sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
08830c04191cb5266b3013274a59d934a754a87e4eac5127f3645e70d6829f7e | Text | 2,725 | 41 | # Intan-RHX
Intan RHX is free, powerful data acquisition software that displays and records electrophysiological signals from any Intan RHD or RHS system using an RHD USB interface board, RHD recording controller, or RHS stim/recording controller.
The most recent binaries are available from the Intan website: https:/... |
a9c37d1701f8e9bf557fd73997073dfcf7241acb5ffbdf4dfaccf2976f03ec19 | Text | 2,735 | 35 | # Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction
Hi-GeoMVP is a deep-leaning model using graph neural networks to represent the drug and cell line features for drug response prediction.
H... |
db094e240496569ea29f633179bd78a3a8f55f0c2c39c443c6466a1fde3765f1 | Text | 2,738 | 29 | # moodie-geneexpression-cognition
This repository contains the R scripts that I wrote in support of
Moodie JE, Harris SE, Harris MA, Buchanan CR, Davies G, Taylor A, Redmond P, Liewald DCM, Valdés Hernández MDC, Shenkin S, Russ TC, Muñoz Maniega S, Luciano M, Corley J, Stolicyn A, Shen X, Steele D, Waiter G, Sandu AL... |
25567b62b5a4fb8d1485924bfb73311127d45bd05564ce461b37b16c7cad2111 | Text | 2,742 | 61 | # FFClust
## Reference paper
This code is the implementation of FFClust: Fast fiber clustering for large tractography datasets for a detailed study of brain connectivity.
https://doi.org/10.1016/j.neuroimage.2020.117070
## Code Dependencies
To use the code, it is necessary to install the following libraries:
- Numpy:... |
7c6f244b85f23afd26a5e57e8f778f790db51f654fd4ca7201291fb751b55d91 | Text | 2,788 | 37 | README for TWristAR (Three Wrist Activity Recognition) Dataset. January 27, 2022
Lee B. Hinkle https://userweb.cs.txstate.edu/~lbh31/ , Gentry Atkinson, and Vangelis Metsis
IMICS research lab at Texas State University, San Marcos, Texas. https://imics.wp.txstate.edu/
Original repository https://doi.org/10.5281/zenod... |
2472f46244c5eb5cbe9fda738abd07b98da5eb7577e0e253041f1b25b788948c | Text | 2,808 | 75 | NEATmap
========
<p align="center">
<img src="Docs/Html/_images/NEATmap_pipeline.png"
height="300">
</p>
*NEATmap* is a toolbox for the semi-automatic analysis of volumetric data from [VISoR](https://github.com/BilabOptics/VISoR_code/).
*NEATmap's* tool box includes functional modules such as data preprocessing, neur... |
ad69431a52120eb716a4425a3514c4b3b1bdf36344e482f12e4fd57dc2c94b24 | Text | 2,828 | 70 | # TTDCapsNet
[](https://zenodo.org/doi/10.5281/zenodo.10613575)
## Contents
1. [Introduction](#introduction)
2. [Usage](#usage)
3. [Results](#results)
4. [Contact Us](#contact-us)
## Introduction
We introduced a three hierachically layerd Capsule Network (CapsNet) str... |
0c43e4894c135ecb828e95390026757ad1de9c77d80bae737ad7e76a1a6ba7aa | Text | 2,829 | 21 | # The Cortical Representation of Language Timescales is Shared between Reading and Listening
Language comprehension involves integrating low-level sensory inputs into a hierarchy of increasingly high-level representations. Although written and s... |
6885942f0236d3e8f8158483c36a1d4b23b2ab9fec9a76aa079c4b33ae365ea3 | Text | 2,833 | 35 | # SBR-Net
This repository contains the python implementations of the paper: **Robust single-shot 3D fluorescence imaging in scattering media with a simulator-trained neural network**. We provide a code in a python package, `sbrnet-core`, that contains functions for generating synthetic data and training models.
<p al... |
c94baef29cd7ed2b2649787992db8eb938c08dacedf6a03e85b8b2262f7f7538 | Text | 2,871 | 72 |
# Protein holography
## Overview
The protein holography package implements efficient rotationally-equivariant encoding of protein structure and minimal rotationally-equivariant processing of protein micr... |
29aaa8fd41148f2b3229cfb7b17ded090dc88558e86753c1569a0508480dcf29 | Text | 2,873 | 78 | # SpatialPPI: Three-dimensional Space Protein-Protein Interaction Prediction With AlphaFold Multimer
[](https://opensource.org/licenses/Apache-2.0)
## How to use
### Install environment
Using [Conda](ht... |
393516d9c517c4d9c69919baf14b6acafd0fc091a398aa507125dae3324d1546 | Text | 2,901 | 81 | # VoxTool 2.0
## Setup
- If you are on windows, you will need to set up WSL first (https://learn.microsoft.com/en-us/windows/wsl/install)
1. Open powershell
1. Run ```wsl --install```
1. Restart your machine
1. Open wsl
- Clone the repository from GitHub
- Make the setup script executable
```
chmod +... |
af305345d31dc934890c82e35a0ec9d9fca82f98d82a7bbd36d7b0bdbccf6e4a | Text | 2,930 | 80 | # DeepBrain
[](https://pypi.org/project/deepbrain/)
> Brain image processing tools using Deep Learning focused on speed and accuracy.
