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06b121380dc07464814318116e7437e701f6231e061d6b2b5893f2f9e1f1a47b | Text | 1,196 | 25 | # gtImputation (Genotype Imputation)
gtImputation (Genotype Imputation) is an application designed to determine the genotypes of missing data
in a VCF or tabular format file using a machine learning procedure based on self-organizing maps (SOMs) called SOM imputation.
In addition, the application is also designed to p... |
9d31530e7b6cce45421e99750419a2f5260ee4bad057b5bad0fab287828341d8 | Text | 1,200 | 17 | # TUS-TMS-Clamp
# 3D-Printed TUS-TMS clamp
***Benjamin R. Kop, Lennart Verhagen, et al., 2022 "preprint in progress - title"***
In this repository you will find .stl and .easm (eDrawing) files for our TUS-TMS clamp. The files provided are designed for use with 2-element annular array transducers with solid water cou... |
a458c9aa3ef2968bee3fadef60001d2bcf90fef4cbeba35d0bacac4c9a0738ff | Text | 1,202 | 1 | The provided code begins by loading a dataset named "cloud final1.csv" using pandas. Then it explores the data, including examining unique values, checking for missing values, and dropping columns with NaN values. It proceeds to visualize the correlation matrix of the dataset using seaborn's heatmap. The data is then p... |
e00aefe1de913fd41f50a468253b18059120c95de57f19f738165898b216acdc | Text | 1,231 | 18 | # HD Astrocyte Paper code
Github repository for the code used in the manuscript Multi-OMIC analysis of Huntington disease reveals a neuroprotective astrocyte state.
## Usage
The directory contains two folders, analysis and function. The analysis section contains portion of codes used for the various analysis perfor... |
5fdc5bd405980743d2467d7883d0b5c5920d23741baf0a4f50c6ac0bd98add6d | Text | 1,232 | 35 | # ElikoPy
[](https://elikopy.readthedocs.io/en/latest/?badge=latest) [](https://pypi.org/project/elikopy//) ](https://zenodo.org/badge/latestdoi/488574180)
In this repository you will find .stl and .easm (eDrawing) files for our TUS-TMS clamp. The files provided are designed for use with 2-element annular array transducers with... |
18335b4a5fbaa7da4817fe3f738a5b2db04177329abc2c916c7281a278ef8bd3 | Text | 1,238 | 21 | design-files
============================================
Repository of the [Wilson Lab](http://wilson.med.harvard.edu) design files.
## terminology:
* "holders" aka "foils" are small pieces of metal that are cut to hold flies. We typically use thin stainless steel shim stock, or titanium foil, see below for more info... |
e2d464cce590005128a8098cc8604e93722fdefcb4821d26f4075f5235a747f0 | Text | 1,241 | 29 | # BCPNNSim
Bayesian Confidence Propagation Neural Network Simulator
This repository provides code for the experiments in the paper
Ravichandran, N., Lansner, A., & Herman, P. (2024). Spiking representation learning for associative memories. Frontiers in Neuroscience, 18, 1439414. (https://www.frontiersin.org/journa... |
05a0e00f1a35ffb8719b58b3beae11af62428c716deb75fafad6d79ce2d8f8e6 | Text | 1,258 | 20 | # multicolumn
This repository contains codes for multicolumnar model paper.
### Folders
- `figs`: contains figures for temporary results. (not necessary)
- `funcs`: contains functions used in study. Usually be called from scripts in other folders.
- `plots`: contains scripts for generate figures in `figs` folder. Code... |
c04afa5cd3ab33367b8677b04703eb1687a4fc799d222baf033062366d606f52 | Text | 1,258 | 23 | # permFDP
An R package for correcting p-values for multiple hypothesis testing in comparative quantitative omics experiments using permutation-based FDP estimation.
## Installation
Once you have the `devtools` package installed, you can install `permFDP` by using the `install_github()` command:
```
install_github('s... |
50376f42e08fc89467988304efda2dd1f6631d4c2065ab6b30e79e05f3409ac8 | Text | 1,270 | 33 | README : VONet for reviewers
This is codes for generate Virtual Organoids(VO), train VONet using VO, and test the performane of it.
Since this code is for research, it is not automatically configured.
I am sorry for not optimizing usage, since I am now doing lots of other works for changing my workplace.
I wrote h... |
2bdb1f5a71f924becda31d084aa227051ab7160579f9ff94516be5d45f35d24c | Text | 1,273 | 22 | # GATK-SV
A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data.
For technical documentation on GATK-SV, including how to run the pipeline, please refer to our [website](https://broadinstitute.github.io/gatk-sv/).
## Repository structure
* `/.github`: Continuous integra... |
de7d8eeda7eae61950b1d202b821a14e7901ac18024225cd15f4bb67c3ac4570 | Text | 1,274 | 49 | # BaseNet
BaseNet: A Transformer-Based Toolkit for Nanopore Sequencing Signal Decoding
# How to install
run the following commands:
```
git clone https://github.com/liqingwen98/BaseNet.git
cd BaseNet
pip install -e .
```
... |
aff1266482521b9b3816efad381a31d00e45805030f54b03e4ea46110944ec4f | Text | 1,285 | 26 | # gtImputation (Genotype Imputation)
gtImputation (Genotype Imputation) is an application designed to determine the genotypes of missing data
in a VCF or tabular format file using a machine learning procedure based on self-organizing maps (SOMs) called SOM imputation.
