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4c1dc93e42685e0d3bab7bb031b9fad3b5aefcd6bff3bb2329e8f982570d455c | Text | 726 | 17 | # What is ct-tools?
This is a set of Matlab tools to segment electrodes in CT images of brains and to determine their anatomical locations.
# Requirements
Matlab R2021a or later with the Image Processing Toolbox, the Optimazation Toolbox and the Computer Vision Toolbox.
# Installation
Make sure that the folder is on ... |
3af17deafff3fddc4a68df05f7730fa2b58800f9dc9fd3504e977a3019b0d721 | Text | 732 | 17 | # CINPLA Allen V1 analysis
Contains code for data analysis and making figures in Atle E Rimehaug et al. (2023) Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex eLife 12:e87169. https://doi.org/10.7554/eLife.87169
Data files are stored with Git Large File... |
9017bdef20efa40080ef6093d860debfeddf88037ae8f629666c61f85eb17d79 | Text | 733 | 13 | # HIPred
HIPred scores for each gene in the human genome are listed in <i>HIPred.tsv</i>.
### Interpretation
Predictions are in the range [0, 1]: values above 0.5 are predicted to be <b><i>haploinsufficient</b></i>, while those below 0.5 are predicted to be <b><i>haplosufficient</b></i>. Scores close to the e... |
0f154cc87bf38e0e970de101c921a14edba1af25dede3da05a2a2d32fe1d22ae | Text | 777 | 19 | # kallistobustools
kallisto | bustools workflow for pre-processing single-cell RNA-seq data
Please visit https://kallistobus.tools for tutorials on how to process single-cell RNA-seq data.
## Contributing
Create a Google Colab notebook and make a pull request. If approved `your_tutorial.ipynb` will be added to a ne... |
3a306def568a1a1f9669695e701a0a20e6c77dea813341dc4ad9a8803c981e85 | Text | 783 | 15 | # My Jupyter notebooks
## Ribosome profiling
* [Multi-frame Ribo-seq and mRNA-seq visualization](ribosome_profiling/ribo_orf_plot.ipynb)
## Gene differential expression
* [Gene differential expression with DESeq2 from Python](deseq_from_python/de.ipynb) and [MA plot](deseq_from_python/de_ma.ipynb). Recommended usag... |
d61c02597c53912a053328481552331a8f40595820ecfe7e6960b929279c68fa | Text | 804 | 23 |
# pycocotools
This is a fork of the original [cocoapi](https://github.com/cocodataset/cocoapi), with bug fixes and packaging improvements.
This is also the "official" source of the pypi package `pycocotools`, available for download at [pypi](https://pypi.org/project/pycocotools/).
Changes in this fork include:
* Ad... |
8686b0f7c163a1a358d8966d3b8f83c4dfc5e767f27499368cefe0d43449ac8a | Text | 821 | 15 | # MultiPatch
IGOR PRO script for quadruple whole-cell recordings
Create a folder somewhere in your user directory called /Igor Stuff/.
Put all these files in /Igor Stuff/.
You also need "Jesper's tools", which is found here:
https://github.com/pj-sjostrom/qMorph/blob/653053f24b4fd660f12791354bdcaa1a01fcd36f/JespersToo... |
4f1be0e111cb84ae6365022f26c9de72c358431410accc46ded31a6c9867c56a | Text | 826 | 8 | This repository contains data analysis scripts and associated files accompanying the manuscript:
"Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal *Caenorhabditis elegans* aging and systemically regulates longevity from serotonergic and GABAergic neurons"
**Manuscript authors:** Mari... |
9a682f1a5114908457f07f0ed759fd4942b40f4586136d82237ae957c69bcf3d | Text | 831 | 18 | # Pophale et al., Nature (2023)
This repository hosts the source code used in the paper.
## Contents
* `probemapper`: A Python library for brain registration and Neuropixels mapping.
* `neuropixels_analysis`: Code to analyze Neuropixels data
* `ephys`: Matlab code for processing Neuropixels data recorded with Spike... |
57f192ef292c8e351fb95949419de3abffca2b9393913c5cab3217dd09ac14f1 | Text | 833 | 11 | # MTLnet
Author: Preya Shah
Welcome! This project carries out core analyses and visualizations for exploring functional and structural network connectivity in the medial temporal lobe (MTL). We have provide a sample dataset, and our methods can be applied to your own datasets of healthy or diseased subjects. Input da... |
fd53474f8faf8941712abce2b8a100ca5ba927fe6e35994d70466a5b7a38c503 | Text | 833 | 18 | # 2023_pancholi_natcomms
Code for Pancholi et al. 2023, Nature Communications
This repository contains the code for figures in Pancholi et al., 2023, Nat.
