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f64a4d6ecc2b4cc9e49be6ae8b5795b79f4dbd94804750f51ecb079bba22156f | Text | 927 | 29 | # Installation
The best way to manage the dependency of this repo is through a conda virtual
environment. Use the following commands in your terminal
```
conda create intactness python=3
conda activate intactness
conda install --file requirements.txt
```
Please check this [site](https://www.anaconda.com/) for inform... |
c3c08a3db22508c6e95118dfe25193f0e75c4b92f2c092ef25920b12bab4e6cf | Text | 932 | 23 | 1) analyze_behavior_Fig1_Fig3_Sfig1.m
This code generates the results of behavioral performance in Figs.1, 3, and sfig.1.
The relevant variables are saved in "Learning_values.mat".
2) analyze_SI_bimodal_Fig2_Sfig3.m
This code plots task-related activity indices in the bimodal task as shown in Fig.2 and sfig.3.... |
a5518c0f61446625e97eb0fcb5743a26191046fa5f1b3ef174cf0731a7664816 | Text | 933 | 11 | # examining-GNN-for-crystal-periodicity
This repo is associated with the paper: https://arxiv.org/abs/2208.05039 (Examining graph neural networks for crystal structures: limitations and opportunities for capturing periodicity)
This repo provides the e3nn and de-e3nn designed specifically for predicting properties of ... |
cd47be3b465ea7a759df98725c225f06f0da4a7ef6fb064bcf2a80e5bb952226 | Text | 933 | 30 | # Implementation of Manuscript "Training large-scale optoelectronic neural networks with dual-neuron optical-artificial learning"
## How to use
### Our DANTE approach:
1. Global artificial learning:
Modify the `server_dir` based on your own environment. Then, run:
`python train_electric_cifar10_readout.py -e 3b -g... |
9739c2af0856361bb797c266f3e2ae3cbf3e4b822f8bf5fca6c23985514bccb3 | Text | 939 | 15 | # DistributedFeedforwardFeedbackProcessing
This repo corresponds to the speech decoding framework in the paper "Distributed Feedforward and Feedback Cortical Processing Supports Human Speech Production" https://www.biorxiv.org/content/10.1101/2021.12.06.471521v1.
## speech decoding
"speech_decoding/" folder is for t... |
78b6313fe711fab5e634f7ddf810deb848a500fc3186703ec56c5e3f0ce76b85 | Text | 965 | 6 | # ML.Proteins.2023
Bioinformatic scripts for IMJS 2023 article concerning both local and secondary protein structures prediction by regression neural networks:
<br><A HREF="https://orcid.org/0009-0000-9585-337X">Yury V. Milchevsky</A>, <A HREF="https://orcid.org/0000-0002-4350-8424">Vladislava Y. Milchevskaya</A>, <A ... |
4f14466e2e06d564b92c81197d9cd2edcefd55e5188c6225eaeebf1cb0b51f10 | Text | 971 | 32 | # Psychotropic drug on *Drosophila* brain at the single cell resolution
This repository contains the **code** for our manuscript being submitted.
## **Codes**
Our scRNASEQ data was mainly processed by Seurat, R codes used for analyses are in the following files:
`01_scRNAseq_flyDrugs_CelltypeCluster.R`
`... |
19eef8cb23fd6a885a0e89dbc62cee71b0e6b46b8aeca0b59e52d681f6b1f460 | Text | 976 | 15 | # SeqDatasets
SeqDatasets is a Python package meant to provide an interface for downloading commonly used machine learning in genomics datasets. We currently support a small but growing list of datasets, including:
1. The RNAComplete2013 dataset used to train DeepBind and ResidualBind
2. DeepSTARR's genome-wide STARR-... |
ecaed5c188162737a3a1ac64bb1d8844fb81467c9abce394f7742796ba431d7d | Text | 983 | 27 | # Resonance Analysis
Analysis code for the RESONANCE microbiome cohort
of the NIH **E**nvironmental influencences on **C**hild **H**ealth **O**utcomes (ECHO) project.
Grant # NIH UG3 OD023313 (VK-C).
## Repo organization
- This repository is a julia package, with reusable code in the [`src/`](src/) directory.
Fo... |
bf263077e4c4153783c522a25a255ee5f98b3270ac5f9f990dd48f2ebc6c4cbd | Text | 984 | 32 | # RT-4K-CGH
<p align="center">
<img src="https://github.com/flyingwolfz/flyingwolfz/blob/main/rt-4k-cgh.png" alt="1920" width='50%' height='50%'/>
</p>
**<p align="center">
Real-time 4K CGH,paper:https://www.nature.com/articles/s41598-023-46575-1**
</p>
## environment set up
The environment is the same as https:... |
1ad81a089632e8f72289155b8de6bc053102fe49df243040d4b57a7e167c70bf | Text | 985 | 43 | BIAS
*****
BIAS is a software application for recording video from IEEE 1394 and USB3
Cameras. BIAS was intially designed as image acquisition software for
experiments in animial behavior. For example, recording the behavior of fruit
flies in a walking arena.
|
.. figure:: /images/bias_charlie.png
:scale: 100 ... |
384fdff056f6cd8a81f810af3443303eb30bc57ec4d0e02594d3b20c3fafa735 | Text | 985 | 16 | # OCDBaseline_public
Public repo for the OCD fear conditioning baseline comparison project code base.