### How to install
```bash
$ pip install d... |
64db8446dda9b7512d3d12233b3d01137f293cd292fd27a05ee150a6e38b78fb | Text | 2,969 | 36 | <!-- badges: start -->
[](https://doi.org/10.5281/zenodo.10030383)
[](https://github.com/DiseaseOntology/HumanDiseaseOntology/actions)
<!-- badges: end --... |
9d88b333c4e0d6a60070fd7b06ab5d09fbc6db12ab859396f948887ef3a7e74b | Text | 2,974 | 42 | # Electric-field-based dosing for TMS
***
Ole Numssen*, Phil Kuhnke*, Konstantin Weise, Gesa Hartwigsen
This repository holds data and scripts for our Imaging Neuroscience perspective *Electric-field-based dosing for TMS* (DOI: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106))
We... |
8ea0e83d6b3880dd9bfe90a358e67eaafe5bd10c4562090bc6b4968c7e9edfae | Text | 2,978 | 67 | # Whole-brain 3D maps of cellular abundance for six canonical cell-types in humans
<p align="center">
<img src="img.png" width="600" height="300">
</p>
High-resolution imputed maps of spatial cell-type distributions can be used to study variations in cell-type density in relation to macroscale phenotypes. These maps ... |
d509d09ae034571549e0fc610f832eb75e42538567315c05e08d04ad38dbdcaa | Text | 2,978 | 54 | # ETDP-CA1
This repository contains the code for the models used in [A voltage-based Event-Timing-Dependent Plasticity rule accounts for LTP subthreshold and suprathreshold for dendritic spikes in CA1 pyramidal neurons](https://doi.org/10.21203/rs.3.rs-3333583/v1) Tomko et al. (preprint, Journal of Computational Neuros... |
0cdf22a1b490961cdf3732090ea43b51cc9e4deb39ef619cc78aa5caf86fb584 | Text | 2,985 | 54 | # ETDP-CA1
This repository contains the code for the models used in [A voltage-based Event-Timing-Dependent Plasticity rule accounts for LTP subthreshold and suprathreshold for dendritic spikes in CA1 pyramidal neurons (Tomko et al. 2023; Journal of Computational Neuroscience)](https://link.springer.com/article/10.1007... |
afb6279f4abe2404fae433455ccb040660d4038a230c71f33921c8258fe71e1d | Text | 2,991 | 67 | # Cardiomyocyte emulator
[](https://github.com/thomgrand/cardiomyocyte_emulator/actions/workflows/python-package.yml)
[](https://github.com/JaneliaSciComp/neuronbridge/actions/workflows/node.js.yml)
[](https://www.biorxiv.org/content/10.1... |
484a3a83a20ded4abae299d717b72ed2e8f454d7800ad00c89ff59facfaf187d | Text | 2,996 | 74 | # <img src="https://raw.githubusercontent.com/predictive-clinical-neuroscience/PCNtoolkit/dev/doc/_static/pcn-icon.png" alt="PCNtoolkit logo" height="52" align="top" style="vertical-align: middle; margin-bottom: 20px;" /> PCNtoolkit
[![Downloads][downloads-badge]][downloads-link]
[![DOI][doi-badge]][doi-link]
[](https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software/releases)
[![License](https:... |
1b07c1eb69dff0759e84bbc13a6f14810d470aed2ea78db538bd1716a688725d | Text | 3,021 | 43 | # cavity-expansion-model
This repo hosts the code for the simple illustrative particle-based 2D model of cavity expansion and its effect on cell density for the paper "Competence for neural crest induction is controlled by hydrostatic pressure through YAP" by Alasaadi & colleagues. All code was written by Jonas Hartma... |
59cb68c2afb468de36bbe4695c1d4c6403b3b42d370ec7d73c064b09b89db070 | Text | 3,028 | 78 | # Nimo
This is the code for the "Nimo: a Nature Inspired Molecular Generative Model Based on Fragments of Natural Products" paper.
The models was based on [OpenNMT-py 2.0](http://opennmt.net/OpenNMT-py/).