In addition, the application is also designed to p... |
7e8018aa394e625bd99686c60a4b11d55f7712b8816ab008d7006c9292b36777 | Text | 1,289 | 18 | # SIRV
## Spatial inference of RNA velocity at the single-cell resolution
### Implementation description
Python implementation can be found in the 'SIRV' folder. The ```SIRV``` function takes as input 1) spatial transcriptomics data as ```scanpy/scvelo Anndata``` object, 2) scRNA-seq data as ```scanpy/scvelo Anndata`... |
69b896decb531c8841a5c463f5e97e3a47933d9b9fb57e93980061c404599f2c | Text | 1,290 | 20 | # kumar-molecular-mechanism
## This is the code used to analyze the data presented in S. Kumar, A. K. Sharma, and A. M. Leifer, titled "An inhibitory acetylcholine receptor gates context dependent mechanosensory processing in *C. elegans*". Here is the link to the preprint: https://doi.org/10.1101/2024.03.21.586204
T... |
4c466c4f3946c5913a807fed4ed02af076bd436b916c068dede14c46f9a165bb | Text | 1,294 | 7 | # Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer
## Abstract
Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe t... |
0b18e24df4581052e0f2c3b0c199cfd975ebe4aa300c47d18355da15c248f07b | Text | 1,298 | 37 | # Near-real time Grape Downy Mildew Segmentation
Repository contains codes and datasets to reproduce results in the IROS 2022 submission on "Near Real-Time Vineyard Downy Mildew Detection and Severity Estimation"
This codebase is an undergoing project. Improvements will be continuesly made.\
Todo: \
-Training instru... |
cb4d31caa6d60796f87d054887daa9e340dfabfcfec9099a449ae6b282b8f332 | Text | 1,300 | 20 | # EpimiRNA
R code and accompanying data files to reproduce miRNA bayesian network analysis as performed in Khemka et al Sci Rep 14, 15313 (2024). https://doi.org/10.1038/s41598-024-66117-7
File descriptions:
Network generation code:
Rcode_network_generation.R : This R script is used to generate the Bayesian network ... |
d48676aaf3f41c72d79a66686dd38861a71116ca763dd189bab3b970e86c4310 | Text | 1,309 | 18 | # SIRV
## Spatial inference of RNA velocity at the single-cell resolution
### Implementation description
Python implementation can be found in the 'SIRV' folder. The ```SIRV``` function takes as input 1) spatial transcriptomics data as ```scanpy/scvelo Anndata``` object, 2) scRNA-seq data as ```scanpy/scvelo Anndata`... |
cce4e635c31870a6e82ad8bbdcf7317b56bf345f6aba6c0961f9241097d18588 | Text | 1,318 | 21 | # Machine Learning of Brain-specific Biomarkers from EEG
This repository contains the research code from [Bomatter et al 2024, eBioMedicine](https://doi.org/10.1016/j.ebiom.2024.105259).
For the software library please checkout the [meeglet](https://roche.github.io/neuro-meeglet/) package.
## Install Instructions
1... |
52ba2df131052e06e60e9689a31e8e4a2108105e7b12fc04d7847e27644256f0 | Text | 1,320 | 13 | # Analysis code for DeepComBat manuscript
This is all code used for development and analysis of the DeepComBat image harmonization method described in more detail here: https://www.biorxiv.org/content/10.1101/2023.04.24.537396v1
In the development process, code/deep_combat.Rmd was used to run DeepComBat, along with p... |
e4e220ab14119e1d30b0c88d4e150009d7ce8b4f89ab2668b75fbd2585727960 | Text | 1,320 | 16 | # StructuredConnectivity
Data and code for manuscript "Structured connectivity in the output of the cerebellar cortex."
Link: https://www.biorxiv.org/content/10.1101/2023.03.17.533173v2
This repository serves to store the data and code for the Gruver et al. 2023 BioRxiv manuscript "Structured connectivity in the out... |
f0f0e9381fce12a76ba4448b18e3b5978d2ca66c953a1783ec89a953753e5697 | Text | 1,327 | 39 | # Initial Code Upload
This repository contains the initial code upload for running on a Windows 11 PC equipped with an RTX 3090 GPU. The environment required for running the code is listed in `environment.yml`.
## Prerequisites
Before running the code, ensure you have the following:
- A PC with Nvidia GPU installed,... |
f3ea38b7bc4f4d4adf5eaee435c9e8aa952d9e78f677872dd266bb4663efe897 | Text | 1,327 | 28 | # torch_pgn
Proximity Graph Networks (torch_pgn) is a pytorch toolkit allowing for the modular application of multiple different encoder architectures to cheminformatic tasks centered around protein-ligand complexes. Alpha version of documentation is available at: <url>https://torch-pgn.readthedocs.io/en/latest/index.h... |
6d5709b5fe5a88a542b61d15dc26464c8cc416a2e21be86822618364471b903e | Text | 1,338 | 18 | # DePasquale *et al* eLife 2024
Data and analysis for [DePasquale *et. al* eLife 2024](https://doi.org/10.7554/eLife.84955).