- Preprint: https://www.medrxiv.org/content/10.1101/2022.09.01.22279518v1
- Final manuscript: TBA
## Summary
We compared people with and without OCD on a fear conditioning fMRI task. We found very limited difference... |
6954bba75f8b003c4e19821aaf970aaa35ab8aba08434f841f0e83f56bee1c60 | Text | 986 | 14 | # WM-connectome-devlopment
This repository provides data and code for reproducing a range of analyses involving our study.
If you use these data and code, please cite our paper:
Guozheng Feng, Rui Chen, Rui Zhao, et al. Longitudinal development of the human white matter structural connectome and its association with br... |
2c70b20867a85879fde088fcc983ec2ecfad6dd830dc926c1d1df2f46f302238 | Text | 988 | 22 | # Supplementary Data of 'The Surface of Electrolyte Solutions is Stratified'
This repository contains input files necesary to reproduce the ab initio and
neural nettwork simulations reported in the manuscript:
"Surface Stratification Determines the Interfacial Water Structure of Simple Electrolyte Solutions"
Yair L... |
ff608ecb2722f090578cce49e2fd17522c0b00531de77c7c9c0d91a65d484fcb | Text | 993 | 22 | # snRNA-seq analyses of postmortem dorsal striatum in opioid use disorder
## Reference & Contact
**Single nuclei transcriptomics in human and non-human primate striatum implicates neuronal DNA damage and proinflammatory signaling in opioid use disorder**
BaDoi N. Phan1,2,3, Madelyn H. Ray4,5, Xiangning Xue6, Madelin... |
dbde8ff86a8e31a395aee9d4a9d8e71f5c697a5d1e39b4e7b68d4e4995872f9c | Text | 1,006 | 15 | <div align="center">
<img width="600" src="/graphical_abstract.png" alt="Graphical Abstract">
</div>
# np_name_finder
[](https://doi.org/10.5281/zenodo.8155759)
A project to use different computational approaches to identify natural product mentions ... |
fbc890ce57d39f10acb5de95d047e03ac93e8a8444c351a8c203c1c9d74bddd4 | Text | 1,010 | 38 | # MLNet🔍
An Automated Deep Learning Pipeline for EMVI and Response Prediction of Rectal Cancer Using Baseline MRI
Paper Link: https://www.nature.com/articles/s41698-024-00516-x
<img src="https://github.com/Liiiii2101/MLNet/blob/main/graphic_abstract.jpg" width="400" />
# Installation💻
in your favourite virtual... |
046425caf0710ee3e0cc8b22286a162ea6d78132af4b6346978bbf412ee702c2 | Text | 1,011 | 18 | # Prenatal_infection_multimodal_imaging
Hi everyone,
This repository contains the computer code for the manuscript: Long-term effects of prenatal infection on the human brain: a prospective multimodal neuroimaging study. Please find the full text article here: Suleri, A., Cecil, C., Rommel, AS. et al. Long-term effe... |
8113977b330306b0482e29388705f3feabdeadb6cabafcdb3e7d594224af7bdc | Text | 1,014 | 15 | # CHEX-seq Data Analysis Scripts
## Overview
This repository contains code for CHEX-seq data analysis to promote transparent science.
For CHEX-seq computational pipeline, see [chex-pipeline](https://github.com/kimpenn/chex-seq).
## Copyright
```
Copyright (c) 2017-2023, Youtao Lu, Kevin L. Bullaughey, Jean G. Rosario,... |
5eb22305482f79c226e4917b328d16f0ddfa5c3f0232fecf48e64ea20849a83b | Text | 1,017 | 28 | ## Code for spiking neural network model from "A developmental increase of inhibition promotes the emergence of hippocampal ripples"
Preprint on biorxiv ([here][spwr_biorxiv]).
[spwr_biorxiv]:https://www.biorxiv.org/content/10.1101/2023.08.11.552951v1
#### Requirements
* brian2 v.2.4.2
* pypet v.0.6.0
#### How-to ... |
13ff8f9264534fa7f275cd069a30f4ea823715ca878171c8953386536c91eb11 | Text | 1,022 | 23 | # Code for analysis of Genesis GBM 001 phase I/II study
**Author:** *Caterina Brighi*
This repository contains python scripts used for the analysis of the Genesis GBM 001 phase I/II study, which aimed at evaluating the role of [68Ga]Ga-PSMA-617 as an imaging biomarker in adult recurrent glioblastoma patients.
## Set... |
524d251f5230a1f681a5ce807eeb733c6c99ef384705684f09854d7eabf2b285 | Text | 1,034 | 21 | # DeepPeptide
Predicting cleaved peptides in protein sequences.
[](https://zenodo.org/badge/latestdoi/593202385)
### Training the model
1. Precompute embeddings using `src/utils/make_embeddings.py`
2. Train the model
```
python3 run.py --embeddings_dir PATH/TO/EMBEDD... |
a937bdf6fd11a81d8ef42956b7c2ef770c1f5aa88e3b37071c74d63b40731e5d | Text | 1,036 | 11 | # 2023_BraunA_Adaptive_biasing_of_action-selective_cortical_build-up_activity_by_stimulus_history
Code for Adaptive biasing of action-selective cortical build-up activity by stimulus history eLife2023;12:RP86740 DOI: https://doi.org/10.7554/eLife.86740.3.