## Environment
- python = 3.6.13
- pytroch = 1.8.1
- RDKit
- numpy
- pandas
#... |
2db187d97313c5135581cb1a0ba03bc73f527203de3c81917a8992af22fbb466 | Text | 3,029 | 61 | microplastic-detection
==============================
ML code for detecting microplastics in sea water from their Raman spectra
See Makefile and run_all.py to run the model training/evaluation
***
Project Organization
------------
├── LICENSE
├── Makefile <- Makefile with commands like `make data... |
88833d82bf8aaa9faa09b64b8ae4a2a10f709922110652670b8e34f5a60885ec | Text | 3,035 | 29 | # ConvNets for Egg Detection in microscopy images
This repository includes training and inference code, as well as pre-trained weights, for the detection of Lymnaea stagnalis eggs in 2D microscopy images. Egg detection is achieved through the combination of image classification architectures (e.g. ResNet) with a bound... |
7ceec242366111505a8d4f1d0ead7354f01792b62f5a1601d8d95305634aab80 | Text | 3,037 | 67 | ## Pycallingcards
[](https://pycallingcards.readthedocs.io/en/latest/)
<p align="center">
<img src="https://github.com/The-Mitra-Lab/pycallingcards/assets/64772552/4eb2fa43-1f69-4a35-8b7e-72568e0f95e7", width="350">
</p>
**Pycallingcards**... |
e6300b2abd2bc5ddfb6c0aa9c46dd2bb43a6c0b597927504c66fd11c0c026571 | Text | 3,044 | 101 | # Flappy Bird for Gymnasium
[](https://pypi.org/project/flappy-bird-gymnasium/)
[](https://githu... |
1da5f8f84de72c0e233037a3d18bbac45356f083c75b6fcce9768a413f097bf5 | Text | 3,051 | 114 | # shadedErrorBar
[](https://uk.mathworks.com/matlabcentral/fileexchange/26311-raacampbell-shadederrorbar) [, such as convolutional kernels and sparse recurrent loops. However, the compromise of ... |
f1474dcd54e45792498e3f1056cdbc755a7bc9328247ee253909ab17b8d614ad | Text | 3,089 | 59 | # Identification of clinical disease trajectories in neurodegenerative disorders with natural language processing
https://www.medrxiv.org/content/10.1101/2022.09.22.22280158v1
---
## Introduction
This repository contains all the code associated with the publication: "Identification of clinical disease trajectories i... |
455012dec4a53cd02be2695f511738d0b755a68e627ad1e86480434c2d826918 | Text | 3,104 | 69 | # Cardiomyocyte Emulator Training Data
The data presented in this repository is the training data (data set #1) used in our work *Neural network emulation of the human ventricular cardiomyocyte action potential: A tool for more efficient computation in pharmacological studies*, available at https://doi.org/10.7554/eLi... |
0b749f1d10398f09f06a0169db902e793b1eac4edf7346b045a06b7ff8b127cd | Text | 3,113 | 93 | # NeuronBridge backend services
[](https://zenodo.org/badge/latestdoi/260239328)
[](https://circleci.com/gh/JaneliaSciComp/neuronbridge-services)
## Deployment
As a prerequisite, you n... |
14ad7c869cc78f3b04b789cd32d483b26fb0b62bb3a814f8e54bfaa1a0137241 | Text | 3,122 | 46 | # 2.5DAttention
This repository is the implementation of our paper [Interpretable 2D Vision Models for 3D Medical Images](https://arxiv.org/abs/2307.06614) and was used for [Private, fair and accurate: Training large-scale, privacy-preserving AI models in medical imaging](https://arxiv.org/abs/2302.01622).
## Setup
... |
e07f134738e1d1bae0439ecd378639a6ff775fe844eda827b3df8501b880247b | Text | 3,129 | 72 | # Pipeline_SpiderMass1D
This Python script written in jupyter notebook performs analysis on mass spectrometry data. It includes various functions for data preprocessing, machine learning model selection, visualization, peak picking, and statistical analysis of significant features.
## Functions and Usages
1. **impor... |
effc49a09b8f0dfe65d4eacc33425471fd306fcb962551c2f880d8ba11f5d34d | Text | 3,132 | 68 | microplastic-detection
==============================
ML code for detecting microplastics in sea water from their Raman spectra
See Makefile and run_all.py to run the model training/evaluation
***
Project Organization
------------
├── LICENSE
├── Makefile <- Makefile with commands like `make data... |
99d672cf19ea9d9a2a8c198c7dcb70a18fffa7cbd92a114f384e9c67a04e7451 | Text | 3,137 | 48 | # Flu Forecaster
An experimental deep learning & genotype network-based system for predicting new influenza protein sequences.
