
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[], we have been using it in the medical imaging domain for hi... |
a5fdf1dfc26aab4017245d0527bbd5fd4cf6da278b45cc2e73e42e0709ec1294 | Text | 1,366 | 82 | # Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology
The DOI for the associated Zenodo data repostitory is 10.5281/zenodo.10729767 . Please download all data and follow below instructions for directory setup to execute code to reproduce figures.
MOUSE
Create a file f... |
2dfc59e5e7260e6d8439d55f3631135316409da8eb10a2b85bd5c733f0e99714 | Text | 1,369 | 39 | # Implementation for FlowGAT model for paper "Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality"
## Overview
This repository contains the PyG implementation of FlowGAT model.
This implementation provides a clear and structured codebase to help researchers and pr... |
795bfc2bfdd749c75fe5fbb16ee13df3ec65ac36e68d44396d8515ce274fdbd0 | Text | 1,382 | 18 | # NeatMS
[](https://pypi.org/project/NeatMS/) [](http://bioconda.github.io/recipes/neatms/README.html) [ and [Kaggle](https://www.kaggle.com/datasets/sartajbhuvaji/brain-tumor-classification-mr... |
94bf5891e8df057a07599be2b349d5f0e82fff78ec359b88045ee5921d69438c | Text | 1,494 | 36 | vegas
-----
The ``vegas`` package is for evaluating multidimensional integrals using
an improved version of the adaptive Monte Carlo vegas algorithm
(G. P. Lepage, J. Comput. Phys. 27(1978) 192).
A tutorial on its use can be found in the documentation:
see ``doc/html/index.html`` or <https://vegas.readthedocs.io>.
Th... |
6b66ae9b609eec2985ff49340b83bc3f1f810aa5303557bbfe1b4221b456e785 | Text | 1,497 | 38 | # Phase locking and correlations in globus pallidus: data and code repository
### Data and code used for analysis, simulations and plots in the article:
* "Phase delays between mouse globus pallidus neurons entrained by common oscillatory drive arise from their intrinsic properties, not their coupling" *
Erick O. O... |
bb2c1cb7fb77d682065c2a0c6611e407ac310ab0279cc8a4bd2234d51d769b63 | Text | 1,506 | 27 | # colony_screening
The 96WP_colony_screening macro is designed to use ImageJ to screen 96-well plates for the presence of colonies after clonal isolation. The macro takes a folder with stitched images of wells as an input and identifies wells containing colonies of adhered cells. The macro generates a TIFF file contai... |
3a9a19e5dd0d30edf2c737bb993240e1925d5f2aa87c1e254d2910742fa7e30d | Text | 1,509 | 6 | # snRNA-seq_hippocampus
Deciphering molecular heterogeneity and dynamics of neural stem cells in human hippocampal development, aging, and injury
This site provides the analysis codes to generate the figures reported in the published paper "Deciphering molecular heterogeneity and dynamics of human hippocampal neural s... |
b19bdc1a654389a97a7c250485e5d83a8b17f3a99bbabe448c4e232d43db211b | Text | 1,511 | 11 | Article URL
https://www.nature.com/articles/s41467-024-46529-9
Title
Remodeling of the postsynaptic proteome in male mice and marmosets during synapse development
Abstract
Postsynaptic proteins play crucial roles in synaptic function and plasticity. During brain development, alterations in synaptic number, shape, ... |
a379eddea5f548fedd67eedb5d4d3eeb2be9673b883fea316585bfb9bc71b39f | Text | 1,519 | 40 | # Stereotyped goal-directed activity patterns in the insular cortex
## Description:
This repository contains the analysis that were used to study the InsCtx activity manifolds.
(DOI: https://doi.org/10.1101/2023.11.13.566809)
The code is written in R and requires RStudio or an equivalent IDE to execute.
### figur... |
ce551d25459b31a58a8f4bdf48cd29dcedc8331918cee385e43608976527ce99 | Text | 1,521 | 22 | # libmpMuelMat
The *libmpMuelMat* library is a multi-platform set of computational tools for polarimetric Mueller matrix image processing.
The library builds on an integration of compiled C codebase and Python for an optimised and streamlined user experience.
The *libmpMuelMat* library embeds high-performance computat... |
b7f5f7e96c6772f76260fae74d1f88f42e0689e4ed26d63f09139fd8f9bb5b25 | Text | 1,559 | 17 | **README ZAK ET AL 2024 NAT COMM **
All imaging datasets are provided as a mean z-scored value of five seconds after the onset of odorant delivery.
Datasets will open as a cell array where each cell is an imaging field organized in a matrix with the following dimensions, region of interest x odorant x trial. Missing... |
195695886f1869aed733694d4db4cac133db8fb0a6d8b18ba1681b1435dec67c | Text | 1,566 | 33 | # Brain-state-shift
This repository includes information relative to the project: Body mass index-dependent shifts along large-scale gradients in human cortical organization explain dietary regulatory success.