The logistic regression model with history bias was fitted usi... |
bd8441010d5a5c43ebe1bbab21fb946f6c5008319d2a59b1d70a45b9ad38e33d | Text | 1,045 | 12 | # brainwide-npix
The goal of this codebase is to provide a lightweight set of functions for working with data from multiple simultaneously acquired Neuropixels and associated histology data. Relies on output formats and folder structures from [SpikeGLX](https://billkarsh.github.io/SpikeGLX/), [Kilosort](https://github... |
753cb1a7412d1379e73295aa3b0827e8cbcccdc2f649927e905dca95b4e34fd9 | Text | 1,050 | 28 | # Population_Integrator
A modular pipeline for segmentation, registration, and analysis of large-scale high-resolution
neuro-anatomical imaging data.
Designed for scalable integration of neuroanatomical connectivity data
across experiments and spatial reference frames.
Raw Data → Segmentation → Registration → Integr... |
2c61a6f8ae94827ad49b585ff1d4f3c7a93ca31e2164a679f4e86c2181ed7d05 | Text | 1,061 | 14 | [](https://badge.fury.io/py/eugene-tools)
[](https://eugene-tools.readthedocs.io/en/latest/?badge=latest)
... |
ba2ee7ab85b6382f4772a758ec34fe5c2a2eb30edf99d7e4ec1c5a2bcd391c51 | Text | 1,063 | 27 | # dev_beta_claw
Analysis code for analysing beta bursts in infant and adult EEG data.
> Rayson, H, Szul, MJ, El-Khoueiry, P, Debnath, R, Gautier-Martins, M, Ferrari, PF, Fox, N, Bonaiuto, JJ<br>
> **Bursting with potential: how sensorimotor beta bursts develop from infancy to adulthood**<br>
> Journal of Neuroscienc... |
9284ca77419bebc1d52241e311a8f82add96d718e535d761517643440d037dd3 | Text | 1,066 | 20 | # Connectomics
[](https://opensource.org/licenses/Apache-2.0)
### _Note: Under heavy development_
_This repository is currently under significant development, and should not be considered stable. Semantic versioning is not guaranteed for now; APIs... |
c2c0235790ddba769c47a1f726a0339776e07cd2077908616bc0df917d4df0a9 | Text | 1,066 | 13 | # MoCsEFC
"Targeting motor cortex high-excitability states defined by functional connectivity with real-time EEG–TMS" paper
Folder contents:
* [`protocol`](https://github.com/connect2brain/MoCsEFC/tree/main/protocol) contains the script `run_MoCsEFC.m` that was used to run the experiment. It uses `MEP_ioresponse.m` an... |
81422d72004c04eed3d6c08daa550c5a111c397088ac7b05fa5afcf185b92764 | Text | 1,070 | 14 | [](https://badge.fury.io/py/eugene-tools)
[](https://eugene-tools.readthedocs.io/en/latest/?badge=latest)
... |
c6033061d2176774cdbea97db039d6ac61177646d6fe8f8d743c6e6b6e959eae | Text | 1,070 | 42 | # LCMnet
Source code for the paper "A Latent Code Based Multi-Variable Modulation Network for Susceptibility Mapping‘’
## A Latent Code Based Multi-Variable Modulation Network for Susceptibility Mapping
The implementation of LCMnet for QSM reconstruction network <br />
This code was built and tested on Centos 7
## Ov... |
05a12ec4a62df49840d8ddc16e1ed31aeacc884bf61d491b26dcb1d1a6f4221e | Text | 1,079 | 28 | Computational model of Hadler et al 2023 Science advances
by Alexandra Tzilivaki alexandra.tzilivaki@charite.de
Requirements to run the simulations:
Neuron software 7.4 version or later
Matlab (view the dataset used for the paper. Listed in the Dataset subfolder)
Folders explanation:
mechanism:
Thi... |
5aa1938a53e2f3b1ce857877e07898dd8ddb56d39ba3fb28735a7430ecf31817 | Text | 1,080 | 8 | we captured the image in each frame during the visual stimulation. Subsequently, we employed the MATLAB Optical Flow block (the mathematical algorithm is given at the end the letter ) from the Computer Vision Toolbox to estimate the optical flow vector for each pixel between two consecutive frames. The direction of pix... |
30fcb6e36b8388e05569c6626b362bb204c62e7ad84f0396471f6e6ee3eb0dc3 | Text | 1,086 | 31 | # ScaffoldGVAE
ScaffoldGVAE: A Variational Autoencoder Based on Multi-View Graph Neural Networks for Scaffold Generation and Scaffold Hopping of Drug Molecules
# Installation
You can use the environment.yml file to create a new conda environment with all the necessary dependencies for Scaffol... |
9b96e6509120f824b308e835243679e0c224619cabfecbaf6fed76b4b2c284dd | Text | 1,095 | 28 | Code to reproduce the spatial proteomic affinity network fusion analysis shown in Figures 3E and 6A in Davis et al, "Deep topographic proteomics of a human brain tumour"
Tested on R version 4.3.0 on macOS Monterey 12.6.5
Directly attached package versions:
magick - 2.7.5
Spectrum - 1.1
ANF - 1.22.0
data.table - 1.14.8... |
857e0c34554037bc2ec21e4cc701643da3886b4cb8397c9cb0899011e0a3b718 | Text | 1,109 | 28 | # HIC Workflow
Snakemake workflow for QC and processing of HIC data. Results in on .cool file and TAD calls for the data. All commands used to QC, and process hic-data are contianed in the main Snakefile.