## Rationale
Flu Forecaster was first fully developed during my time as an Insight Health Data Fellow. The projected business use case is to predict what future strains of flu will look ... |
4035037e4006d1433523669d352c46603e0c49c24c2d2009ec822e94b91ae3dd | Text | 3,145 | 68 | # JETS for Diffusion MRI at 7 T
Demonstration on Joint k-q-slice rEconsTruction framework for Shift-encoded (JETS) Diffusion MRI at 7 T
## Pulse Sequence
### Complementary k-q-space sampling
**Figure 1**. **(A)** An example diffusion-weighted magnetic resonance imaging (DWI, or ... |
4d944975d0b1e91d9d87b66c5f31c0f8b5056ef166358d970e4e4af5126077b9 | Text | 3,189 | 63 | ## Circadian Analysis: Rhythmicity detection and DE analysis
The purpose of this software is to demonstrate rhythmicity detection of circadian patterns in gene expression profiles as well as differential expression (DE) analysis using a random intercept model with gene specific covariate selection. Full analysis using... |
075e0e6fa82bffa892b85ccffa65e41665b0319432769c22f6f06c8115b046b5 | Text | 3,209 | 26 | This software package includes the codes used for population decoding of single-unit responses of freely-behaving mice to different social stimuli, as well as example data files for illustrating the running of each functions. The codes were written as MATLAB .m scripts, and tested under MATLAB R2023a with Windows 10 v2... |
a585170c3cf6d05830d56d6e0e5c0bc46be87ee922a9a8a461080c1cedea0445 | Text | 3,218 | 78 | # Preserving fairness and diagnostic accuracy in private large-scale AI models for medical imaging
Overview
------
* This is the official repository of the paper [**Preserving fairness and diagnostic accuracy in private large-scale AI models for medical imaging**](https://doi.org/10.1038/s43856-024-00462-6).
* Pre-p... |
130a6bb1f54203c50698abe461d53e589dc4126988dde99c571e7fa6f0dd1ae8 | Text | 3,223 | 43 | # ClimbFiber_InstructSignals
Centralized data used for the bioRxiv article "Neural instructive signals for associative cerebellar learning" (Silva et al., 2022).
Each folder in this repository contains a Pickled Python dictionary (version 3.6) containing all the data used for the experimental analysis involving Purki... |
f05ed7379368db5cfafdf768fcf4694017feae7eec2521bc3cfbd9244c3e9154 | Text | 3,245 | 107 | =========
mtoolnote
=========
.. image:: https://www.repostatus.org/badges/latest/wip.svg
:alt: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.
:target: https://www.repostatus.org/#wip
Variant annotator for MToolBox.
* ... |
f641fe4ffd92b6915279175ace9f26e1eaf0d2ee7f595c0bfac5e955f81409bb | Text | 3,252 | 62 | ## Setup
First,`bowtie2` and `bedtools` must be installed and accessible from the terminal.
Additionally, large files with experimental data used in this project are hosted on GitHUB LFS server. To be able to pull this project
you must follow [the instructions](https://docs.github.com/en/repositories/working-with-fi... |
3ccb649796bd318b006a5cb54c8bd6ebb838ec33c762337fef9f6bd6933467d8 | Text | 3,302 | 93 | # Color Depth MIP Search Tools
[](https://github.com/JaneliaSciComp/colormipsearch/actions/workflows/maven.yml)
This is a set of tools for precomputing color depth searches using the same algorithms as [ColorM... |
39aee8d7b29e68070f9d0493250e5742b845baf0743079e1628e41ba1b9a3ee9 | Text | 3,311 | 47 | # C.-elegans_locomotive_simulator
Ready to install and run MatLab app (CelegansLocomotion.mlappinstall) simulates the forward and backward locomotive neural network dynamics with multiple control variables.
The user can specify the type of networks used (electron micrograph connectivit... |
95644f15a853522b957a0bc0e066f1ddb4287515a1bbb3699e3ba252a529819e | Text | 3,321 | 58 | # T-DAPIA: Two-dimensional Analysis Pipeline for MSI Artificial Intelligence (T-DAPIA)
T-DAPIA is a Python-based Two-dimensional Analysis Pipeline designed for Artificial Intelligence (AI) applications in mass spectrometry imaging (MSI).
This pipeline provides functionality for processing and analyzing MSI data, inclu... |
188b41fd8f9f1fa95a49809a227a1ebfc0b56b9f6ec950511cd04b53af1bb838 | Text | 3,325 | 56 | # NeuronBridge
[](https://zenodo.org/badge/latestdoi/257408159)
[](https://github.com/JaneliaSciComp/neuronbridge/actions/workflows/node.js.yml)
[ lesions in the white matter (WM) of the brain have not been resolved to date. Using several high throughput molecular profiling technologies, snRNASeq, snATACSeq and spatial transc... |
bbfc5c71dcc194ff01cb18b430740748c522ec5aade58e104df5bb8f77159934 | Text | 3,365 | 67 | ## 3D fetal MRI altases of the fetal body
This repository contains 3D fetal MRI atlases of the fetal body cretated at King's College London from 3D DSVR reconstructed images.
-----
### Structural 3D T2w MRI altas of fetal body at 3T
The fetal body atlas was created from 3D DSVR-reconstructed images of 17 normal f... |
4f68f71d984e3e5f5afe6e7fddf5c21be4bd7a2fd2ab3c4fdc02acdc0ee1773b | Text | 3,389 | 32 | # narratives_reading_listening_fmri
This folder contains stimuli, models, and fMRI data originally created for and collected in Deniz et al. 2019 (see below for full reference).
