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539ffdb9db4f0e227773fd8c505dbb1e07ae9930fc72bb8444b5824ac12bd462 | Text | 333 | 2 | # Development_ConnectomeGradient
This repository provides core code and relevant toolboxes for data analysis in the article entitled "Development of Sensorimotor-Visual Connectome Gradient at Birth Predicts Cognitive Outcomes at 2 Years of Age" by Xia et al. 2023. Please check the paper for the latest description of da... |
d4012b41d5ae42095d935defe69d51f29032bd86f7c875b2fe7b51198bb0f894 | Text | 335 | 8 | trinityrnaseq
=============
Trinity RNA-Seq de novo transcriptome assembly see the Trinity [wiki](https://github.com/trinityrnaseq/trinityrnaseq/wiki)
## Contributing
We encourage you to contribute to Trinity! Please check out the [Contributing](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Contributing) for t... |
2459718da0a13be460eeb99db13df210843350c43aca26302dc02b04f9effd0f | Text | 338 | 11 | This folder contains the EEG and MRI raw data related to the paper
*"Alpha-frequency feedback to early visual cortex orchestrates coherent naturalistic vision"*
by Lixiang Chen, Radoslaw Martin Cichy, and Daniel Kaiser
### EEG data
EEG raw data are found in */eeg_data/*.
### MRI data
MRI raw data are foun... |
f77ca4c907f71ca9258f040ee5ecef7a1a3b87c9e0e97a654db2a36b68a31ca6 | Text | 343 | 11 | # Fiber Photometry Data Processing Scripts
## Python Scripts
`input_to_extract.py`
Try it out: [Jupyter Notebook](https://colab.research.google.com/drive/1KvO_jYotG1x_XblHG85TF8xfqD0f-WQ2?usp=sharing)
Usage: Modify the `tankdir`, `blockname`, and `filenames` variables in the script and then run
```{bash}
$ python3 i... |
2bb9363795a277a51d14a35c442818cbb699ab9cf1bd150ca2551f82fe058a85 | Text | 346 | 7 | # FusionGAN
## Codes for FusionGAN, a GAN model for infrared and visible image fusion
### Please refer to our following paper for algorithm details:
> Jiayi Ma, Wei Yu, Pengwei Liang, Chang Li, and Junjun Jiang. "FusionGAN: A generative adversarial network for infrared and visible image fusion", Information Fusion,... |
1777365229352b7f6180004eb2dd5dffe911c174b020883c131641bd1b598603 | Text | 347 | 10 | # physio_benchmark
This repo contain notbooks to reproducde figures of the paper
"A unifying method to study Respiratory Sinus Arrhythmia dynamics implemented in a new toolbox"
Authors : Valentin Ghibaudo, Jules Granget, Matthias Dereli, Nathalie Buonviso, Samuel Garcia
The dataset can be downloaded from https://z... |
880599d5c75be17d0ff35954543c42c1be80c2b844f82ecafdf98146442b476e | Text | 349 | 19 | # PTIC
PTIC tool for texts classification, uses following statistical model:
* point-wise mutual information for word and a class
* tf-idf (term frequency-inverse document frequency) for word in a text
## Installation
### From PyPi
```bash
pip install ptic
```
### From source
```bash
pip install git+https://githu... |
8bc4b16166626988692c2e8331d5217c6ebd325a25cb73a47d1646f81c6d6b9b | Text | 368 | 7 | # micro_ecog_phoneme_decoding
[](https://zenodo.org/badge/latestdoi/680109211)
The folders contain necessary m-files to process micro-ecog recordings and decode speech features.
Obtain data files from corresponding authors to run the decoder files.
Refer phonemeDecoder.m ... |
03a666816178a07a02f6e5d97d5c5f5508544e4abbf85ba0e9a8b6d4bb8934b9 | Text | 381 | 8 | # Assembly Spectrograms and MFCC
Autor: Carlos Alberto Hernández Nava
The database used for this work is ASVspoof 2017 V2, available at: https://datashare.ed.ac.uk/handle/10283/3055
The database used is under Creative Commons Attribution-NonCommercial License (CC-BY-NC).
This repository has a folder called ASV... |
f737239d4a81c653e42e3de4e9b6dccf69545b0acf23afae3f43e7dadfa24208 | Text | 398 | 5 | - code_and_metadata.zip contains all the source code used to analyse the data and generate the figures
- high-resolution_videos.zip contains the videos used for the DeepLabCut / BSOiD analysis in Jones et al.
- The jones2023_db_files.zip archive contains the raw ethoscope data used in the same paper. Due to the overall... |
15309df446ea6e63f8022c5e9b49929bd4ccdb522134c5152037a0d1f4e1a40f | Text | 407 | 4 | To plot FigS8 panels run FigS8
Data was obtained from fig 8 for GLs L and R. For the other maze sections data was calculated running Fig_Bootstrapping_summary_Delay.m Fig_Bootstrapping_summary_Goalc.m
and Fig_Bootstrapping_summary_ITI.m. 'Scr' or 'KD' option should be selected before running those scripts for contro... |
1642979c34e90776aace517abd5a7b79cf77dc401f6ee971cbd40b70772676f6 | Text | 433 | 5 | To plot panels of Fig.6 "TRPC4 supports persistent activity of spatial cells when animals stay in a place for an extended duration".
1) Open Zenodo_Fig6_main.m
2) Run PlaceCellAna by uncommenting the corresponding line.