After you clone the repository to your local machine, further steps are needed to run these notebooks. Several Julia libraries are necessary to run the analyses in each notebook. To instantiat... |
4de91e7feaf9ad098863fc344f964e6828675299cadb27835e462f3e54d6174d | Text | 1,343 | 7 | FRASE-bot is a collection of protocols developed in Pipeline Pilot, a data processing software featuring its own programming language (Pilot Script). Pipeline Pilot requires a commercial license from 3DS Biovia (www.3ds.com/products-services/biovia/). Pipeline Pilot is a client-server software; client can be run on a W... |
3ba7f6ccae25acc8521fc3278893b0d69c6eaff9234b4faa9f68d88a9c1eb4ae | Text | 1,350 | 30 | # <p align="center">HIFI: Heterogeneous Spiking Framework<br>with Self-Inhibiting Neurons<br>
This is the official PyTorch implementation for [Biologically inspired heterogeneous learning for accurate, efficient and low-latency neural network](https://doi.org/10.1093/nsr/nwae301).
The paper has been accepted by [**Na... |
f0631f7c86419be339b0b4745783913a951bd08c3fd573a29d6451fd799f9fb6 | Text | 1,359 | 15 | # DRUG-seq toolbox
This is a toolbox for processing raw sequencing output from multiplexed RNA-seq experiments into a digital gene expression matrix that will contain integer counts of the number of transcripts per barcode. It provides a bash script that serves as a wrapper for multiple analysis steps, including demul... |
298245174e3f4a3e337484ee773f17ad7a4e6bbf947a33ba785eba6e947ea9f1 | Text | 1,380 | 53 | # Seizy
:snake: **Seizy** uses a simple thresholding method to easily find :detective: seizures from EEG recordings.
After the seizures are detected, they can be manually verified with a user-friendly GUI. It currently works on recordings stored in [Labchart (.adicht)](https://www.adinstruments.com/products/labchart) f... |
9828928c515af51ce5de5306d2d8820aebfa56a63045f7bce8d729744d8b9bd3 | Text | 1,381 | 29 | # Analysis pipelines for allele specific expression (ASE) in pigs
## 1. Introduction
The utitlities for unbiased allele-specific read mapping, discovery of Parent-of-origin effect (POE) genes and Allele-genotype effect (AGE) genes and exploring the characteristics of allelic patterns in chromatin accessibility and me... |
673807e18dd64b741e207e9ff9b87e35c9a123f3bb471368f1016b5f49ea1462 | Text | 1,387 | 20 | # OxygenDynamics
Optical investigation of oxygen dynamics in the murine cortex
This is a collection of analysis scripts for the detection and analysis of oxygen sinks and surges in the mouse barrel cortex
OxygenDynamics_Wrapper imports and csv file with paths and metadata of data folders that contain motion corrected... |
f29dad7ef5f17c02aaa360280ca1114e3bc5e03ce4cb80edbf18bc8ea530998d | Text | 1,395 | 17 | # ALS PLRNN classification
MATLAB Code and data for Thome et al. (2021), Human Brain Mapping
"Classification of amyotrophic lateral sclerosis by brain volume, connectivity, and network dynamics"
In case of questions or comments, please contact georgia.koppe@zi-mannheim.de or janine.thome@zi-mannheim.de.
Copyright: 2... |
04db9e90039ba55ce6ca11d656704296dbbc83f274a8f3f0086754deaa45b660 | Text | 1,403 | 17 | {\rtf1\ansi\ansicpg1252\cocoartf2761
\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 ArialMT;}
{\colortbl;\red255\green255\blue255;\red0\green0\blue0;\red24\green24\blue24;\red12\green93\blue161;
}
{\*\expandedcolortbl;;\cssrgb\c0\c0\c0;\cssrgb\c12157\c12157\c12157;\cssrgb\c784\c44706\c69412;
}
\paperw11... |
f92ff549fb62a9853f89737b69c8e07178acb1e110a772100774ae695a0538ff | Text | 1,422 | 12 | # Fatecode
Hello, here you can find the codes related to our paper (“Fatecode: Cell fate regulator prediction using classification autoencoder perturbation”). Fatecode focuses on cell fate decision making, which is a fundamental process in the development of organisms. This process involves the regulation of gene expre... |
97d5e1b05b0ae45624c04a7708e9f56af65321ea1f0fb342059e410355940cb8 | Text | 1,427 | 79 | # ImputeHiFI
## ImputeHiFI: an imputation method for single-cell multiplexed DNA FISH data by utilizing single-cell Hi-C and RNA FISH data
ImputeHiFI has three modes to accommodate different data scenarios.
The workflow of ImputeHiFI mode 1.
![Mode 1](./assets/Mode%2... |
3afc1982a9be2702ec1f23abc0335f4a6f30fe274deb9d80977b80ba123e4d5a | Text | 1,440 | 11 | # residuals_spectral_analysis
This repository shares the Matlab code associated with the preprint "Detecting rhythmic spiking through the power spectra of point process model residuals."
This code enables regeneration of all manuscript figures and tables, and the analyses and simulations that inform them. Additional ... |
30b1aeeeb30267aac6b34a94b91a7df089019d961b2c3a0ce9f9d9dcfc9b28df | Text | 1,454 | 64 | **Development Status:** 3 - Alpha. Some features still need to be added and tested.
==========
EDGE OF PY
==========
Package for assessing the distance to criticality in brain dynamics.