**Prep**:
Place raw HIC reads in a new directory data/raw
```
mkdir -p data/raw
ln -s /path/to/some/data/*.fast... |
d6f741625c9140434eb7be0c3069ffd201ca1e357a6421516a7bf52f2ef77932 | Text | 1,109 | 49 | # biccn-broca-I46
Code used to generate a cellular resolution atlas of Broca's area (sample I46)
This code relates to the paper:
> **A cellular resolution atlas of Broca’s area**
>
> Irene Costantini<sup>‡</sup>,
> Leah Morgan<sup>‡</sup>,
> Jiarui Yang<sup>‡</sup>,
> Yael Balbastre<sup>‡</sup>,
> Divya Varadaraj... |
2d878a9655cfd6151725445fac444851b6973b3d3f21b50132ccb0d1b5916294 | Text | 1,115 | 30 | ## Code for spiking neural network model from "A developmental increase of inhibition promotes the emergence of hippocampal ripples"
[](https://zenodo.org/doi/10.5281/zenodo.10424460)
Preprint on biorxiv ([here][spwr_biorxiv]).
[spwr_biorxiv]:https://www.biorxiv.org/cont... |
eb84999f243fa03fffa1df2075dd8a7f0f071a8ee7f05f79bf4cc5feb6c74e75 | Text | 1,116 | 15 | To plot Fig 8 panels A to C for control and E to G for KD
Run Fig8_m with the following parameters
- Set line 22 to 'Scr'for control and 'KD' for TRPC4KD.
- Run line 94 with the following parameters:[observed{1}, bootstrap{1}, tests{1}, info{1}] = bootstrapRf_goalMode_allScopesSideStratified_v5(Rf{1}, ...
... |
a0bb145d377236a6ea98a5d64f195f03393bcb7c638a396453046c7166bdab24 | Text | 1,119 | 40 | # NOCICEPTRA_Tool
# Beta Version:
Tool in Python that should visualize the Analysis of miRNAs, mRNAs, ncRNAs.
<br>
<img src="Images/Readme.png" alt="StartingPage">
<br>
## Details:
Data is provided using the DuckDB OLAP Database.
Tool was updated to use interactive libraries instead of Matplotlib such as Altair and ... |
bde3633d18698f5b0eadceece9ff35da4566a3e8cb2eefddc9f65d57cc715a92 | Text | 1,119 | 6 | # Downstream network transformations dissociate neural activity from causal functional contributions
## Authors:
Kayson Fakhar, Shrey Dixit, Fatemeh Hadaeghi, Konrad P. Kording, Claus C. Hilgetag
## Abstract:
Neuroscientists rely on distributed spatio-temporal patterns of neural activity to understand how neural units... |
71809f7f6c2f13cfeb9afad46c873d5148b8d61d062f4f4719014ca94bf6d15d | Text | 1,120 | 18 | # synthetic_promoter_mavenn
Notebooks and data associated with Loell, et al. 2023, 'Transcription factor interactions explain the context-dependent activity of CRX binding sites'.
This repository contains:
(1) a jupyter notebook and associated files needed to load all saved models and reproduce all of the figures fr... |
4a80a9672afb5dc481e51308d45d86bdc6123ff1bd08e4057f0e6300fc9d031d | Text | 1,130 | 29 | # eTC-PCT image enhancement techniques
This repository contains an implementation of diffusion reversal methods for thermo-photonic images.
## Testing
Perform deconvolution and save the resulting image for second derivative analysis. Zero-padding the images may be necessary to eliminate edge artifacts.
After apply... |
d88fdeac57db4c472bfeca5a6cd70238e4151934e2bdae9059e74ac48fc1ae19 | Text | 1,134 | 42 | # organage
A package to estimate organ-specific biological age using aging models trained on SomaScan plasma proteomics data (Oh and Rutledge et al. _Nature_ 2023 https://doi.org/10.1038/s41586-023-06802-1)
## System requirements
### Hardware requirements
organage package requires only a standard computer with en... |
d67016e232783847d1e50fa7bbcc8c425ad6c91d0400f2c8701938298007ebda | Text | 1,138 | 22 | Nearest neighbor suspect spectral library
=========================================
For more information:
* [Official code website](https://github.com/bittremieux/gnps_suspect_library)
The nearest neighbor suspect spectral library is a spectral library that was created in a data-driven fashion by propagating annotat... |
0acdbedf9b597eb58d82725a35f47f754d871c0179864a3f9c9ee832b5d553b4 | Text | 1,139 | 24 |
# Pipeline for DePTH
[code_for_data](https://github.com/Sun-lab/DePTH_pipeline/tree/main/code_for_data)
Code files for processing Emerson data and generating TCR-HLA pairs used for developing DePTH models, processing Zheng 2021 single cell potentially cancer-related TCRs, preparing pairs based on Szeto 2020 solved s... |
f855acb7bbbfe6cc31dcb125fe01e453acdf025134cd3ca2fcf0cc4670016753 | Text | 1,149 | 18 | # :mortar_board: [AngoraPy](https://github.com/ccnmaastricht/angorapy) Documentation & Tutorials
Currently up-to-date with version `0.11.0`
A growing collections of examples and notebook tutorials on how to use [AngoraPy](https://github.com/ccnmaastricht/angorapy).
_DISCLAIMER: This documentation is work in progres... |
5c90ff3978c5f6e5e879f06687dd84d33fb02bdf531d0aba90d1bd1320438584 | Text | 1,153 | 7 | The directory code is the original content of parameter optimization, single model, combined model respectively, and does not contain data, where the specific points are shown below.