3) Run PlotBinFirRateFig7 by uncommenting the corresponding line. This plots Fig. 6A and prepa... |
ee600ca0a0b9d5a2c60d7f883065c4e0e558f9d3c03e9be848e41850a040e4d5 | Text | 442 | 12 | # fmriprep2BV
Simple script to convert preprocessed functional files from fmriPrep to BrainVoyager.
This MATLAB script is based on Neuroelf functions (https://neuroelf.net/).
## Requirements
- Have Neuroelf installed and in MATLAB's path.
- One or more functional .nii.gz from fmriPrep (example provided)
- Protocol ... |
a9a58ec8658858c2e8f633810a868907ede82a67cc46cce316f0da9e31057fdb | Text | 456 | 3 | 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 University.
The proof of concept (POC) for epileptic seizure detection in long term EEG signal is tested on Android platfo... |
0f274990f79d155111f8edcc12917051489e5cb842e575542470dca1d0f8e0e6 | Text | 460 | 8 | # OfflineEnsembles
Detecting offline synchronous neuronal ensembles in two-photon calcium imaging data.
Companion code for:
Chang, H., Esteves, I. M., Neumann, A. R., Mohajerani, M. H., McNaughton, B. L. (2022), Cortical Reactivation of Non-Spatial and Spatial Memory Representations Coordinate with Hippocampus to For... |
449da68f7a20ad725be291cded63141a5e2e14c3687fdab228452b9f9360ec56 | Text | 460 | 10 | # CHA_Cross-Movie_Prediction
## Overview
This repository contains open data for analyses in the manuscript by Guo Jiahui, Ma Feilong, Samuel A. Nastase, James V. Haxby, & M. Ida Gobbini (2022). https://doi.org/10.1101/2022.11.21.517253
The open data can be downloaded from the Release of the repository: https://githu... |
43be592c5f09c46d5018f0e8088cfa82645059ccb3316dd9888d780b2ae3b7f4 | Text | 463 | 2 | # lagonet
LagoNet is a simple Convolutional Neural Network with 3 layers, designed to distinguish individuals with lagophthalmos from those who do not. It runs with an 80:10:10 split between training, validation, and testing sets. The 1,008 total input facial images were 256x256 RGB photos. The model expects the images... |
eae74187f5085d306c903c5e9b23c5b147cfb8d2e0ba24f5199dd54ab1d6c010 | Text | 465 | 17 | # PairsDB.jl
Access package for UsreyLab RGC-LGN paired recordings database. See below for helpful links.
## Install
Launch Julia and then:
```julia
using Pkg
Pkg.add(PackageSpec(url="https://github.com/scottiealexander/PairsDB.jl.git"))
```
## See also:
* [RelayGLM.jl](https://github.com/scottiealexander/RelayGLM... |
0d30876a555fad7ed7f673a57a03035da71a6bb14bdb826894cd97260b86fd14 | Text | 466 | 2 | # Dynamic FDG PET clustering
This repository holds the codes and some additional info from paper "Segmentation of dynamic total-body [<sup>18</sup>F]-FDG PET images using unsupervised clustering". Files Jaccard30.csv and ProcessingTimes30.csv include the Jaccard indices and running times of the tested methods for all 3... |
116b239e9d7872a07a5c3100a3af60787175f9d7a5f9ee3d4025403ebec5a9ff | Text | 485 | 17 | Contact info: jens.schwamborn@uni.lu or isabel.rosety@uni.lu
Please cite: https://www.nature.com/articles/s41531-023-00616-8
Complete dataset can be found here: https://doi.org/10.17881/xfh3-a153
Data processing and plotting:
- Figure 1B - GCase activity
- Figure 4A - DA ELISA
- Figure 5A - DA genes
- Figure 5G -... |
3ee1d1b2639c19afbcb51ba11f476ffa2fa965cdc3d1fc1ff20cb16a910be03b | Text | 493 | 6 | # Pairwise Ratio of Gaussians
MATLAB Toolbox and code to reproduce the results in our paper, Modeling the Diverse Effects of Divisive Normalization on Noise Correlations.
**bioRxiv Link** [](https://doi.org/10.110... |
ed85c0a409b7a68224954d35209c4935ea8dd609e5213cde44a6433c5a162af5 | Text | 493 | 3 | # Survival_Analysis_Kidney_Cancer
The purpose of this research is to determine whether or not a CT scan can accurately predict a patient's chance of survival after a diagnosis of kidney cancer.
This study utilizes two deep learning networks, one for extracting features from images and another for predicting how long an... |
4c6acd0916a2ff8b31d9c31542f3c05fa002a70448f421b4701baea7207a3bbc | Text | 496 | 9 | # IDSL.GOA
# Gene Ontology Analysis for Metabolomics
Input is a list of InChiKeys separated by semi-colons.
```
metabolites_to_go_inchikey(iklist = "AADLTHQNYQJHQV-SVLGDMRNSA-N;ABVVZYXTZLEOHP-CMDGGOBGSA-O;AEUCYCQYAUFAKH-YEUCEMRASA-N;AFSHUZFNMVJNKX-CLFAGFIQSA-N;AFWBWPCXSWUCLB-WDSKDSINSA-N;AWUCVROLDVIAJX-VKHMYHEASA-N;... |
4cb84512aac8848899ee0881f2d0d360d3f78cf651220195996a0e06634a893a | Text | 496 | 5 | The image data and the ROIs (if necessary) in each folder follow a figure or table or graph, mentioned with the name of the folder.