Features
--------
- Avalanche criticality measures
- Avalanche detection
- Avalanche distribution plotting
- Power-law ... |
e9b1d8c5b31d3ac2d29d0eb40a9df9709a23b6285f4ee829d9eeb7b0734a5c66 | Text | 1,459 | 38 | ## Autoencoded Vocal Analysis v0.3.1
#### Modeling animal vocalizations with VAEs
<img src="docs/source/logo.png" width="300" align="middle" alt="logo">
See our article for details:
> Goffinet, J., Brudner, S., Mooney, R., & Pearson, J. (2021). Low-dimensional learned feature spaces quantify individual and group dif... |
b72f9d9787f6810c249ad56d4ea052cde6c94a513760961271f08f30a193976e | Text | 1,462 | 42 | ## Direct amplitude-only hologram realized by broken symmetry
### Requirements
Required packages to reproduce the results are as follows:
- numpy==1.22.2
- torch==1.13.0
- opencv-contrib-python==4.6.0.66
- torchvision==0.14.0
- kornia==0.7.0
- tqdm==4.64.1
- imageio==2.26.0
- pandas==1.4.3
Required system to run the... |
845db3f85d8c1e020d67a53a19ed906240c02eee413e72823aa026b7b73a3c59 | Text | 1,477 | 44 | Training and prediction of atomic polar tensors using the e3nn framework implementing E(3) equivariant neural network on top of torch.
Note that the code is working and tested on liquid ambient water (see publication below), but still in beta. It is therefore not optimized and might be subject to change in the future. ... |
d589dae1990b3c976e21a4a0cda6786c9c8aa0cb6ad853a3766db15bbd3dbdc3 | Text | 1,499 | 33 | # Introduction
Discernas: Differential Interpretation of Single-cell RNA-seq Signatures in Human iPSC-derived Neural Differentiation
Single-cell RNA sequencing workflow used at the Erasmus Medical Center, department of Psychiatry in the lab of Steven Kushner and Femke de Vrij.
This repository is linked with github.co... |
b7c2d2800f22bd1bb3f4e19c5daf25d32f2d57b80eeab5fa81f2b4680f3db85c | Text | 1,504 | 25 | # Affine-transformation
Find the affine transformation between two channels in a localization microscopy image
Associated publication:
Please cite
Steen, P.R., Unterauer, E.M., Masullo, L.A. *et al.* The DNA-PAINT palette: a comprehensive performance analysis of fluorescent dyes. *Nat Methods* (2024). https://doi.... |
dbccefe23fc94c403465b50b60e1848afbbb71526dc95531beb1388b2db68686 | Text | 1,511 | 33 | # SMR Neurofeedback Pilot Study - Healthy Subjects Analysis
[](LICENSE.md)
## ENGLISH
## Prerequisites
- Python 3.8 or higher
- pip install colorama matplotlib mne numpy pandas
## User Manual
To function, the data to be analyzed must be in the 'D... |
cd9e45cee7bab505a8dffcfe7734f2ff9d34618b1cffddac90650e1fce51b931 | Text | 1,516 | 18 | # smart home dataset
Dataset for Smart Home Appliances:
1. Unix Timestamp: Represents the Unix timestamp corresponding to each data entry, providing a standardized time format.
2. Transaction ID: Assigns a unique identifier to each transaction or entry in the dataset, ensuring distinction between different observatio... |
47dcddc0a0567b342e3bbf865d21af9b9db0f8c10bfbe6c970598e94a894d1c2 | Text | 1,518 | 25 | # Joint Propagation Model
The Joint propagation model (JPM) is a model developed for deriving a harmonized quantification of tau PET data across different tracers. The JPM estimates equations for mapping regional SUVRs across multiple PET tracers to a harmonized scale named *CenTauRs*. The JPM simultaneously estimates ... |
12389e8ee62018d34b2e75f1f69b809a388bec1758d2a3a04ed9111d68a1c682 | Text | 1,519 | 22 | # FLEX
Code for Cone, Clopath and Shouval 2024 "Learning to Express Reward Prediction Error-like Dopaminergic Activity Requires Plastic Representations of Time"
The code for the main FLEX model is located in \main_model.