The folder SubjectContrasts includes all participants' contrasts for the Natural (NC=contrast_0001.nii) and H... |
5fc64704b89bf1f957bd035898caa0acef2bc3bc2a3a3b063b06fb73d29b4c54 | Text | 1,575 | 40 | First generate the tract profiles by following the steps outlined here:
https://github.com/36000/OR_aging_ukbb
To process individual subjects, follow all of the instructions in the
afq_processing folder of that repository.
To generate the tract profiles, follow the steps in the
analysis_and_figures folder up to ... |
e4038e166ee8a5871e4e78627f42da698d0c5a515cdf471fb2fd6ec42bef8d1a | Text | 1,579 | 38 | ---
### Adapted UK biobank pipeline for the DPUK cohorts
---
The `Adapted UK biobank pipeline` project is a image processing pipeline to generate UK biobank-like image derived phenotypes (IDPs) from dementia cohorts. This pipeline can generate more than 4000 IDPs per subject from different brain MRI modalities.
---... |
9a42045fcc3c5721541f90e79d227f3f6b33fbf02be453c77e6187e3655bb857 | Text | 1,589 | 46 | # Predictive Coding Networks for Temporal Prediction
Repository for experiments with the temporal predictive coding model
## 1. Description
This repository contains code to perform experiments with temporal predictive coding models.
## 2. Installation
To run the code, you should first install... |
d760b3f12793cda00b58d8afb8ed5198ba84594187b1b9c80151a2e6eea54342 | Text | 1,592 | 47 | # DeepLearning-_TF
# DeepReg
The next code presents a new model hybrid to Predict Transcription Factors.
It has the next architecture:
a) A 4CNN Module
b) A BiLSTM Module
C) A Attetion Mechanism Module
Th... |
73c190205b6ac2707edf73bca7c730743483823c94630a772e840d556ebe0c8f | Text | 1,596 | 17 | # Optic Lobe Connectome
This repository is a collection of code for analyzing the optic lobe in the new Male Brain dataset ([Janelia FlyEM](https://neuprint.janelia.org/?dataset=optic-lobe:v1.0&qt=findneurons)). You can find the preprint at [bioRxiv](https://doi.org/10.1101/2024.04.16.589741).
Please also visit our [... |
d7b11db0fb621481ec5eef8139a4d9bd203678058179cff31d1a72fe074b49b7 | Text | 1,597 | 36 | #Augur
Augur is a blood-brain barrier penetrating peptide(B3PPs) classification prediction tool that can determine whether an input amino acid sequence belongs to B3PPs.
# Data
The original B3PPs sequences and non-B3PPs data are stored in ./B3PPs/Augur Data/Raw data/Training.txt(2851 sequences) and ./B3PPs/Augur D... |
97ac6b47b8ed8d3884f09920e83f54f3a2d772c9740f3091ea344df0e1a6d0c5 | Text | 1,609 | 72 | # ECG Digitize
A library for generating digital signals from electrocardiogram images.
## Getting Started
If you have already followed the `paper-ecg` setup guide, just set `pyenv local paper-ecg` in the repository root directory and you are good to go.
This assumes a working version of [PyEnv](https://github.com/... |
238c5c3cfed195e8151c3fa3fcd4ab3b4f6e00eb5014edeffd160298678c894e | Text | 1,614 | 13 | # Tissue-specific genetic variation suggests distinct molecular pathways between body shape phenotypes and colorectal cancer
This repository contains the codes to perform the analyses included in our manuscript entitled "Tissue-specific genetic variation suggests distinct molecular pathways between body shape phenotyp... |
073e5980d6ac7daf4d9936e1632080661ba036531975baa2f34bb4a4bd1e27ae | Text | 1,616 | 20 | # On the importance of data transformation for data integration in single-cell RNA sequencing analysis
This repository is for the investigation of the impact of data normalization in integrative analysis of the single-cell RNA-seq data.
Check out this [document](https://iron-lion.github.io/scRNAseq-preprocessing-impa... |
464e3308ec81798e3c18e009b237c80343a86c3b59c9778ad55e3c3f1c2023d3 | Text | 1,616 | 36 | # QBMG: Quasi-Biogenic Molecule Generator with Deep Recurrent Network
## Introduction
This is a PyTorch implementation of the paper: [QBMG: quasi-biogenic molecule generator with deep recurrent neural network](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0328-9)
.