ARIMA, LM, SCG，LSTM and BR are respectively models established by using the monthly incidence data of hepatitis C in China, among which M... |
41a25a3f776a2df492be7638b0b6adf89b305ae49d3cb734b067c03d696f686b | Text | 1,155 | 34 | # ECG-AI_Heart_Failure_Prediction
ECG-AI: Electrocardiographic Artificial Intelligence Model for Prediction of Heart Failure
# Requirements
* Python 3.7.7
* lightgbm 2.3.1
* scikit-learn 0.22.1
* scipy 1.5.2
* tensorflow 1.15.0
* tensorflow-bas... |
02467c3bcd70b9628a3f648343bd9b1a4d4ce565d3412878913ceec8a91d045a | Text | 1,159 | 21 | # Some extra useful info ...
# RN052: photo for the experiment setup
# BDA089: QuickNii example
# BDA091 : ilastik example (axons)
# BDA069_215 : ilastik example (injection)
# BDA061left: flatmap & top view
# for figure H: red is BDA046left and yellow BDA050 right
# BDA046 - left - red, BDA050 - right - light ye... |
bef3155f83233584d544d56f1b4a62750bfd509e59a86331e105458811a50a0e | Text | 1,162 | 15 | # Scheer_Bargmann2023 README
This repository contains code pertaining to Scheer, E. and Bargmann, C. I. (2023).
Questions about this repository can be directed towards Elias Scheer at elias.scheer@gmail.com or Cori Bargmann at cori@rockefeller.edu
These data were collected in the Bargmann Lab at Rockefeller Univer... |
a98ec5b184f36a7ef7c71db382be9d71681731425397c9a06975a6cca3eff98b | Text | 1,171 | 24 | # BM_sim_fit
Bloch-McConnell simulation (full numerical and analytical) and fit (multi B1)
preRelease 2017
the code was used and is documented for the paper:
Zaiss, M., Angelovski, G., Demetriou, E., McMahon, M. T., Golay, X. and Scheffler, K. (2017), QUESP and QUEST revisited – fast and accurate quantitative CEST ex... |
19a66e078a7efea4c86098eb1694dbc618a26ac91b388a392e06f99e32587e3e | Text | 1,173 | 6 | # NR-Analysis
Scripts and data used in the creation of "[A Thalamic-Hippocampal CA1 Signal for Contextual Fear Memory Suppression, Extinction, and Discrimination](https://www.biorxiv.org/content/10.1101/2023.03.27.534420v1)"
Contained in this repository are the Python and R scripts used in the creation of this [paper]... |
c2d357f41aaea5946d50120dcfee6513dbd9d394f330b4697a30d3b27d186ee8 | Text | 1,176 | 33 | 
[](https://github.com/nebiolabs/tasmanian/blob/master/LICENSE)
[](https://www.python.... |
1ee78f1162172bb5407b63eb352fd2cc10139f545cac4d80942fe2628d42aeb7 | Text | 1,182 | 20 | # Multiview Opinion Fusion Machine Learning
<img src="mvof-ml-logo.png" alt="logo" width="300"/>
This repository implements the Multiview Opinion Fusion Machine Learning (MVOF-ML) that automatically identifies crystal system from electron diffraction patterns with arbitrary orientations, as proposed in the following ... |
dcd298cb0edc5b6f5b777f162621d96d1a29497f0e4620206c192360aa3c3827 | Text | 1,182 | 19 | # USPerceptionBrain
U.S. Public Perceptions of the Sensitivity of Brain Data
This project examines how the public perceives the sensitivity of a wide range of information items, including data on their brain and mental states.
Files in this repo:
- _USPerceptionBrain_analysis.Rmd_
- Rmarkdown file with code for ... |
f9a04fb2e3c4e5c08565b9ab5fd7074aba6e6608b75205d7bf441d730ba33dba | Text | 1,184 | 22 | # DomAdapt_BrainNetFusion
This repository stores code and analyses for the [preprint](https://www.medrxiv.org/content/10.1101/2023.01.26.23285055v1) entitled
> *Signatures of pubertal brain development and health revealed through domain adapted brain network fusion*
Before running the code, please make sure to set... |
58020e48c109fcc490655ebdb9a83c129a8c8e5d1006808756e7fb132d7f9690 | Text | 1,187 | 47 | `coeffnet`
---------------
Equivariant Neural Network to predict transition state properties with knowledge of only the reactant and product graphs and coefficient matrice... |
679595083e0b030adb1c2b7cccd981e4517d63ed82d99e82b33b0ab11327e44b | Text | 1,191 | 25 | # Resonance Analysis
Analysis code for the RESONANCE microbiome cohort
of the NIH **E**nvironmental influencences on **C**hild **H**ealth **O**utcomes (ECHO) project.
Grant # NIH UG3 OD023313 (VK-C).
[](https://zenodo.org/badge/latestdoi/448058945)
[ has moved to the fork at [https://github.com/vufuma/FUMA-webapp](https://github.com/vufuma/FUMA-webapp). Please refer to this repository in future.
The rest of... |
95ec16becc7c58ee9a029e9361de3814527908c54a7011b2b1c15b3713015698 | Text | 1,201 | 20 | # HCP structural analysis
HCP_racial_identity_analysis.Rmd: Pipelines of the brain structural analysis by racial identity of HCP restricted database
Pipeline can be consulted at R-pubs website: https://rpubs.com/Daniel_atilano/898523
For more information related to the database refer to:
https://wiki.humanc... |
105de50a53b7ee7c37169d766fb6257595845ef213127c5e2b06334f4c2b45f5 | Text | 1,209 | 33 | **Looking for maintainers** - I no longer have the capacity to maintain this project. If you would like to take over maintenence, please get in touch. I will either forward to your fork, or add you as a maintainer for the project. Thanks.