"Main_vectorized_simple_dopa.m" includes the main code for the simulations - a running the progra... |
8d3b1f5eb802df058018365b6680e3dbf13a0f388046575c78286b66df8bafbf | Text | 1,524 | 29 | <div align="center">
# Axisymmetric diffusion kurtosis imaging with Rician bias correction: A simulation study
</div>
# Description
Run simulation, data analysis and create figures of "Axisymmetric diffusion kurtosis imaging with Rician bias correction: a simulation study" paper
# Installation
## Clone repository
`... |
0a1137c884f4e8f7a746163250493dd3ee484a3d654c5ca2d069743e94800a26 | Text | 1,527 | 16 | # Winchester_EVENTER
Data and code for:
Winchester, G.†, Steele, O.G.†*, Liu, S., Chagas, A.M., Aziz, W., Penn, A.C. (2024) Reproducible supervised learning-assisted classification of spontaneous synaptic waveforms with Eventer. *Front Neuroinform*. Submitted
† These authors contributed equally to this work and sha... |
6de0893efb0275a5d03156aacb710fe055d0369d439003ec0989dbdd44efb8bc | Text | 1,530 | 8 | # Spike2-Scripts
Spike-Delay (31/07/2020):
This Spike2-script measures the delay between two events in separate channels. To extract events from a recording (waveform channel) the Spike2-software offers several searching mode: peak (maximum detection), through (minimum detection), signal rising through a level and sig... |
5e2fb5c9c9a06f085e7d7bd21b61463b3290a1f7b8e95dafbf5e0bd890dca9a2 | Text | 1,536 | 54 | # toxify
deep learning approach to classify animal toxins
# Installation
1. Get the repository for toxify
```bash
git clone https://github.com/tijeco/toxify.git
```
2. Change into toxify repository
```bash
cd toxify
```
3. Create conda environment with dependencies needed to run toxify
```bash
conda env create -f ... |
6185e4b03b3f991fe696d9a438be0763de9a39a36bc95dc2aa40631b92f65ba4 | Text | 1,550 | 20 | # PLRNN_SSM
#Welcome
This folder contains MATLAB code and data files from
Koppe G, Toutounji H, Kirsch P, Lis S, Durstewitz D. (2019). Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI. PLOS Computational Biology
Copyright:
2019 Georgia Koppe, Dept. of Theor... |
192b5d5a43de8b5198bb8cde6aa38c962534144ab95de11949c8549646d4f660 | Text | 1,558 | 13 | # phaistos/ProCS-15
Version of ProCS-15 with added support for phosphorylated amino acids SER (SEP), THR (TPO) and TYR (PTR) as used in:
Bakker, M. J.; Gaffour A.; Juhas, M.; Zapletal, V.; Stosek, J.; Bratholm, L. A.; Precechtelova Pavlikova, J. Streamlining NMR Chemical Shift Predictions for Intrinsically Disordere... |
a5843aa5c38a3928bd792f5cb3129aeece6efab12a010cc21d817ef47bfde234 | Text | 1,566 | 5 | ## Differential increase of hippocampal subfield volume after socio-affective mental training relates to reductions in diurnal cortisol
The hippocampus forms a central modulator of the HPA-axis, impacting the regulation of stress on brain structure, function, and behavior. In the current study, we assessed whether thr... |
b7b08f1873568f9616ba11f54c42797d1158355f46e2d5740ec846f19da2593d | Text | 1,568 | 56 | # 基于深度学习Pytorch框架的文本分类
## 1、修改配置文件
在config.py文件中对常规参数进行修改。
```python
# data preprocess
data_path = 'dataset'
train_file = 'train.csv'
valid_file = 'valid.csv'
test_file = 'test.csv'
fix_length = 256
batch_size = 64
# data label list
label_list = ['低危', '中危', '高危', '超危']
class_number = len(label_list)
# train details... |
33e720a88f19c557878c1d457c615c0c033fd50c12b00687ac5c2e82e3756b75 | Text | 1,585 | 34 | # Comparing the representation of a simple visual stimulus across the cerebellar network
Analysis code and notebooks for the analysis and figures of the paper "Comparing the representation of a simple visual stimulus across the cerebellar network" (Prat, Petrucco, Štih, Portugues).
## Installation instructions
Downlo... |
dcbd68dedcaa0d760961687eec3cf76b92fe349a9f78918f6d0f581e7b6b3e84 | Text | 1,607 | 48 | ### FlyTracker
#### System requirements:
* OSX 64-bit, Linux 64-bit, or Windows 64-bit
* Matlab R2013b or later (you can try your earlier version but functionality
such as parallel processing may not work)
#### Quick start:
1. Add FlyTracker to your Matlab path by navigating to its dire... |
0b99ac7e169994fbc4d40279751526fd3ccb51ff5912465708fe22b392f23eee | Text | 1,616 | 27 | # omicverse-reproducibility
Reproducibility of results/figures from omicverse paper. **`OmicVerse`** is the fundamental package for multi omics included **bulk ,single cell and spatial RNA-seq** analysis with Python. For more information, please read our paper: [OmicVerse: A single pipeline for exploring the entire tr... |
f642f7fb8d4cccb63ffacbc8b3ba06ec7a91472e6120f3f4f336e390c40b65db | Text | 1,621 | 44 | # DeepIRES
DeepIRES: a hybird deep learning model for indentifying internal ribosome entry site in mRNA
## EXPLANATION
This repository contains four folders: model, dataset, weights, data, and result.
### Model
This folder contains python code files for constructing model.
### Dataset
This folder contains orginal data,... |
5684b554b163e2c0a323038dd4cf8589aea405491987733d81a5c6b8efad7379 | Text | 1,623 | 37 | # Dual-Channel RNN
================================
A Recurrent Neural Network architecture designed to study the effect of mixed synaptic and diffusive signaling in a population of neurons. Released in conjuction with the publication "Adaptive robustness through incoherent signaling mechanisms in a regenerating brain... |
1014ec74f7600c0f36f87a647adb5a036505f0b46257d1d21a146a20d198f222 | Text | 1,624 | 7 | # CLA-Nurr1
This repository contains all the necessary code required to run the Spatial Transcriptomics data analysis for the data in the study "**_Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice_**"
Once the count matrices have bee... |
e9575a2dccaaf59151a76cdc7b3d74c7f2c8d9657fcea04101b8d437b534325d | Text | 1,626 | 37 | # Dental-Loop-Real-time-Facial-Landmark-Tracking-for-Clinical-Research
Dental Loop is a Python-based facial landmark detection application for dental research. It uses computer vision techniques to analyze real-time or stored videos of human faces, extracting measurements from facial landmarks. The application tracks ... |
1289f67d71f4811c68a155f0f0c9fa616c0235420b53b8602cd285e0cc8bad74 | Text | 1,636 | 38 | # rcnn-sat
Code for feedforward and recurrent neural network models used in
the paper [Recurrent neural networks can explain flexible trading of speed and accuracy in biological vision](https://doi.org/10.1371/journal.pcbi.1008215).