Some results from this study can be viewed online at:
https://www.gallantlab.org/brainviewer/Deniz2019/
# Stimuli
The stimuli folder cont... |
94a014f67421e1b2374742420be7b0a32d02cbb2a522e9a3a7f8acf6d6d98134 | Text | 3,431 | 40 | # xCAPT5 for Protein-Protein Interaction Prediction
This repo is for the paper: `Dang, T.H., Vu, T.A. xCAPT5: protein–protein interaction prediction using deep and wide multi-kernel pooling convolutional neural networks with protein language model. BMC Bioinformatics 25, 106 (2024). https://doi.org/10.1186/s12859-024-0... |
66a3ce2304c7a01cb9ac438c0e9174a9cbce98bd84f839908f664404998a84ae | Text | 3,439 | 68 | # TraSE-IN
Tracking and Spike Estimation of Individual Neurons
This is the official code implementation of `Automatic monitoring of neural activity with single-cell resolution in behaving Hydra` (See below for the full reference).
The tracking code is published as a re-usable python library: [ByoTrack](https://githu... |
6f93cc32ba3a8ed31a76e6657328dc1270dec3612f5e16a72d9441b6c68436fe | Text | 3,441 | 81 | # Public scRNA-Seq Datasets
This repository is used to build [scater](http://bioconductor.org/packages/scater/) objects and reports (in continuous integration manner) for various publicly available scRNA-Seq datasets used by our group. This pipeline is implemented using docker containers and cloud computing. The resul... |
5ccbb4ceb40fb137de5c92f98f5cea9ffe29cc44369f3405f73ab1f0bd8328e5 | Text | 3,447 | 49 | # Multimodal brain age prediction using machine learning: combining structural MRI and 5-HT2AR PET derived features
Scripts and documentation for the paper "Multimodal brain age prediction using machine learning: combining structural MRI and 5-HT2AR PET derived features".
bioRxiv: [https://www.biorxiv.org/content/10.1... |
c7ff6fa23e733a8abbfb22a6ab6cc13aae5062f94c8cc0efaaa21dc0b8fb67b5 | Text | 3,450 | 65 | <h1 align="center">
<a href="https://mol.dev">Mol.dev</a>
</h1>
[](https://openreview.net/forum?id=pCbCRfUSoh)
[](https://lbes... |
1d71f601cb697a84bbc5c1c7de5a661f94c66125c3be7b587c619e195c061a2e | Text | 3,451 | 47 | # Whole-heart electromechanical simulations using Latent Neural Ordinary Differential Equations
This repository contains the code accompanying the paper [1]. We employ Latent Neural Ordinary Differential Equations (LNODEs) to learn the atrial and ventricular pressure-volume temporal dynamics of 400 four-chamber heart ... |
648bbac4c9f7e42cd23d0e3a0e42673f65280866becccca95b653cb2e9bb2ca3 | Text | 3,454 | 83 | # DREDDA: Drug Repositioning through Expression Data Domain Adaptation
## Overview
This repository contains the implementation of DREDDA from
```
Zhongxiao Li, Antonella Napolitano, Monica Fedele, Xin Gao*, Francesco Napolitano*
"AI identifies potent inducers of breast cancer stem cell differentiation based on adver... |
937c188280328cc9587f8e26c4e22bb976ff76ee291991adfa9bc94a41e80b8e | Text | 3,479 | 86 | # gradient-decoding
Methods for decoding cortical gradients of functional connectivity
## Summary
This repository contains all code required to reproduce the analyses and figures of the
"Methods for decoding cortical gradients of functional connectivity" paper.
Please refer to the paper for further details: https://... |
922a517d57115f23064f4a12b90c6f569ae52c6910679d2e0b8101267ebaad20 | Text | 3,516 | 92 | # `AIgarMIC`
[](https://doi.org/10.21105/joss.06826)
## Introduction
`AIgarMIC` is a Python package and collection of commandline scripts designed to facilitate the automation of agar dilution minimum inhibitory concentration image interpretation.
... |
ba534ddccb8b414208200922c54128e6db21d0923aa027dd10bb0db351ebffd0 | Text | 3,517 | 68 | # Verilog UART Readme
[](https://github.com/alexforencich/verilog-uart/actions/)
For more information and updates: http://alexforencich.com/wiki/en/verilog/uart/start
GitHub repository: https://github.c... |
caf10e490f58fc53db2f2b8751483add0eb9d0047a499c5828ae8ad16fdb3b04 | Text | 3,566 | 39 | # Cellular-functional decoupling in marmosets
This repository contains code created to conduct the main analyses described in the paper "**Decomposing Cortical Activity through Neuronal Tracing Connectome-eigenmodes in Marmosets**".