---
# VGGish
A `torch`-compatible port of [VGGish](https://github.com/tensorfl... |
184c5f9df7c69e8c5cdfaf53a704e891a7dd8f18a927f44f9f18b683fdb6cb7f | Text | 1,217 | 53 | # Detecting changes of sound pressure level for automatic volume control using EEG
Code for Kimura et al. 2023
## Reference
An auditory brain-computer interface to detect changes in sound pressure level for automatic volume control
Kimura et al. 2023
## Data
Preprocessed data are available from the following for... |
fb35c052b3b58c26e81347325d89efd419bb7b0882efa977f6d2c94e76d39751 | Text | 1,220 | 44 | # Kelluwen
Open AI library for research and education designed to be easy to use and develop with.
## Installation
```python
pip install kelluwen
```
## Usage
```python
from kelluwen.functions.transforms import generate_affine, apply_affine
from kelluwen.functions.tools import show_midplanes
from torch import rand... |
bb796da4d416705390d19464e25aa903cf75b45649884cb7a6b0e63f40c7876e | Text | 1,224 | 38 | # Background
This repository contains code for the paper found [here], which used in silico analyses of publically available transcriptomic data to investigate the relationships between genes encoding the NSL complex and genes associated with Parkinson's disease.
# Citation
# License
The code in this repository is... |
5f5eab3b6b252d61c37963400e4d2a3147218d4a6f927359d7269584cf6e8c4e | Text | 1,225 | 18 | # NNucleate
This is the release version of NNucleate. NNucleate is a Python package developed for the training of GNN-based models approximating computationally expensive collective variables (CV). The primary intended application is enhanced sampling simulations of nucleation events. These types of simulations are ty... |
b9b7434be6cb4ebcf4b5deccf53956378910b964b0b1da8b3b7ec9e70865c0e3 | Text | 1,226 | 29 | ## Code for the paper "Unconscious brain dynamics – auditory inputs modulate intrinsic neuronal timescales during sleep"
# Requirements
I used this on MATLAB R2023a on a Windows 11 laptop. Haven't tested on previous versions but it doesn't include anything fancy so should work on earlier versions as well. The figures... |
45950478260c8cf9ed4f049ca69d727601b737a404f83ced9edd1588f83144a4 | Text | 1,227 | 37 | A minimal toolset for analyzing protein localization patterns and tissue structure in the _Xenopus laevis_ neural plate epithelium, supporting
- **"Mechanical control of neural plate folding by apical domain alteration"**. <br>
Miho Matsuda, Jan Rozman, Sassan Ostvar, Karen Kasza, Sergei Sokol. <br>
Nature Communicat... |
6a34e5ff28b93c315303a0dbe2ab73c53b946dcad632bc10fe777125c83db8fa | Text | 1,232 | 27 | # Multiomics data analysis and code for ketogenic diet therapy for pediatric epilepsy
This github page contains source code used for multiomics data analysis in <br>
"Ketogenic diet therapy for pediatric epilepsy
is associated with alterations in the human gut microbiome
that confer seizure resistance in mice"
Ea... |
4e6bedef6ec64619183dc5c7839e09586e62e39fbeac50be69ae40be9655529d | Text | 1,244 | 15 | ## Overview
We share PyTorch and C code that produced our results in Kang L, Toyoizumi T. "Distinguishing examples while building concepts in hippocampal and artificial networks." *Nat Commun* 15, 647 (2024). [doi:10.1038/s41467-024-44877-0](https://doi.org/10.1038/s41467-024-44877-0).
<!--
> This GitHub repository c... |
894fd0259002e638e2066fb99544bd67bcae4492f914d0ecc969760e5487cf7e | Text | 1,244 | 42 | # SimplyFire
A customizable analysis package for electrophysiologists
Read the full manual [here](https://simplyfire.readthedocs.io/).
## .exe Installation
Download the software zip file from the recent [release](https://github.com/HaghighiLabBuck/SimplyFire/releases).
You only need to download the zip file.
Extrac... |
c56a96a1eeb607343889a255097338fdb7da6e51eb8f83043c25bcf8a9f8f3fc | Text | 1,245 | 26 | # PtychoNN: Deep learning of ptychographic imaging
PtychoNN is a two-headed encoder-decoder network that simultaneously predicts sample amplitude and phase from input diffraction data alone. PtychoNN is 100s of times faster than iterative phase retrieval and can work with as little as **25X less data.**
Companion re... |
4a74dc3b717bc91e74abc0d69a1d859e4cb64277d9aac566da8407625190868a | Text | 1,247 | 34 | # BC-GNN
Zero-Shot Learning of Aerosol Optical Properties with Graph Neural Networks
## Overview
This repository contains a PyTorch implementation of the code for the paper "Zero-Shot learning of aerosol optical properties with graph neural networks".