Comms. "Learning in a sensory cortical microstimulation task is associated
with elevated representational stability".
If you only downloaded the code, you will ne... |
1422a31b0a6bff5eb59112a30d49082cb26825b1aa16bc3d4885a3839f7fd63c | Text | 839 | 14 | # PyL3dMD
PyL3dMD - Python LAMMPS 3D Molecular Descriptors Package
A Python-based post-processing routines, called PyL3dMD, for calculating 3D molecular descriptors from molecular dynamics (MD) simulations. PyL3dMD is compatible with the popular simulation package LAMMPS and enables users to compute more than 2000 3D ... |
ccfaf88983cc528c189357b4fdac03359fba47c53797a8ea81ae7dd058d0ec0a | Text | 859 | 13 | # communication_public
The repository contains a the code for simulation (communication_sim.ipynb) and analyzing empirical data (communication_empirical.ipynb) from the Midnight Scan Club.
For the detailed rationale of the emthods, see manuscript "From correlation to communication: disentangling hidden factors from ... |
8d106a0be0c6a329d12f32d4496370835d7e3ab4f027a53930c1ee9e567cb118 | Text | 877 | 20 | # SHS_NET
Suguru Honda, Koichiro Yano, Eiichi Tanaka, Katsunori Ikari, Masayoshi Harigai
The objective of this project is to predict the Sharp/van der Heijde score (SHS) for hand radiographs through three phases, orientation, joint detection, damage prediction. The results of this analysis have been posted on Medrxiv ... |
1c78e02e5eb836c79fdaa5b5e1048b400299fbbd613fca6a9501677a347b5db0 | Text | 882 | 13 | # qMorph
<I>Igor code for quantification of reconstructed neuronal morphologies</I>
<BR><B>QUANTIFY MORPHOLOGY</B>
<BR>by Jesper Sjöström, begun 7 Nov 2010
<BR>Reads folders of SWC files, where each folder corresponds to one condition, and averages those.
<BR>See <A HREF="http://www.sciencedirect.com/science/article... |
d0bd0a5d3d828a8a1bb3cbc903ffef339bf24272710433c788d35b516245c661 | Text | 886 | 15 | # M1_Preparatory_Movement_Representation
Data and code for the paper BachschmidRomano, Hatsopoulos, Brunel, 2023 - eLife
Data:
Firing_rates.mat contains electrophysiological recordings from the primary motor cortex of a macaque monkey performing a center-out reaching task. Recordings were performed by Doug Rubino in ... |
0b038f431924c8d54ee425133727b9f97cf723b7e777227979d55beb3c200a1e | Text | 889 | 5 | # subdiagnostic-autism-variants
You will find here the python scripts developped for the post-processing analyses reported in the "Sub-diagnostic effects of genetic variants associated with autism" manuscript.
All raw genetic data are available upon request from [SFARI-base](https://sfari.org/sfari-base), [UK-Biobank... |
fa9954991161a81991e0dfd01690f27777816a89837f5d77dcfb4b4b455641d2 | Text | 892 | 4 | # mvar-analysis
set variable appropriately in global_vars.m. running the analyses for RS, RAW (raw RS data), and the sleep stages (WS, N1, N2, N3, R) must each be run separately. For each of these three options, run the scripts in the following order: compute_gpdc.m, compute_ssgc.m, compute_mse.m, compute_cosine.m, ... |
eada609bde7091cad82fe63bd5cfea5a2c9cd854ae3b1dfd2b13b692c581597b | Text | 895 | 28 | # pinn2022
Code for paper published in Communications Biology.
## Inputs
The `inputs` folder contains input files for the first case demonstrated in the paper.
- `volume.dat` is the volume mesh for the finite element model
- `surface.dat` is the surface mesh for the finite element model where it inter... |
db72b025c842547cf44359e5b80c4e37fee3243f183d513c163c5eb508ba8894 | Text | 910 | 20 | % to use the stimuli in the four sets of images considered in the study,
% please make sure that the folder '\black_and_white_stimuli_Sets_1_to_4\' is
% located in the current folder where the code is called
% to display the stimuli used in the experiments:
display_BW_processed_stimuli;
% to run a simulation w... |
e1c2af85bc97bc276ccace949a0947cd35247994141d6ab1bbecfd28a0a9620e | Text | 914 | 9 | # Using the fly liquid interaction counter (FLIC) to record feeding behavior in Drosophila melanogaster
## Summary
We used the fly liquid interaction counter (FLIC) to record feeding behavior of the fruit fly (Drosophila melanogaster). The benefits of FLIC over other methods is that it is a high throughput and unbias... |
2b95a34806050d1fa3a61e05dc693c4de3cd738c042e0cd9aae8a17ee5d0ecc1 | Text | 923 | 27 | Matlab implementation to remove skulls of head CT and CTA images.