Uses an eigenmode-based analysis to study how neuronal tracing connectome (cellul... |
5beba26819b903f328a51bdf593576b8c8f510301d7d820a7bb367c867e4f75d | Text | 3,586 | 86 | ## SVision-pro-Utils
The utilities and scripts in SVision-pro paper, including
* Running commands
* Comparison criteria
* Model training and interpreting
* Figure plotting
## License
SVision-pro and its utilities are free for non-commercial use by academic, government, and non-profit/not-for-profit institutions. ... |
c5eda3dbaeec1acd14cdc2d3afaa635201ae31d352ee19586d245a64777d4c48 | Text | 3,626 | 98 | # moseq-reports
### Interactive interrogation of Moseq models.
In short, moseq reports exists to democratize moseq data. Computational biologists often produce data which is difficult to parse without the proper tools or context making, increasing barriers to access for others to simply pick up and use. Moseq reports a... |
3ba7dadf34e8f95ece62282e446ec897c0115314492a6bfb3c5e0902f94f46d1 | Text | 3,627 | 89 | # LiMCA: **L**inking **m**RNA to **C**hromatin **A**rchitecture
<img src="images/limca.png" width="275"/><br>
[](https://doi.org/10.5281/zenodo.10862950)
LiMCA is a new single-cell sequencing method that can simultaneously profile the 3D genome structure and transcriptome... |
e6ad42b6248a24d7710b8101916aa0dc1932b40b286c17160dcd11d5c9afffde | Text | 3,710 | 127 | Kernel Current Source Density
=============================
This is version 2.0 of kCSD-python implementing kCSD method and related functionality.
Only supported for python 3.
Relevant Papers
---------------
Paper 1: "Kernel Current Source Density
Method", J. Potworowski, W. Jakuczun, S. Łȩski, D. K. Wójcik; Neur... |
c794c7f796d39307c371c377a838b430f45045ccd0d755b9f46fefb68e4af5db | Text | 3,712 | 78 | # Collective Relational Inference (CRI)
Our proposed **Collective Relational Inference** model learns the heterogeneous pairwise interactions from the trajectories of interacting particles.
This repository includes the implementation of the three proposed methods in our paper: CRI, Evolving-CRI and Var-CRI.
Author... |
bb80578d076c6bcf109b84ca4a37bd0285af2df250a233a687dcb0fa8ee433af | Text | 3,734 | 107 | # NeuronBridge backend services
[](https://circleci.com/gh/JaneliaSciComp/neuronbridge-services)
## Deployment
As a prerequisite, you need to have the [AWS CLI](https://aws.amazon.com/cli/) installed and configured with proper AWS... |
3d9f0ba3a707b3972b1f81c318295b44dd3ca440577c4a6d825ec90b3bf93268 | Text | 3,808 | 73 | README for ModelBlocks
======================
This is the `Modelblocks` software package. It includes several
resources for constructing and evaluating broad-coverage probabilistic
models of cognitive processes, organized into projects centered around
different tasks and data sets.
Documentation is available at: htt... |
eb4583b7b7a1fc473e46072716e4acb21d2f0566f575d07605d5cede63cd40cc | Text | 3,825 | 81 | # DISSECT
DISSECT is a deep semi-supervised learning framework that performs complete deconvolution of gene expression mixtures such as bulk RNAseq, proteomics and spatial transcriptomics. The manuscript is available at [Genome Biology](https://link.springer.com/article/10.1186/s13059-024-03251-5).
This repositor... |
1f95d72526b11109766149aadfda532a8081b19987c72f0cc1fee7062a64d20a | Text | 3,829 | 75 | # T1T2
**by Tim J. Hartung, Darko Komnenic, Graham Cooper, Valentin Jünger, Michael Scheel and Carsten Finke**
*Cognitive Neurology Lab, Charité - Universitätsmedizin Berlin*
*August 2023*
## Introduction
This is a fully automated script to derive the standardized T1-weighted / T2-weighted (T1T2) ratio from T1-... |
ae2bdaf3b98f7345344eee0c5cb4b191aadfd45ea11a2fc7cba26d529c4333f8 | Text | 3,831 | 45 | ## Centripetal propagation of calcium signals in astrocytes
Custom code to compute **centripetal propagation** patterns (delay maps) from **astrocytic calcium** recordings using pixel-wise **correlation functions**.
<p align="center"><img src="https://github.com/HelmchenLabSoftware/Centripetal_propagation_astrocytes/... |
c270860fc5efac44a3e99135bf5abeba09440e7fc1b746877ccd31c1527733f1 | Text | 3,870 | 50 | # ML Malaria prediction
This repository provides the implementation of our machine learning model for predicting Plasmodium liver stage development in vitro using microscopy imaging.
In our work, we delve into the liver stage development of the P. berghei parasite responsible for the Malaria virus and examine the hos... |
df0db31bc492cb0a9e175557b129f6a0a8b3e757a5e8927cbaca577c22c17237 | Text | 3,898 | 47 | Updated 4/4/24
This repository contains the code and data to calculate STAMPR measurements from barcode frequency counts. If you have a question or are having trouble running the code, don't hesitate to email me at hullahalli[at]g.harvard.edu.