The code has been tested with TensorFlow 1.13 and Python 3.6.
## Using the code
The... |
b746bbfd761041962c4e1e0f78687648ad9509ef0cb2f690e00bbeb54c59db51 | Text | 1,638 | 38 | # motionmapperpy : Modified Python 3.0 implementation of [MotionMapper](https://github.com/gordonberman/MotionMapper)
This package is a GPU accelerated implementation of the MotionMapper pipeline for creating low dimensional density maps using tSNE or UMAP. Some methodologies
may differ from the original implementati... |
bca0d679c26153ea310d2d65c686c03dcd72019a4b66fd6bfce300672ffedd02 | Text | 1,642 | 43 | **Please star this repository if you like it :)**
**Feel free to leave feedbacks and ask questions. We want to make the repository helpful for your research.**
**We will keep updating this repository for pretrained models and weights.**
# UKBiobank_deep_pretrain
Pretrained neural networks for UK Biobank brain MRI im... |
510ff26c386d5b78eb22f79e8b3b7cd6c097bd97335de1f2ddfa702864866a1f | Text | 1,655 | 31 | # RST-saliency
This is the source code for our paper in ICCV 2017: 'Saliency Pattern Detection by Ranking Structured Trees'. Lei Zhu, Haibin Ling, Jin Wu, Huiping Deng and Jin Liu.
# Requirements
The project is build on MATLAB and is validated on both Windows 10 and Ubuntu 16.04 with CUDA 8. While in Windows system, v... |
6698fc6556e6710bb7a35b0b0a4158296b69f80a8eb03ecc8ba57f115e1a2995 | Text | 1,655 | 7 | # CLA-Nurr1
This repository contains all the necessary code required to run the Spatial Transcriptomics data analysis for the data in the study "**_Claustrum/dorsal Endopiriform cortex complex cell identity is determined 1 by Nurr1 and regulates hallucinogenic-like states_**"
Once the count matrices have been generate... |
9e0193a24835db4cb7434b188361a7250da14bf6b34974a69611fdcff4cdc746 | Text | 1,660 | 40 | <img src="logo_motum.png" width="250">
This repository serves as the official source for the MOTUM dataset, a sustained effort to make a diverse collection of multi-origin brain tumor MRI scans from multiple centers publicly available, along with corresponding clinical non-imaging data, for research purposes.
### Do... |
248e767042bc8ec4476f17e7c9aeb788d05067ff99a1452fbc9e366e87d99f25 | Text | 1,667 | 42 | # mobility-mapper
- This app allows allows for the scoring of behavioral videos involving mobility (or any other binary behavior).
- The behavior state is stored for each frame of the video to allow for in depth analysis.
- Total time immobile and latency to immobility are calculated in the app, but the raw fame-wise... |
de4b4860cb1c69d659d3d868911a3707bb9055965ebe79cc870faa61617f2c65 | Text | 1,683 | 46 | # ROGUE (Ratio of Global Unshifted Entropy)
## Contents
- [Overview](#overview)
- [Installation Guide](#installation-guide)
- [Tutorial](#tutorial)
- [Reproduction instructions](#Reproduction-instructions)
- [License](./LICENSE)
- [Citation](#citation)
- [Contact](#Contact)
## Overview
Often, it is not even clear wh... |
2e4872fb0c4632b439f08c9e0001db7a39e399bfe2511cbb6cb342616b7b1211 | Text | 1,700 | 25 |
## Dependencies
This code relies on the usual python scientific computing environment and on
one of my other repositories: [general](https://github.com/wj2/general-neural).
Once you have these two repositories on your path and all the additional python
packages downloaded, the code here should work.
## Generating ... |
07dc6c10876e1f6d9353c8162caee17b0714f5b648d69c3be1bbcc8084b0656e | Text | 1,702 | 28 | # Code to Accompany the Journal Article: Estimation of Ground Reaction Forces Using Commercial Wearable Sensors and Deep Learning During Varied Treadmill Running
Setup Anaconda Environment using the accompanying environment.yml file (Python Version: 3.8.12)
When moving this code and accompanying dataset onto your loc... |
ddec56c3d3d8d44cd571d250b3ff0f62e0158c3f73441f76fb8ef77213a0761b | Text | 1,709 | 11 | ## Repository for the manuscript "Characterization of non-monotonic relationships between tumor mutational burden and clinical outcomes", https://www.biorxiv.org/content/10.1101/2024.01.16.575937v1
In cancer research survival analyses are often performed with a simple Cox regression or splitting patients by a single c... |
632431f4b046f6dc9285ace623b33fd8e3b7290b65814f18f8d897803b49d43e | Text | 1,720 | 28 | # Life course investigation of structural neurodevelopment at the individual level
*demo.txt*: Due to data usage regulations, we are unable to upload raw data. However, researchers can obtain access to all the datasets by submitting applications. Here, we provided a simulated dataset to demo the clustering analysis. G... |
f7a45b8d006e9bd7b6222c4101eda7122c45bf539b90d22ca6c78bb86bc3a7e0 | Text | 1,722 | 36 | # Brain Genomics TWAS Web App
Simple web application for parsing TWAS results from [_Hoang, et al._](https://osf.io/xefru) (regional brain volumes in the UK Biobank)
_last code update: Jan 30, 2024_
## How to Run
App was developed using Python version 3.7.2 and [Plotly/Dash](https://dash.plotly.com/)
Tasks to do ... |
b67d3c76b16564a837d400bb1c92547b5a0324d6c923fc3748103cccc482defb | Text | 1,736 | 56 | # app-trekker-roi-tracking
Trekker implements a state-of-the-art tractography algorithm, parallel transport tractography (PTT). This repo wraps Baran Ayodogan's Trekker github repo so that it can be executed on brainlife.io. All credits for this App belongs to Baran Ayodogan <baran.aydogan@aalto.fi>
# How does it wor... |
3a73f1a82fc98fe07e22b89b91498745e2c2d0c0213515800c746eaf67df357c | Text | 1,743 | 29 | # Social Reward Processing Across the Lifespan (SRPAL)
This repository contains the code for managing and processing the imaging data tied to our Social Reward Processing Across the Lifespan (SRPAL) project, which is funded by the National Institute on Aging (R01-AG067011 to David V. Smith).