These are unmodified data, meaning the auto-white balance macro has not been applied to them
neither any: zoom-in, rotation, contrast modification, stitching, z-projection, kept-stack, ... |
3ff6fe254e9456d488c80dced13e3f409bc732601b84a6576ed5d251655a0206 | Text | 507 | 4 | # Decision making in dynamic, continuously evolving environments
EEG and behavioural analysis code for "Decision-making in dynamic, continuously evolving environments: quantifying the flexibility of human choice", Ruesseler et al., bioRxiv preprint 2022
This repository is currently under construction. An online resour... |
4aa21f62c937cdde3639a39719c72685c243f3274ff20d1ffb77a18bcb487087 | Text | 509 | 13 | # RegisterStack
Affine registration of 3D image stacks with manually selected control
points in [Matlab].
`RegisterStack` is an interactive tool that loads a pair of image stacks,
helps with manual control point selection and displays affine transformation
results.
It requires [`TIFFStack`] to load TIFF files. Inte... |
57273f827e3b745b4c2bcb97f69260a14c99b3bd807f9f22c74241959530d262 | Text | 515 | 8 | # YH_NK01_APOE4_HMGB1_paper
Huang lab Nicole snRNA-seq analysis for APOE4/HMGB1 paper
**Huang lab members:** Yadong Huang, Nicole Koutsodendris
**Bioinformatics core members:** Reuben Thomas, Michela Traglia, Ayushi Agrawal
**Type of expreiment:** Single-nucleus RNA sequencing on isolated hippocampi from 9.5-month... |
4e523dd00e93157de967e2554290a15078a9ab15d6be5aacbb554b166dbea86d | Text | 516 | 5 | # PARENT
Cite this work by Shah, S. T. H., Shah, S. A. H., Qureshi, S. A., Di Terlizzi, A., & Deriu, M. A. (2023). Automated facial characterization and image retrieval by convolutional neural networks. Frontiers in Artificial Intelligence, 6, 1230383, doihttps://doi.org/10.3389/frai.2023.1230383.
The PARENT proj... |
46d61ee33877ca544adcdb488f1f3aa194f1eadeaf8193f16b99ab58bcc77ff3 | Text | 529 | 15 | # CCInx
Build predicted cell-cell interaction networks from single-cell data.
Uses the [Bader lab ligand-receptor database](http://baderlab.org/CellCellInteractions) (DOI:[10.5281/zenodo.7589953](https://doi.org/10.5281/zenodo.7589953)) generated by Ruth Isserlin.
## Installation
```r
devtools::install_github("BaderLa... |
8e4c11c2795febd5ae38f8dc03a59ae024c1b83707e276467595d44096d97311 | Text | 529 | 8 | # RNA-seq of GR manipulation in A549 cells
This repository contains the RNA-seq processing and differential expression analysis for the paper
Gazorpak*, Hugentobler* et al., "Harnessing PROTAC technology to combat stress hormone receptor activation".
The expression data can be obtained as a SummarizedExperiment [her... |
a9c1c209b6b9a3c5b963054af3b0df451a2914ee4203aa4efd1b2ef06f98e33d | Text | 535 | 10 | #readme
Each directory is a MERFISH sample.
countsPerCellExactIn.csv: number of mRNA counts exact in each cell
countsPerCellCorrectedIn.csv: number of mRNA counts in each cell
featureNames.csv: the names of all cells
geneNames.csv: the gene names include in the MERFISH library
feature_metadata.csv: metadata of all ce... |
b70214ce08054a650bbcc122e4181f1db2cd047e105fe4f92ec4778006578007 | Text | 535 | 10 | # nmo-bibliometric-analysis
Back-end API for Bibliometric Analysis of NMO Describing, Citing and Using Literature. </br></br>
#Build and run the container: </br>
docker-compose up -d --build </br></br>
#Connect backend to network: </br>
docker network connect nmo_network nmo_bibliometric_analysis_web_1 </br></br>
#co... |
d33586a3e4d1ec58b9226f791dda98590a7c0b958a00afd2c5cdf8db3e7f637e | Text | 535 | 7 | This code is for the model in "Latent Representations in Hippocampal Network Model Co-Evolve with Behavioral Exploration of Task Structure".
"plateau_splitters_code.m" includes the main code for the simulations - a running the program will run a demo simulation and plot relevant figures afterwards. Comments are includ... |
13b29a33ccf209e547f369430ca05f9cb35b3bfcb40fe5b76ee3e5b4a0c8bd9d | Text | 538 | 6 | # Neural Network Sound Discrimination Models
In this repository, we explore simple neural networks to model behavioral performance of mice in a sound discrimination task.
The models are defined in `models.py` and explored in the `fresh_analysis.ipynb` notebook.
The results of this analysis are published in: Christian... |
e063fbd2b40a8886ec72a39645c0d13f2ae2f77a7d0edf8d7a38cbf771ddae9c | Text | 542 | 8 | # JEDI-1P_Widefield_Figures_data_scripts
This repository contains data and scripts used to generate figures (Fig 3-6, Supplementary Fig 8-12) related to in vivo widefield imaging in manuscript: detecting rapid pan-cortical voltage dynamics in vivo under widefield one-photon imaging with a brighter and faster voltage in... |
2ee6db0e55c15ad62da5ec2a5d2c4f2b8bae58732e63a696680cc75ec34dd1b5 | Text | 543 | 7 | # Cellograph
Cellograph is a graph neural network model that uses a two-layer graph convolutional network to analyze single-cell RNA sequencing data (but can extended to other single-cell modalities). You can read more about it in our preprint on bioRxiv: [Shahir et al, 2023](https://www.biorxiv.org/content/10.1101/20... |
35be4c7f6731e645c078d0c70e4f46f1f210b07064c4b01f259b50f6eef41b9c | Text | 554 | 18 | # Module: Topological Neuron Synthesis
# --------------------------------------------
# Generation of artificial neuronal trees
# based on the topology of biological cells
# and their statistical properties
# --------------------------------------------
# Instalation instructions
--------------------------------
```... |
5426425c7e0d5b043259d4c0d1679be892436164ad216ca1d12760df51c9a4a8 | Text | 555 | 20 | # Neural substrates of parallel devaluation-sensitive and devaluation-insensitive Pavlovian learning in humans
The repository contains all scripts needed to reproduce the results reported in the above study.