## Citation
The preprint for this paper can be fo... |
dcfe03019eada747495053aba4307ef2e6c1e62082914ecdc47857be533a9d1e | Text | 1,248 | 21 | ********************************************************************************************************************
This is a part of PhD thesis titled "Automated detection of epileptic seizures for remote monitoring using optimal
cross-database classification model" to obtain the degree of Doctor at Maasstricht Unive... |
394d52982611a15d7de6f04ff72a2510163eeb0a01b59df2b974efb25eb95a81 | Text | 1,251 | 6 | # optimal_schistosomiasis_model
Optimized strategy for schistosomiasis elimination: results from marginal benefit modeling
The integrated control strategy is a proven and effective strategy for the national schistosomiasis control program in China. However, the optimization of the integrated control measures under the ... |
ae7f2eacfd3192fbe585fb55cd01cc8bbfb63d4f23cff330fdecfa0a2813cf0d | Text | 1,253 | 24 | # Monomers to Polymers (m2p)
A simple interface for converting monomers to polymers using SMILES representation.
## Related Work
1. [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://arxiv.org/abs/1509.09292)
2. [Neural Message Passing for Quantum Chemistry](https://arxiv.org/pdf/1704.012... |
ca91ea90f9e183c8ca35bf928223323cc33f03a80a82b3393a3474e20d851d02 | Text | 1,256 | 23 | # Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain - Code and data repository
## 1. [Brain Dissection Region CCF Registration](dissection_region_ccf/)
This directory contains the CCF registration of 117 brain dissection regions,
which can be used to quantify the anatomical composition of eac... |
f026c5e79555fce5c23102025a52923d31434981bdb4ad55ceeef2cf343202c1 | Text | 1,256 | 28 | **LEfSe**
==============
LEfSe (Linear discriminant analysis Effect Size) determines the features
(organisms, clades, operational taxonomic units, genes, or functions)
most likely to explain differences between classes by coupling standard
tests for statistical significance with additional tests encoding
biological co... |
48d460c7d74d70a715518dae76dbf529a047c84ce674db085da1d75804885c1c | Text | 1,258 | 29 | # NLM-HiLo
> This content is based on our work titled ["Multiplane HiLo microscopy with speckle illumination and non-local means denoising"](https://www.spiedigitallibrary.org/journals/journal-of-biomedical-optics/volume-28/issue-11/116502/Multiplane-HiLo-microscopy-with-speckle-illumination-and-non-local-means/10.111... |
fb41695186b17aef137c3a90faa923cd7e3c700beea145227d579cb175804c6e | Text | 1,261 | 16 | This pack of functions correspond to the EEG and ECG preprocessing pipeline to obtain Random Forests binary classification of 2 classes of patients using as inputs Heartbeat-Evoked Responses. Additional functions are included to perform classification controls
Copyright (C) 2020 Diego Candia-Rivera
These codes are fr... |
829fb6ac1a05a126db32a6f35681b3b665cee0619a8949528294c14dbe734ee3 | Text | 1,283 | 27 | # DomAdapt_BrainNetFusion
This repository stores code and analyses for the [preprint](https://www.medrxiv.org/content/10.1101/2023.01.26.23285055v1) entitled
> *Signatures of pubertal brain development and health revealed through domain adapted brain network fusion*
Before running the code, please make sure to set... |
c81cfdd577645a58cbd538de14f3b5d7b1d8ab11156ed931732552e33133f09a | Text | 1,288 | 36 | # Brain_Iso-Seq
Repository of programs used for iso-seq analysis of brain samples.
The programs in this repository are the ones we used in our research (doi: ). Its purpose is to format and analyze data from a merged file that includes the results of sample chaining using [TALON](https://github.com/mortazavilab/TALON)... |
d536e652f81aa9068cafb8617939ab4075f351aaca4497cca60d2f74efba45b4 | Text | 1,289 | 30 | # SpacoR
[](https://doi.org/10.1016/j.patter.2023.100915)
[](https://doi.org/10.1016/j.xpro.2024.103062)
R version of [BrainStOrmics/Spaco](https://github.com/BrainStOrmics/... |
c536e22303961277fb24ee83404376c77896fc2a795ee78ddcd7d3e9d288c196 | Text | 1,293 | 23 | # mg-segmentation
Adrian et al Nat Comms 2023 - Fiji scripts for microglia segmentation
This simple repro contains the ImageJ/Fiji macros for the following publication:
Adrian, M., Weber, M., Tsai, MC. et al. Polarized microtubule remodeling transforms the morphology of reactive microglia and drives cytokine release. ... |
5ed7606c322ba23e2e0b88797553513d0bb9ad4aea1c598dccde4217cf07d629 | Text | 1,299 | 17 | # deepLungFoam
[](https://zenodo.org/badge/latestdoi/432129853)
Here, we have implemented a repository for coupling a 3D respiratory CFD model to a lumped-parameter model for downstream flow. This model accounts for pleural-pressure change with time and varying capacitan... |
b4365895300a5fda325cf9b5967d8dd7f5d841254d5367c0c1cd67fab6f0fdbd | Text | 1,309 | 36 | # Brain_Iso-Seq
Repository of programs used for iso-seq analysis of brain samples.
The programs in this repository are the ones we used in our research (doi:10.1126/sciadv.adj5279). Its purpose is to format and analyze data from a merged file that includes the results of sample chaining using [TALON](https://github.co... |
959da3d4ec20fdff808dd11d160e489c93894f281bb29247c6fb39c38c97b57c | Text | 1,312 | 18 | lifespan
========
Code associated with:
Yeatman JD, Wandell BA & Mezer AM (2014). Lifespan maturation and degeneration of human brain white matter. Nature Communications.