The data is available on O... |
27596bb63340ed9f46707ae57e930fe45e2221a19db24746f8ce38acd8b49d29 | Text | 1,763 | 41 | # spatiotemporalPRFs
Code repository to reconstruct, fit, and use spatiotemporal pRF models.
This code is used in the following two papers:
* Characteristics of spatiotemporal population receptive fields across human visual streams
by Insub Kim, Eline Kupers, and Kalanit Grill-Spector [add link to paper]
* Rethinkin... |
2d3321dd5fcf85c8e70b480dcd8450c528b61e0db8d4c844f15a80fd9a0df318 | Text | 1,765 | 46 | This repository contains MATLAB code for analyzing calcium imaging data. The program generates ΔF/F per stimulation, averages neural responses from three stimulations per neuron, generates a time series for each neuron, and computes an average time series across all neurons.
# Table of Contents
## Overview
## Features... |
a0ccae515c2e395f6391f8538863ad5b9100bc398b07267a2b96547a29d46312 | Text | 1,769 | 20 | # FICLE (Full Isoform Characterisation from (Targeted) Long-read Experiments)
<img align="left" src="https://github.com/SziKayLeung/FICLE/assets/33493350/c998696c-6820-4b36-950f-603cbe2b93e3" width="400" height="450">
Developed for analysing short-read RNA-Seq data, existing tools for assessing alternative splicing e... |
20efc3040c09616d082b726ba09598c3df95860975938e5bae05f2c647acb44f | Text | 1,772 | 53 | neuroGLM
=========================
Supports flexible regression analyses of trial-based spike train data
using a Generalized Linear Model (GLM). This modeling framework aims
to discover how neural responses encode both external (e.g., sensory,
motor, reward variables) and internal (e.g., spike history, LFP
signals) co... |
eaea52b5009b4d55314ee44927181ade47d43fb31feb77fb8ca53cb7a35c0ab1 | Text | 1,777 | 30 | **Description**
This repository contains a balanced network of inhibitory and excitatory neurons adapted from "Sadeh, Sadra, et al.
"Assessing the role of inhibition in stabilizing neocortical networks requires large-scale perturbation of the
inhibitory population." Journal of Neuroscience 37.49 (2017): 12050-12067.... |
233ca371ca1077b61c4afecd1e6525cc5dccc3574058629d91e44c9fdaf2c0b7 | Text | 1,788 | 14 | [](https://zenodo.org/doi/10.5281/zenodo.11262980)
# InVivoPhotometry
Folder "doric_photometry_analysis" contains the functions for analysis of the recorded photometry signals. We used similar algorithms for calculating the dFF (see Methods), but structured these functions ... |
0cfdff9f84c0733d1571d1c26f9123752bbca29a8cc3a95435ad35d93b1e8408 | Text | 1,793 | 21 | All files used to create the artifacts are in artifact_creation. The files are labeled by their respective artifact type:
createfscvartifactrctype_railtype creates a rail type artifact and saves as a CSC file for processing in plexon, for a clean input CSC file.
createfscvartifactrctype_RCtype creates an RC type arti... |
fe2ef2062fd77ce25595e8df8ccc9e04097d483777b31aa427009973ea58ff5a | Text | 1,820 | 58 | # About
Codes pertaining to the results in our paper *Predictive Modeling of Evoked Intracranial EEG Response to Medial Temporal Lobe Stimulation in Patients with Epilepsy*.
Authors: Gagan Acharya<sup>1</sup>, Kathryn A. Davis<sup>2</sup>, Erfan Nozari<sup>1</sup>
<sup>1</sup> University of California, Riverside \
<... |
677f9d00bfeb1e975157ec59ecd0f32092dd2ac412dc4ae1f3ab26a9fa48209f | Text | 1,836 | 44 | 
# Dinosaur: differentiable dynamics for global atmospheric modeling
Authors: Jamie A. Smith, Dmitrii Kochkov, Peter Norgaard, Janni Yuval, Stephan Hoyer
Dinosaur is a spectral dynamical core for global atmospheric modeling written in
JAX:
- *Dynamics*: Dinosaur solves the shallow water equa... |
dc6408232e5998416c76578c133ec18c1d80d0fb4889ce31f6c96d390045d34b | Text | 1,840 | 54 | # scoreCT
Automated Cell Type Annotation.