# Data
the fMRI dataset can be found here: https://doi.org/10.26037/yareta:dyhmmxkwkfbwvaq4yotxziszva
# Code... |
8ecbddeb98f923425acb66cf99cbb90d9545324f2bbff53182badcfa1eda1997 | Text | 555 | 8 | This repository codes used for data analysis in the manuscript: “Neuronal sensorimotor integration guiding salt concentration navigation in Caenorhabditis elegans” by Ayaka Matsumoto, Yu Toyoshima, Chenqi Zhang, Akihiro Isozaki, Keisuke Goda and Yuichi Iino.
All codes are written in Matlab (MathWorks).
- Figure_... |
03cd1888b365140e8306d9ba54718c07e9c7afdbb23286475f4a573f639a2b41 | Text | 560 | 11 | This code requires Pytorch, Pandas, Numpy library installed.
To run the code set the following input arguments:
--trainingset_list <a file containing the list of sites downloaded from MetalPDB>
--trainingset_dir <the path of the directory contanining the sites downloaded from MetalPDB>
--to_predict_list <a file contai... |
d4239fa8b988c6abdb058d98547eaab773bd296f21e3405524d2da98b7559c2a | Text | 578 | 7 | # sam
Code for paper Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing.
Read the paper [here](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03162-x). Paper by Kavi Gupta, Chenxi Yang, Kayla McCue, Osbert Bastani, Phillip A Sharp, Christopher B Burge... |
c58ca775855569a50704f0bd9079798315ef4fbfb4ffc2bdca384b8b88e0c20f | Text | 593 | 10 | This dataset contains the raw electrogastrography (EGG) signals that were used in our research paper, titled 'Quantifying the Effects of Vagus Nerve Stimulation on Gastric Myoelectric Activity in Ferrets Using an Interpretable Machine Learning Approach.'
Data Structure:
The data is organized in the following hierarchy... |
258e441294b213c9ba519202d18295c27a9a4c2280b0b4ba589b4b133c585b6e | Text | 594 | 16 | # PONDR AI QC
This repository contains the quality control of the raw T1W images from a collection of
public datasets, totaling approximately 40,000.
Images are rated on a 6 point scale, with 1 being good and 6 being bad.
Manuela Costantino performed the manual quality control rating on 10-slice stacks of
Axial, Cor... |
5134a67972b8ef3071b540eaaba7ebaa9c87b9d024183d7f5bbeca3b27d520b1 | Text | 611 | 10 | [](https://zenodo.org/badge/latestdoi/686073472)
# YH_NK01_APOE4_HMGB1_paper
Huang lab Nicole snRNA-seq analysis for APOE4/HMGB1 paper
**Huang lab members:** Yadong Huang, Nicole Koutsodendris
**Bioinformatics core members:** Reuben Thomas, Michela Traglia, Ayushi Agraw... |
cf2339b3583ced30b4afb50b056dbbb630fb370a09deb4b0eee0d6a64b724cff | Text | 612 | 11 | # YH_NM01_NatureNeuroscience_paper
Huang lab Maxine's snRNA-seq analysis for Nature Neuroscience paper
**Huang lab members:** Yadong Huang, Maxine Nelson
**Bioinformatics core members:** Reuben Thomas, Michela Traglia, Ayushi Agrawal
**Type of expreiment:** To study how the APOE-R136S (Christchurch) mutation might... |
fd93c0333f846b886e224305077d5079234fdf3a7a5ec338d6f4701fb224617a | Text | 612 | 10 | # HeterACh-STDP
Repository for study: Acetylcholine facilitates localized synaptic potentiation and location specific feature binding
You need Python 3.7 (or above) to run the scripts.
This directory consists of:
* Neuro2Nets.py: a Python code containing the methods and the class to run and analyze the simulations
*... |
a151a72dd1d150b82a3796981943a80ef58db24a79f5fbccea8c683cd1ffe27a | Text | 615 | 18 | # LeGUI
Fast, easy-to-use intracranial electrode localization software built entirely in MATLAB with core image processing performed using SPM12 and support for Windows, Mac, and Linux platforms
Latest release:
https://github.com/Rolston-Lab/LeGUI/releases/latest#user-content-downloads
Installation guide:
ht... |
a7b97b5d11a4d12f6d03dab14f7ea882130c7a27e5af2c188932f18a24be4f75 | Text | 616 | 26 | # WESAD Processed Dataset
## Processing
- Total windows: 86,583
- Stress windows: 9,966 (11.5%)
- Non-stress windows: 76,617 (88.5%)
- Subjects processed: 15
## Files
1. **features.csv** - Hand-crafted features (16 features + subject_id + label)
2. **labels.npy** - Binary labels
3. **subjects.npy** - S... |
b90d840b86e9c6d43a0ba40b6c9286ee3b1ced1240a071adb4b2c600e097e40f | Text | 620 | 12 | # ThomasYangEtAL2023NC
MATLAB code related to Thomas and Yang et al, 2023, Nat Communications (in press).