Papers that have deposited code into this repository include:
1) [The de... |
1e34d7b63026b4c35c44b61eed7ceed7965772b9a1a075ebeebfb93332ee51b9 | Text | 3,926 | 45 | ## Centripetal propagation of calcium signals in astrocytes
Custom code to compute **centripetal propagation** patterns (delay maps) from **astrocytic calcium** recordings using pixel-wise **correlation functions**.
<p align="center"><img src="https://github.com/HelmchenLabSoftware/Centripetal_propagation_astrocytes/... |
d0962ddc7cd63b3b886f5ed403b6148019aae9a1d6c64c002ddb26c70b03a12a | Text | 3,926 | 96 | <p align="center">
<img src="imgs/logo.png" width="300">
</p>
# Diffusion Deep Learning for Brain Age Prediction and Longitudinal Tracking in Children though Adulthood
Here, we leveraged 32,851 T1-weighted MRI scans(Fig A) from healthy children and adolescents aged 3 to 30 from 16 multisite datasets to develop a... |
6be84db36f7a8fb3769337164ca977c3d9ae135de1d98687d68d3aa6371cfac0 | Text | 3,936 | 102 | # About
SlicerRadiomics is an extension for [3D Slicer](http://slicer.org) that
encapsulates [pyradiomics](https://github.com/radiomics/pyradiomics) library that calculates a variety of
[radiomics](https://www.radiomics.io/) features.
See list and detailed description of computed features in **[pyradiomics library do... |
3f1e4a0d2e167260b09757ceefa438927a1923b32fb0748a42539bc6ef81e685 | Text | 3,941 | 116 | # Wavenet research
Code base for the paper (when available): [Empirical modelling and prediction of neuronal dynamics]()
___
## Table of Contents
- [Description](#description)
- [Installation](#installation)
- [Documentation](#documentation)
- [Authors](#authors)
___
## Description
The respository is a Wavelet Neu... |
636a44964434c45511f38d7945dd4106acb493d373948afd55125ad9535e9c6b | Text | 3,944 | 35 | # PCDHA9-ALS-Candidate-Gene-Functional-Identification
Here is the code of our paper: **Functional identification of protocadherin alpha 9 (PCDHA9) as a candidate causative gene for amyotrophic lateral sclerosis**
**If you have any questions, please contact us：*... |
70fc14a6451fba413b7227a7d4e7a685e7f5b33750f2813ee99009417cdafea0 | Text | 3,961 | 76 | # Periodic Graph Transformers for Crystal Material Property Prediction
<!-- [](https://github.com/MinkaiXu/GeoDiff/blob/main/LICENSE) -->
[[OpenReview](https://openreview.net/forum?id=pqCT3L-BU9T)] [[arXiv](https://arxiv.org/abs/2209.11807)] [[Code](... |
7714f1af341644a0a51d5f6284968475d0789ca3004ec4d98482fda237c1c246 | Text | 3,962 | 107 | # image-registration
A MATLAB library/toolbox providing access to image registration,
initially developed for use with medical images.
# Copyright
Copyright (c) 2015 Daniel Forsberg
danne.forsberg@outlook.com
# About
This toolbox was written during my PhD at Linköping University, Sweden.
However, although develo... |
8ba560cf21c13c163dbfb60efc3937ff8e633104bf02947f9d4fec28505902d3 | Text | 4,003 | 67 | # VINNA4neonates
Newborn Whole Brain Segmentation with the Voxel size independent neural network VINNA.
This README contains all information needed to run VINNA4neonates - a fast deep-learning based whole brain segmentation network.
VINNA4neonates provides a dHCP alternative for volumetric analysis (within minutes) w... |
6463b75bafb1415084b1a87ecdb632865a3b55208cb5f465864d7f8aa4977e91 | Text | 4,010 | 36 | # Schneider et al. 2024
Code for all data analyses in Schenider et al. 2024. Data files are available at: [OSF | Bap1_Schneider2024](https://osf.io/jgnve/)
# Analyses
The analyses for this paper are separated into three main components:
## `Seurat/`
Pre-processing, integration, cluster markers, and differential exp... |
5b5307d63cf52783894af8a99d9ef5802407bbf919f0e45ac7229c074a79a14e | Text | 4,060 | 49 | # Explainability of deep neural networks for MRI analysis of brain tumors
Artificial intelligence (AI), in particular deep neural networks, has achieved remarkable results for medical image analysis in several applications. Yet the lack of explainability of deep neural models is considered the principal restriction be... |
fe299562e2aa491e2772006a43c8a144ac664c94f4f226309b4eba62e51a6695 | Text | 4,076 | 101 | # Dataset Access for PLOS ONE
This repository contains the raw data associated with the PLOS ONE paper:
📄 [Read the paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0299873)
📄 DOI: https://doi.org/10.1371/journal.pone.0299873 ... |
853df7958d8eb39cee411140f9df156fff571e1770854e22621cedb301963b0e | Text | 4,092 | 127 | # fiberphotopy
Code for analyzing fiber photometry data collected on the Doric Fiber
Photometery acquisition system.