The Python streamer allows to stream on a TCP socket at at specific frequency, and wi... |
c1dc4ad75d92ba8a0cb30385c895b86dc40febad05b8bdf0bc42e6277e4e8258 | Text | 1,628 | 30 | # ExaFlexHH
source code of the ExaFlexHH paper
There are three main projects:
- HHmc: For the simulations of HHmc kernels \
DFE code in the HHmc folder, CPU code in the HHmcCPU folder
- HHmcg: For the simulations of HHmcg kernels on a single DFE (without MaxRing) \
DFE code in the HHmcg folder, CPU code in the HHm... |
e8fa86130703adf126182147b7a719037fd68d010332bd5ee4e0ba906a3cfb53 | Text | 1,629 | 45 | # Dengue Virus Genome Evolution Predictor
Predict the sequence of the evolving serotype through generative models and identify its closest match using a classification model.
## Introduction
The process of evolution in viral genomes poses challenges in diagnosis and vaccine effectiveness. This work focuses on the De... |
fbae095988239525d1beba3887360b1075aea3c4935040b47b8cee7e63d41e51 | Text | 1,674 | 23 | This repository contains the scripts used for the following study:
## CD20 is a mammalian odorant receptor expressed in a subset of olfactory sensory neurons that mediates innate avoidance of predators
### Hao-Ching Jiang<sup>1,2,3,8</sup>, Sung Jin Park<sup>1,8</sup>, I-Hao Wang<sup>1,2,4</sup>, Daniel M. Bear<sup>5... |
ebcae237c8b72dbdf901cb79dd9e6fb14801bd6708af12066273e72e4cb90d52 | Text | 1,687 | 34 | # Spatial Navigation Simulation using Hippocampome Resources
This software simulates neural activites in rodents that occur during spatial navigation.
## Version
This is version 1.03.
## Articles
This software was used in the article:
<br>Sutton, N. M., Gutiérrez-Guzmán, B. E., Dannenberg, H., & Ascoli, G. A. (2024)... |
baf73acd203e2b7c2fc00624aaad57979c9b923724259a44d4d9a561359dacd5 | Text | 1,696 | 53 | # Code used for article: Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks
Everton J. Agnes (1,2) and Tim P. Vogels (1,3)
1 - Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, United Kingdom
2 - Biozentrum, University o... |
3064e2b15c25f738b1be794c80fc7809af049a7cb1fb77c96469aa5605e8a2cb | Text | 1,725 | 37 | # Mares_etal_Cortex_2022
Mares I, Ewing L, Papasavva E, Ducrocq E, Smith FW, Smith MLS (in press).
Face recognition ability is manifest in early dynamic decoding of face-orientation
selectivity – evidence from multi-variate pattern analysis of the neural
response. Cortex.
## Description
This code performs linear SVM d... |
67d9df5fd758b8712cae46c801a97965a6fbd7d13d3174eb72e5c5f42a5c0b54 | Text | 1,737 | 38 | # Gradec
A Python library for meta-analytic functional decoding of cortical gradient of functional
connectivity.
[](https://opensource.org/license/apache-2-0)
[. DOI: TBC.
The repository has the following structure:
- [processing](processing) - location of scripts for (pre)processing of data (view [README](processing/README.txt))
- [analysis](analysis) - location of scripts for analysis of ... |
51b6cc4319b806c537716c5132a61e09b261d939416be957012d8299886dabe0 | Text | 1,755 | 39 | ## Quality Control Interface
Implementation of a graphical interface in a jupyter notebook for the annotation of 3D T1w brain MRI for the quality control of a clinical dataset.
This repository contains the jupyter notebook of the implementation described in Bottani et al. 2021 (full reference below) for the quality co... |
b362e14c22e14585ee1d9aeeb0af1e59535dfe6d6c0ed2995ac72cc4fcbd4bbf | Text | 1,766 | 36 | <table>
<tr>
<td width="250" height="250"><img src="https://github.com/AntonioMG99/IPTP-paper-code/assets/52926867/bb92795a-7016-4814-98dd-833bc9a38e5d" alt="logo" /></td>
<!-- Use span with styles to mimic h1 -->
<td><h1>IPTP-paper-code: Inverse Problems in Turing Patterns</h1> Code for the paper: "Unrav... |
8740700678cbd1c44abccec0455b085dbd20ae52cf9226608886611690af204e | Text | 1,767 | 46 | # Final Data All Excipients — Fast Disintegrating Tablet Dataset
## Description
This dataset provides detailed information on the formulation and physical characteristics of **Fast Disintegrating Tablets (FDTs)**, including:
- Active pharmaceutical ingredients (APIs)
- A wide range of excipients (binders, disin... |
e92201c1cd33d3351aaa522067212af043b6c4d3c102e479d7d26b22dcdcaff2 | Text | 1,787 | 50 | # encoding_surprise
Repository containing data for PLOS CompBio 2024 paper, "Encoding surprise by retinal ganglion cells", by Danica Despotović, Corentin Joffrois, Olivier Marre, and Matthew Chalk.
This repository contains the following data:
- spike times (1 file per cell), for original and repeated experiment
- mod... |
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