This repository contains the code for figures in Thomas and Yang et al., 2023 'Superior colliculus cell types bidirectionally modulate choice activity in frontal cortex'.
Before running code, make sure:
1) dow... |
d34e7667439be5fa2e7bcf70b4b952fb35a110c9ea846279ba22db641e6918a4 | Text | 625 | 13 | # OfflineEnsembles
[](https://zenodo.org/doi/10.5281/zenodo.10030861)
Detecting offline synchronous neuronal ensembles in two-photon calcium imaging data.
Companion code for:
Chang, H., Esteves, I. M., Neumann, A. R., Mohajerani, M. H., McNaughton, B. L. (2023), Corti... |
69ddda379937d8f67f5d57c291fdf7ea2fdc0fc491955b3952bbfc10957e8922 | Text | 626 | 5 | # Population analysis
Here we present the code related to the manuscript
"Dynamics and maintainance of categorical responses in primary auditory cortex during task-engagement"
The script 'tutorial_run.m' shows how to perform the population analysis (both classifiers and linear regression) using chronic recordings from... |
39804b05eced5ce1acbcee0b8e92f7c87e2d0acc57d4b30d63afa81037e35f16 | Text | 640 | 3 | # Image data analysis of zebrafish avatars
This repository is related to the manuscript "Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma", by Lise Finotto, Basiel Cole, Wolfgang Giese, Elisabeth Baumann, Annelies Claeys, Maxime Vanmechelen, Brecht Decraene, Marleen ... |
be012e99fbc9cb4b711372082e306b77fe3d1a5e79d8997700f71d470a9080f5 | Text | 644 | 20 | # Time-To-Contact project
**Authors:** Ignacio Polti ¤, Matthias Nau ¤, Raphael Kaplan, Virginie Van Wassenhove, Christian F. Doeller
¤ shared first-authors
## Folder Structure
`/Raw_fMRI_data`: raw human fMRI dataset
. . . |--`/sub-0xx`: individual subject *0xx* folder.
. . . . . . |--`/anat`: anatomy imaging dat... |
8284034a85ab4b5f106e5e1b96d82ef843c3a65004a40dc51f81763401f57e1e | Text | 647 | 6 | # ethoscopeCodes_eLife
Custom scripts to compute sleep from raw ethoscope data.
There are three files in this repository. The first script, the Yoked_notebook_LD_10sec_bins_NEW.Rmd file is required to convert raw ethoscope files to RDS files for downstream processing. The second script (CreateSleepDataFilesFromRawEtho... |
c3af010803a2c178255ba3b049c05d9968e5d790601987f0d44124a3a11cf888 | Text | 650 | 17 | # Examples for [BrainPy](https://github.com/brainpy/BrainPy) computation
Examples needs ``brainpy>=2.3.0``.
### Recent activities
- 2023/10/06, [Discrete Hopfield Network](./attractors/discrete_hopfiled_network.ipynb)
- 2023/10/06, [Discrete Hopfield Network Demo for Image Reconstruction](./attractors/discrete_ho... |
aabd61eb201e03dbc3a5ffd7d532ffde208afc111006af8cf83825b9ba2c7e3b | Text | 654 | 10 | # Neuron_Aligner
Given a list of publicly available morphologies whose soma location resides in an anatomical area of interest, Neuron Aligner finds a target neuron that is the most morphologically similar to a source neuron that has been pre-selected by a user.
![Schematic Overview](figures/Figure_3_SBA_plots_updated... |
7374c5d17ab219ea09a98f96304cfeed2e7f55b31459e9c47abef23bc2496af3 | Text | 662 | 9 | # ICH_Biomarkers_Meta_Analysis
This repository contains a walkthrough of the meta-analysis performed for our systematic review determining the association between circulating inflammatory biomarkers and outcome following intracerebral haemorrhage.
You will find the code in the Output/WBC.rmd file and the filtering str... |
3555483514f5959f5e5857164170c58d0909196b6293d7766d0d054f20c44a5c | Text | 666 | 14 | # Master-of-metals
Tool for the prediction of metal binding sites in protein structures
This code requires Pytorch, Pandas, Numpy libraries installed.
To run the code set the following input arguments:
* --trainingset_list "a file containing the list of sites downloaded from MetalPDB"
* --trainingset_dir "the path... |
daf2f77ac0d759098dd9623a58ad2e65162e6fde040fcd5b7dcd9faee124c6d8 | Text | 670 | 15 | # Rate map quantification
Code used to generate, and quantify the accuracy of, two-dimensional firing rate maps.
Used for the publication "Estimating neuronal firing density: a quantitative analysis of firing rate map algorithms"
## figures
Code used to generate the main figures for the publication and carry out s... |
453fc85d41e68153e952768b6edeeb555c28753e84ae20645dbc0c8f1a374472 | Text | 674 | 18 | Part of the accompanying code repository to the "Hierarchical temporal prediction captures motion processing along the visual pathway" paper. This repo contains the code for the modified hierarchical temporal prediction model and the slowness and sparse autoencoder control models.