## Installation
The simplest way to install fiberphotopy is by cloning the repository and installing the requirements:
```bash
git clone https://github.com/kpeez/fiberphotopy.git
cd fiberphotopy
pip ... |
84e279cb20f426fe7ca8cc11a923203722ae2ba8054b5882e7eeb370a33d13f9 | Text | 4,122 | 61 | # AbFlex
AbFlex is a CDR design method for a given antibody-antigen complex.
Paper: Woosung Jeon, Dongsup Kim, AbFlex: designing antibody complementarity determining regions with flexible CDR definition, Bioinformatics, Volume 40, Issue 3, March 2024, btae122, https://doi.org/10.1093/bioinformatics/btae122
## Preparat... |
189b84e05c5a78decaffa6299c5958fcf10701e76636fa13813afe165adf704a | Text | 4,139 | 135 | # MMGX: Multiple Molecular Graph eXplainable Discovery
Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction
## Update 🔔
- 2026/03/... |
9e53a9fdebbd03700e09dcc32aaf8d22f5e359bae11d459ef75709334e97f64f | Text | 4,139 | 93 | # Bacon
A comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies
For more information, see our [Bacon](https://csuligroup.com/Bacon) webpage.
Zenodo DOI: [10.5281/zenodo.5607035](https://zenodo.org/record/5607035#.YbVnGX1BwUs).
## Contents
-... |
c12d94392e459cfcaedb121cb107c5546f5140550946543f74972964be17b82f | Text | 4,151 | 67 | <a href="https://zenodo.org/badge/latestdoi/285637037"><img src="https://zenodo.org/badge/285637037.svg" alt="DOI"></a>
# BrainJ
An accessible tool for automated brain reconstruction, mesoscale mapping, and cell analysis.
**Please read the [BrainJ Guide.pdf](https://github.com/lahammond/BrainJ/blob/master/BrainJ%20Gu... |
298e282599153bb946f008d357a2eb4e73f783d3acd77c9d88ca47d79bf57e0f | Text | 4,166 | 101 | # Neurodegeneration Vacuole Quantification
Scripts for vacuole quantification in 3D whole-mount 2-photon images of D. melanogaster brains
(Original publication: https://www.cell.com/iscience/fulltext/S2589-0042(23)02129-6)
Citation : Elguero, J. E., Liu, G., Tiemeyer, K., Bandyadka, S., Gandevia, H., Duro, L., Yan, Z... |
c813ab4b585233a00d457cc1a139b1acc11dc241a89062a76f33aae7d37d2f1d | Text | 4,201 | 138 | # tnn
Matrix-Mimetic Tensor Neural Networks
## Citation
The paper is published [here](https://www.frontiersin.org/journals/big-data/articles/10.3389/fdata.2024.1363978/full).
```
@article{newman_stable_2024,
title = {Stable tensor neural networks for efficient deep learning},
volume = {7},
issn = {2624-909X},
ur... |
5be00eb79183e4e67562567a9d1573ec58f9ec064dcfee66656376e6aa664fbb | Text | 4,229 | 125 | # Manual correction
This repository contains scripts for the manual correction of spinal cord labels.
Currently supported labels are:
- spinal cord segmentation
- gray matter segmentation
- lesion segmentation (e.g., MS or SCI lesions)
- disc labels
- compression labels
- ponto-medullary junction (PMJ) label
- root... |
d9e605203f2a2e1d84da70f89f0eea56ba90b983e4ba3124efa520f1d787f9e7 | Text | 4,232 | 97 | <p align="center">
<img src="imgs/logo.png" width="300">
</p>
# Diffusion Deep Learning for Brain Age Prediction and Longitudinal Tracking in Children through Adulthood
[What is this about?](https://guessmybrainage.webflow.io/)
Here, we leveraged 32,851 T1-weighted MRI scans(Fig A) from healthy children and adol... |
a2186dab8f9e5d520e07a8c437cca4d260382933555a989f28b2a15c95418296 | Text | 4,297 | 98 | # The Actigraphy Project
## Contents
- [Overview](#overview)
- [Repo Contents](#repo-contents)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Reading Materials and Citations](#reading-materials-and-citations)
- [License](./LICENSE)
# Overview
Actigraphy allows a non-inv... |
deb679690981c0ac940c254fb32cd43052a5f1b8565ace69c6e794611ca3703b | Text | 4,357 | 65 | # Intro
GraphSite is a novel framework for sequence-based protein-DNA binding site prediction using graph transformer and predicted protein structures from AlphaFold2. We recommend you to use the [web server (new version)](http://bio-web1.nscc-gz.cn/app/graphsite) of GraphSite if your input is small.
![GraphSite_fr... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.