This is currently a work in progress and eventually there will be code to reproduce each figure and calculation in the manuscript. I am in the pro... |
09171d1a4643012b22be11f0c753bd6e168bf6b0c824a7a4af2e589ce314d572 | Text | 1,313 | 13 | # EUGENe manuscript Zenodo upload
This upload contains the data needed to reproduce the results for the use cases presented in the preprint "EUGENe: A Python toolkit for predictive analyses of regulatory sequences." There are three zipped folders in this upload, one for each use case. You can unzip them in Linux using... |
896d4a97dc47a52968d98aa0a19f520daaed6cad593ab57771a7abe26065a994 | Text | 1,323 | 44 | |impose|
========
|PyPI Version| |Build Status| |Coverage Status| |Docs Status|
Align microscopy images using custom-defined structural patterns and superimpose those on data from other imaging modalities.
Documentation
-------------
The documentation is available at `impose.readthedocs.io <https://impose.readthe... |
31145608949c7768aa0b5295d643e339a04c7a0ede0d085ec67148f6ef4b6413 | Text | 1,339 | 38 | # MyelinCalcium
Code used for analysis of data in Krasnow, Ford, Valdivia, Wilson & Attwell (2017) Nature Neuroscience
Run Code_transient_and_parameters.m (in MATLAB files folder) to plot calcium imaging data from GECIquant results for ROIs in sheaths, processes and somata.
This code requires the following functi... |
2ee9d38c8e1e7a03245a6839780cda4660581f19869bd21d55408e571fb70067 | Text | 1,340 | 34 | # Reliability of developmental MRI
Contains data and analysis towards:
> Drobinin, V., Gestel, H. V., Helmick, C. A., Schmidt, M. H., Bowen, C. V., & Uher, R. (2020). Reliability of multimodal MRI brain measures in youth at risk for mental illness. Brain and Behavior, e01609. https://doi.org/10.1002/brb3.1609
.
## Copyright
```
Copyright (c) 2017-2023, Youtao Lu, Kevin L. Bullaughey, Jean G. Rosario,... |
7c52df14676035dc7ab03730aea96ab4d8c905d3ad2a61b8df74baa0e129d650 | Text | 1,343 | 38 | |PyJibe|
========
|PyPI Version| |Tests Status| |Coverage Status| |Docs Status|
**PyJibe** is a graphical end-user software for the analysis of atomic force
microscopy data.
Documentation
-------------
The documentation, including the code reference and examples, is available at
`pyjibe.readthedocs.io <https://pyj... |
154268ef5aee2793ea5b00ee9687a77708944bbdb10cc8f46b595b54321a0d76 | Text | 1,347 | 13 | :warning: **Please don't submit bug reports for JOSS here. Instead please submit them to [the JOSS repo](https://github.com/openjournals/joss/issues)** :warning:
# Reviews for the Journal of Open Source Software
This is the GitHub repository used to track the progress of reviews for The Journal of Open Source Softwar... |
aaae1bb6bede0b4b9ee5629d79ef311a93d586df4e07383c23caaed74b5bfe95 | Text | 1,350 | 56 | # comoRbidity
`comoRbidity` is an R package to analyze comorbidities from clinical data
## What is this repository for?
This report is used for `comoRbidity` package distribution while we walk thought publication process.
## Package' Status
* __Version__: 1.1.1
* __Authors__: Alba Gutierrez-Sacristan (GRIB-UPF... |
9b9ec1a9fa969d71f372b4e1215d3129842241d7feace6b1a7299e36dc3e6de1 | Text | 1,358 | 31 | # PFC-MERFISH
## Spatially resolved single cell transcriptome profiling of mouse PFC
We employed [MERFISH](https://www.science.org/doi/10.1126/science.aaa6090), an imaging-based single cell spatial transcriptome technology, to decode organizational heterogeneity of cells in mouse prefrontal cortex (PFC).
![cover](Cove... |
b39a687e95bf67892e173a6d53ff2951670a09891cf094c0c69230fa51c802d1 | Text | 1,367 | 36 | # Coincidence Detection and Integration Behavior in Spiking Neural Networks
This repository contains the code generated during the study "Coincidence Detection and Integration Behavior in Spiking Neural Networks". The paper has been published in the journal "Cognitive Neurodynamics": https://doi.org/10.1007/s11571-023... |
bf8e833f2d2e955843bf60e41b989f72788081f5fd75246eb51fe9dc39d0620a | Text | 1,370 | 41 | Real-Time Neurofeedback Environment in Python
=============================================
This is the **rtime** part of the NF tools
A typical workflow exists of, when it comes to the real-time computer:
```
conda activate rt
cd nf-stim
jupyter lab
```
At this stage you should load in one of the ipython notebook... |
2453e2fad71beac4800f97fa4567c15438474669b1ce757d1ff1204ab5b62ae3 | Text | 1,380 | 46 | |PyJibe|
========
|PyPI Version| |Tests Status Unix| |Tests Status Win| |Coverage Status| |Docs Status|
**PyJibe** is a graphical end-user software for the analysis of atomic force
microscopy data.
Documentation
-------------
The documentation, including the code reference and examples, is available at
`pyjibe.re... |
f2a320ac03081652c5fc614db926a50f92fcd8c12948ee1138c8dfc0a85b39ee | Text | 1,384 | 23 | # Code repository for the manuscript 'Improving MR image quality with a multi-task model, using convolutional losses.'
Submitted to BMC Medical Imaging.
The code uses the artefact augmentations from the repository: https://github.com/SimoneRuiter/artefacts
### Data generation
The fastMRI dataset is processed in 'd... |
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