## Installation
```bash
conda env cre... |
3bbce72dedd13cff0b3be38bb8e952559ff91bd452931b210581365062ed965f | Text | 682 | 14 | # Citation
This ReadMe is for the following commentary paper:
Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, Kristen R. Maynard. "Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single cell RNA-sequencing d... |
a91c481f9773f7f8bed471bb29f1541a191f06a290171b2538fb4e40c994bbe6 | Text | 687 | 17 | # SSNNMM
Scripts for our single-step NN-MM paper. Julia version 1.8.2 was used.
Below is the description of each folder:
| Folder name | Description |
| ----------- | ----------- |
| data | data and scripts to simulate phenotypes |
| analysis | scripts to run SSNNMM and conventional single-step |
... |
acd46ab38e19b16558503b19f82a24b16b413d27119bbfb4467af0b6d17f7664 | Text | 691 | 15 | # Asymmetric Student-t model for neuropil decontamination
This repository provides an experimental algorithm to remove neuropil signal in
calcium signal acquired with 2-photon imaging.
To get started, just download or `git clone` this repository and add the `src`
folder to your MATLAB path.
Decontamination is done b... |
082076b82281cb1341c86e50390c4f0c99ab28ce92f4344318e33cb75b35a138 | Text | 692 | 14 | # Quantifying evaluation leakage in motor imagery decoding
Code for the manuscript of the same title (Chadha, submitted to J. Neural Eng.).
Setup: `python -m pip install -r requirements.txt`
- `run_pipeline.py --ptp 400` — main pipeline (Tables 3–5, Figures 2–10)
- `check_leakage.py` — synthetic leakage experiment (... |
f2ae0ca65c138138da519fb4254b65b7ab2bbefc34b9c34686315292f5d3e4e9 | Text | 696 | 7 | # ICMSconnectivity
Analysis code for "Microstimulation of human somatosensory cortex evokes task-dependent, spatially patterned responses in motor cortex"
Published in Nature Communications, 2023
Natalya D. Shelchkova*, John E. Downey*, Charles M. Greenspon*, Elizaveta V. Okorokova, Anton R. Sobinov, Ceci Verbaarschot... |
67bd6f8b6e4d8c0b05b319f4d239c726240935e4af224156913364434e57120e | Text | 701 | 6 | # WMH distribution memory clinic
This repository contains code to replicate our work related to the distribution of White Matter Hyperintensities (WMH) of presumed vascular origin in memory clinic cohorts.
## Spatial distributions of white matter hyperintensities on brain MRI: a pooled analysis of individual partici... |
ebea8602e3dcb5f6e945799c1d7da200afc67cd97c33a55137da081fa49965b9 | Text | 708 | 13 | [](https://zenodo.org/badge/latestdoi/694891486)
# YH_NM01_NatureNeuroscience_paper
Huang lab Maxine's snRNA-seq analysis for Nature Neuroscience paper
**Huang lab members:** Yadong Huang, Maxine Nelson
**Bioinformatics core members:** Reuben Thomas, Michela Traglia, Ay... |
7a48c6e5a4812676ade8072d7c34b509c69ffdd07653b42c1c8df02dfae98cb8 | Text | 713 | 8 | # Brain control of bimanual movement enabled by recurrent neural networks
# Overview
This repo is associated with this [paper](https://www.nature.com/articles/s41598-024-51617-3) and [dataset](https://doi.org/... |
a9a305b5bafdc0a2e1b6a8c671a8b45b217f7a6fbf68869b4d88251a095f8fd4 | Text | 715 | 9 | ## Welcome to the PM 2.5 Correction MLP Network Repository!
This repository houses a Multilayer Perceptron (MLP) network designed to correct PM 2.5 data. The dataset used in this project is available for access via Zenodo at the following DOI: https://doi.org/10.5281/zenodo.10037781.
For detailed insights into the da... |
fdf9c425cf9c13571d354cf8bd028e7ad11aaeecbf15439e372d83a5fec45a68 | Text | 726 | 7 | # ICMSconnectivity
Analysis code for "Microstimulation of human somatosensory cortex evokes task-dependent, spatially patterned responses in motor cortex"
Published in Nature Communications, 2023
Natalya D. Shelchkova*, John E. Downey*, Charles M. Greenspon*, Elizaveta V. Okorokova, Anton R. Sobinov, Ceci Verbaarschot... |
270033fc225fadda3729d10c01843cc7504a5f4643acbb47fe0adc4fbf27bfc2 | Text | 734 | 43 | # SOMTimeS: Self-Organizing Maps for TIME Series
## Other relevant papers
If you use this code please cite SOMTimeS paper.
@misc{javed2021somtimes,
title={SOMTimeS: Self Organizing Maps for Time Series Clustering and its Application to Serious Illness Conversations},
author={Ali Javed and Donna M. Rizz... |
7a99e670bd5f40b685d6ad8c3a4d4309c0acb69ceb7a825c7a85dae61ce6b8cd | Text | 736 | 27 | ## The project devotes to predict the DNA Bendability
### 0 DataSet Loc
```
cd ./Data
```
### 1 pip install environment
```
pip freeze > reqirements.txt
```
### 2 predict
```
cd ./BendNet/Code/
python ... |
8af752e533672bc5f9bae7340b99bdf6e932a156d85d7cc49e55cc6bbad8fc15 | Text | 736 | 22 | # ElectroPhyAnalysis (EPA)
EPA is a set of python scripts to analyse in-vivo electrophysiolgoy recordings (whole cell patch clamp)
The three main axis are:
- data analysis of raw signal from AxonBinaryFormat (abf)
- statistics method
- visualization
The different types of recordings analyzed are spontaneous rec... |
76b77bba2a0254cb907f19ce23fce9f1589eec7100c7f948c5d4588897aa1080 | Text | 752 | 10 | # Joint transcriptome and regulome analysis in the developing human brain cortex at the single cell level
## Description
- ```merge_samples.R``` describes the process of creating a single Seurat object from Cell Ranger ARC outputs of different samples.