Script to automate cell type annotation on scRNA-seq data analyzed with the Scanpy package (https://github.com/theislab/scanpy).
The script uses a reference CSV provided by user with markers associated to curated cell types, which is used to score and assign a cell type to eac... |
8e1f96dfb81e82f45513ea9ebd43d51e4b8bfe67f68c396fb33bfbc179ea3d3d | Text | 1,841 | 50 | # fmri-autoreg
This repo contains the code for the paper [A benchmark of individual auto-regressive models in a massive fMRI dataset](https://doi.org/10.1162/imag_a_00228).
Several deep learning architectures are trained to predict the evolution of BOLD time serie... |
884895d6eacdeb2df6bc194d40942cf132a73b8e488be0da294a1d6cf5a53206 | Text | 1,843 | 53 | # A 3D approach to understanding heterogeneity in early developing autisms
This repository has all the code for the analyses in **Mandelli, V., Severino, I., Eyler, L., Pierce, K., Courchesne, E., & Lombardo, M. V. A 3D approach to understanding heterogeneity in early developing autisms.**
## Requirements
> Python =... |
13c8b4c1b5b8c44029f7569679bc1c4f91348b05e1350560f49295a931beb03c | Text | 1,850 | 55 | # twoPhotonAcquisitionCode
Acquisition Code for two-photon experiments on updated 2P deux
twoPhotonSettings
Function that contains all the constants for a two-photon experiment. Returns the
settings in a struct called settings as well as directory paths dataDir and exptFnDir.
Called at the start of runExpt, the m... |
dea211f1bdfc084acfe20269cbb91ae63e24afbcde5bf1e299721e7ab8f9762f | Text | 1,858 | 49 | Lavaburst
=========
Chromatin domains bursting with flavor!
Let's get started! See `IPython
Notebook <http://nbviewer.ipython.org/github/nezar-compbio/lavaburst/blob/master/example/example.ipynb>`__.
Optimal domain segmentation
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Produce the highest scoring domain segmentation according to... |
37e14558f53df6140f5186ff514928a16ac0000bbefa5d216ff475c6ce7cc2fd | Text | 1,860 | 67 | # RNAlogo
A biological sequence logo generator in SVG format, for the usage as a header-only library for cpp programs.
The alphabets are given as any kinds of Unicode strings, such as "Ψ" (Greek) or "AU" (two characters).
## Download & Run sample code
```bash
$ git clone htpps://github.com/iyak/RNAlogo.git
$ cd RNAl... |
12490960276ea71184d19b533f8f872025dc4744cd3823a516fa7ca52b46c61e | Text | 1,879 | 24 | [](https://doi.org/10.5281/zenodo.17990782)
# Boeken Tau aggregate interactome
This repository contains the analysis code associated with the tau aggregate interactome proteomics and single-molecule characterisation project, led by Dorothea Böken. This manuscript has bee... |
734cd090c451c7614dc93b4cc90838b616d988e449153177f21994c77861262d | Text | 1,911 | 68 | NosaAnalysis
------------------
The NosaAnalysis package is specifically designed to provide the results of the [NOSA software tool](https://github.com/DavideR2020/NOSA) as R objects.
Various analysis methods for the (paired) input data are provided.
NOSA analysis should be used with care. It will not check every use... |
429e79d1ede36310a3528c9141626942d9591b4f673af78c0fe3de3ca75edb5a | Text | 1,914 | 24 | ## About this repository
This repository has MATLAB scripts that will produce plots for our Cheng's Task 2C CA1 neuroscience paper titled ***"Distinct neural mechanisms for heading retrieval and context recognition in the hippocampus during spatial reorientation"***. Other repos referenced in the paper will produce th... |
779fee03da5cdedd1de724e244fcef745cc445758368a66198e0b7ee76e777ad | Text | 1,918 | 43 | NOL_cerebellum
==============================
No Evidence for Semantic Prediction Deficits in Individuals with Cerebellar Degeneration.
Maedbh King, Sienna Bruinsma, Richard Ivry (2022).
Project Organization
------------
├── LICENSE
├── Makefile <- Makefile with commands like `make data` or `make ... |
c01b7a1fbc49b48d3798a44d92809f253223977f778eb4bd236bbe25e3982f0a | Text | 1,929 | 27 | Subject: Data for 3D RCAN Paper
Release date: xx-xx-2021 (MM-DD-YYYY)
Contacts: Jiji Chen (jiji.chen@nih.gov), Hari Shroff (hari.shroff@nih.gov)
Organization: Advanced Imaging and Microscopy (AIM) Resource, National Institutes of Health
This data release contains all training and testing data for the 3D RCAN pa... |
447772232a5e7d03fb030453f630a7ed1bb62bbd18f59e771b4bf66bfb873651 | Text | 1,930 | 26 | # Zebrafish_SCI_Atlas Codes
This repository contains all the codes that are used in the manuscript titled "Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair" by Saraswathy VM et al. 2024. The instructions to run each code is provide inside the respective folders. A... |
1b900a15042b8e7d82235e1af7c1f19d99aafdafc349c1cbab085562c230dcd9 | Text | 1,931 | 27 | # Splam
This repository hosts data and scripts for the Splam project as follows:
* `model/`: Contains the trained Splam model files:
- `splam_cpu.pt`: CPU-optimized model.
- `splam.pt`: the original model that requires the original model script to load and run.
- `splam_script.pt`: the Torchscripted Splam model... |
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