- ```preprocessing.R``` includes quality control, pre-processing ... |
f1e696852daa8eac79b582cb4f1525f9a254a4e886ba7d66720540202d77726e | Text | 760 | 26 | # LSFP-Net
**Zhao, He, et al., *A deep unrolled neural network for real-time MRI-guided brain intervention.***
## Requirements
We provide a requirements file requirements.txt. You can create a new conda environment or virtual environment and execute install the requirements using the following command.
```
pip inst... |
45dfa7b7c08cdc0999d98e8f13e71f6108d4e51cc105695fb0a5ca489fe68098 | Text | 766 | 14 | # Congenital_CMV-ZIKV_infections
Data and code for the CMV/ZIKV congenital infections manuscript
Zip file includes most of the input files and R code. Expression values (in TPM), and human hg38 and mouse mm10 annotation files used in the analysis are available as separate GoogleDrive links:
expression https://drive.g... |
ec17724aff264ad2f7ae63d95a217c1e4e1e7592befb82d0a9b3b84811f4f2cf | Text | 766 | 14 | # FMS_evaluation
## steps to run
1. data used in this project can be downloaded from [here](https://doi.org/10.25452/figshare.plus.c.5774969)
1. use conda to build experiment environment
```shell
conda env create -f conda_env.yml
```
1. cd evaluation/st_gcn
1. you can run the following pythons scripts in that directo... |
e80a3e681c7b9b4ca86c2bf4bbfa995af1385fef6f033d33dc86a8b7c2a052d9 | Text | 769 | 29 | # 2PCISz_RecDetect
Repository for two-photon calcium imaging data analysis code to determine population event times (Pre-Ictal Spikes, Seizure and Terminal Spreading Waves) and individual cell recruitment to those events.
## CODE ITEMS
### SzRecTime_processing.m
MATLAB script to process suite2P .m output files along... |
5f0f9cc659af343f695d64af04a978e714c26457035cde2006ee27f3de37bc3e | Text | 776 | 16 | [](https://zenodo.org/doi/10.5281/zenodo.10085496)
# Citation
This ReadMe is for the following review paper:
Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, Kristen R. Maynard. "Challenges and opportunities to computationa... |
76c219d33a44afa4fedc503341fa4679d9b023020ac5a19d8dc5eddf82b597ac | Text | 789 | 9 |
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://spitfire.readthedocs.io/en/latest/?badge=latest)
Spitfire is an open source Python/C++ scientific computi... |
707bdd91801fe5c6ec631d04ad635314e48cedd96c6caaae733bf9784f8a44dc | Text | 809 | 16 | # Gene-Geometry
**MM 230722**
Code and data for analysis of gene expression patterns among retinal ganglion cells using Cartesian models.
- Read the enclosed preprint:
- Hahn, J., Monavarfeshani, A., Qiao, M., Kao, A., Kölsch, Y., Kumar, A., Kunze, V.P., Rasys, A.M., Richardson, R., Baier, H., et al. (2023). Ev... |
a8690e8170c65339d208ada16382c416dfcf461c72f3dc95038c906b493e4cb8 | Text | 820 | 10 | [](https://pypi.org/project/csbdeep)
[](https://anaconda.org/conda-forge/csbdeep)
[](https://github.com/CSBDeep/CS... |
45c641905605f353bc8d5841d55658ca9d1cfff87a296bbbc6422dc2d8d3a89e | Text | 845 | 21 | # GFDF: Multi-Focus Images Fusion
Multi-focus images fusion using Guided Filter and mean filter. This is the MATLAB code for "[Guided filter-based multi-focus image fusion through focus region detection](http://www.sciencedirect.com/science/article/pii/S0923596518302832)" in Signal Processing: Image Communication (SPI... |
d6ca6ba7570f516cd63dab69b816089c030058f7ff8fa7a7196d42821823659f | Text | 846 | 18 | # 2023_Zhu_et_al
#### Scripts for:<br/>
#### PTBP2 attenuation facillitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes<br/>
DOI: 10.1016/j.stemcr.2023.09.012<br/>
<br/>
Authors:<br/>
Binglin Zhu<sup>1,2,3*</sup>, Emily Fisher<sup>2*</sup>, Li Li<sup>2*</sup>, Ping Zhong<sup>2</s... |
7765faef832c07b60a0807b1cef71867ac0a67053468c05c5c0d902e2b309c8c | Text | 853 | 18 | # 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... |
124f3f3704cc1a29310f81e7accd321dee2f4e6478ecd65726475545a20f812e | Text | 858 | 39 | # rogue-wave-discovery
Code for the paper "Machine-Guided Discovery of a Real-World Rogue Wave Model" (Häfner et al., 2023).
## Installation
Requires Python 3.8 or higher.
1. Clone the repository
2. Install the requirements: `pip install -r requirements.txt`
## Download the data
```bash
$ bash get_rogue_data.sh
``... |
9c789272b167e1594fab6919cf045d0d66aeb45066531d58bff845c12cc2d8d2 | Text | 859 | 9 | # ELife_MovieTuning
Code and datasets generated and needed to reproduce results in upcoming ELife paper - 10.7554/eLife.85069.3 or https://elifesciences.org/reviewed-preprints/85069
The main function to generate figures is called "Movie_Tuning_FigCreator_v24_June20_2023.m". This script relies on the SupporingScripts w... |
76249e17f6dceec1be0109d9456a2803a60ce29f7c9fc895a16c236812f86561 | Text | 867 | 17 | Paper can be found here: https://www.nature.com/articles/s42003-023-05548-w
We used custom Matlab codes for metabolic model generation and model analysis and R script for data analysis and visualization:
DEGS_IPD.Rmd : for analysis of RNA sequencing data
Flux_change_visualisation.Rmd : visualisation of flux changes... |
3983c5163c5d33c14fca0f1a432ed6fb11ab302e02018038cb9b64b8531c23db | Text | 881 | 26 | # SPIN-CGNN
**SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network**
This repository contains codes and pre-trained weight for SPIN-CGNN and corresponding datasets.
## Reference
If you find our work useful in your research or if you ... |
a90b048e1df930dde7c18267f62f284049f0a76dc098cc642e0d423278f16471 | Text | 882 | 13 | 
# NeurospecTriggerBox-Unity
This Unity plugin is used to send triggers with the [MMBT-S Trigger Box](https://shop.neurospec.com/mmbt-s-trigger-interface-box) from [Neurospec AG](https://neurospec.com/).
Many devices require triggers to be sent via a parallel port, but these... |
17d85c543e36fd9595d260522e19ba3335bc7d4d891c487ae0f9003ff6ca0939 | Text | 891 | 33 | # MG-HEADSUP <img src="pics/headsup_logo.png" width="150px" align="right"/>
Hemmorrhage Evaluation And Detector System for Underserved Populations, a collaboration project with the joint efforts from Neurologists, and Machine Learning Scientist from the Mayo Clinic.
[Journal Link](https://www.sciencedirect.com/science... |
d114f7ba0dc788cc6933f866b361339b8ed2797b7de18d37acd187545fb41a86 | Text | 903 | 6 | # MultiTracker
This repository contains the C# code of the tracking program used to track fish in multiwell plates in [Randlett et al., Current Biology, 2018](https://www.cell.com/current-biology/fulltext/S0960-9822(19)30209-X).
Please note that this code is likely not very useful as a whole. It is strongly dependend ... |
2655dcf09cc7b2cb53e1e742c2dc62d9ec7c6831fc543d24ed06cad2b7b58a48 | Text | 905 | 11 | # Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity
This repository contains data related to the manuscript "Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity".
The file `20230611_export_3.h5` contains data from 6 ind... |
5ea0adcdadecb9fe849f127d198d1679e6db44f52f0eda902461f226de4535c9 | Text | 910 | 16 | # Data Source
The data for these experiments were derived from these sources:
* Hosmer Jr DW, Lemeshow S, May S. Applied Survival Analysis: Regression Modeling of Time-to-Event Data. 2nd ed: John Wiley & Sons; 2008.
* Jd K, Prentice R. The statistical analysis of failure time data. New York: John Wiley and Son... |
9f5f79a70d0e257f2ba1d55004fe73c5dbc66330593f0d13d21086f4b2a57489 | Text | 915 | 41 | # CSDGI
Unravelling Cancer Subtype-specific Driver Genes in Single-cell Transcriptomics Data with CSDGI
## Description of each directory
data: the preprocessed data from three real scRNA-seq data in GEO.
comparison: the utility of comparison with di... |
0a5d28e5a2728fec7a06697fd8d47e1a55ebb238a18c66a28b67735c184d9e5f | Text | 918 | 33 | <img src="/visuals/logo.svg" width=250 align="right" />
# PyDeface
A tool to remove facial structure from MRI images.
## Dependencies:
| Package | Tested version |
|--------------------------------------------------|----------------|
| [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslw... |
60bbb04f0b52563a79c365c73943d1576998e3ad31ee10cf568ff44d270113ec | Text | 918 | 24 | # Image Foveation Python
Python implementation of image retina transformation. For detailed algorithm, please refer to the following papers:
> Perry, Jeffrey S., and Wilson S. Geisler. "Gaze-contingent real-time simulation of arbitrary visual fields." Human vision and electronic imaging VII. Vol. 4662. International S... |
1885c947f55e4a963fceec1c350b3eaa7a4912ef70918313048721f877bb003c | Text | 919 | 33 | # The Deep Generative Decoder
DGD is a package for probabilistic representation learning. It can be applied to various tasks. The implementation for Fashion-MNIST and single-cell expression counts can be found in branch ```paper```.
## Installation
```
pip install git+https://github.com/Center-for-Health-Data-Scienc... |
5a027054cc8d7aa5920bafbe6ac73522c362e5a8b46d6558a54f84639559709f | Text | 922 | 16 | # gBGC-drives-accelerated-evolution-of-UCEs
- Anguo Liu
- Yu Wang
This repository contains scripts and pipelines used in gBGC-drives-accelerated-evolution-of-UCEs project. Most of the scripts were specially designed to perform the analyses in the paper ```GC-biased gene conversion drives accelerated evolution of ult... |
1da1b049cfac04bc534d6ca40753c9397c1ce248b64a347f729b7608c3371624 | Text | 925 | 11 | # neural-landscape-diffusion
Functions and example notebook associated with the landscape diffusion model developed in Richman et al., Neural landscape diffusion resolves conflicts between needs across time. Nature (2023). Please find the published paper [here](https://www.nature.com/articles/s41586-023-06715-z). This... |
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