Citing this project
If you use this code in your work, please:
@article{NAJM20191,
title = "Automated brain extraction from head CT and CTA images using convex optimization with shape propagation",
journal = "Computer Methods and Programs in Biomedici... |
a58f218041f778e7fed464e3215807a0c5a575fd4e29edf8902dcd20a9565c8f | Text | 952 | 18 | # What is htrdetector?
This is an algorithm to detect the head-twitch response (HTR) or "wet dog shakes" in rodents using accelerometer signals. The HTR is commonly used in neuroscience research to investigate activation of the 5-HT2A receptor.
# Documentation
Please see the script [demo.m](https://github.com/NRC-Lund... |
b81ee25f02361a116ace2dc242ccf975f6eeb6b6f35ac6c021d61f57f7067a09 | Text | 954 | 21 | # Dynamic SPHARM: software for dynamic spherical harmonic analysis
[](https://doi.org/10.5281/zenodo.3387142)
Author: *Anna Medyukhina*
Affiliation: *Research Group Applied Systems Biology - Head: Prof. Dr. Marc Thilo Figge
https://www.leibniz-hki.de/e... |
85c0420ab92a5029171c0681a24f3776f63b06dd868f7df105f80d147bc8db94 | Text | 963 | 18 | <?xml version="1.0" encoding="UTF-8"?>
<metadata
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<dc:title>Reaching and grasping objects in depth for people with stereovision deficits and healthy controls. </dc:title>
<dc:creator>Cristina Simon-Martinez</dc:crea... |
907e66d42e4dc66f3069cd39c94a71fc80641865c70d7526082375af22fc05d7 | Text | 975 | 18 | # ST_hESC_DA_analysis
This repository contain code for analysis of hESC derived dopaminergic transplants with ST.
### 'SC_processing' folder
This folder should be run first to generate reference datasets for SingleR, cell2location deconvolution and for correlation analysis.
'subset_reference_loom_dataset'and... |
43750a8d45e37e6b731ee7264890214e4f43736ac170904861de7074b227cdfc | Text | 1,000 | 19 | # The spatial landscape of gene expression isoforms in tissue sections
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, exploration of alternative splicing and full-length sequence heterogeneity i... |
41c812132f4999321489788277018f6814473ca5363fb10afbe4f966d2e54ef3 | Text | 1,048 | 39 | [](https://zenodo.org/badge/latestdoi/47563497)
<img src="/visuals/logo.svg" width=250 align="right" />
# PyDeface
A tool to remove facial structure from MRI images.
## Dependencies:
| Package | Tested version |
|------------------... |
18434fa3f18f1b8c06f19a06e5974bf751bf33e23ced84afc37d6c2294b29782 | Text | 1,075 | 16 | # Chen-Wu-eLife-Drosophila-Image-Capture
Labview software to record images to MMF compressed format and to interface with various external stimuli
(c) Marc Gershow; licensed under terms of the GPL v2 license (see LICENSE in this directory)
This software is derived from software developed by Marc Gershow while a membe... |
4cd5d44bcf2d4b15b968c9dcbf6c4c03bd569c1267b1f0c44d68ae2c31782f21 | Text | 1,085 | 16 | ## Sulcal morphology of posteromedial cortex substantially differs between humans and chimpanzees
Associated data for the *Communications Biology* manuscript Willbrand, Maboudian et al. (2023) *Sulcal morphology of posteromedial cortex substantially differs between humans and chimpanzees*.
For questions and/or addit... |
13a8a125e96871973357a048b461d894fab96f128f3cbd2c7f5406f1443abde9 | Text | 1,105 | 13 | # LPS-induced systemic inflammation affects the dynamic interactions of astrocytes and microglia with the vasculature of the mouse brain cortex
We provide in this repository the image analysis scripts to quantify morphological changes of perivascular microglia/astrocytes and their interactions with the brain vasculatu... |
6f4a70bfd505720b948176c00dd152dfa44a565c68f9ba138c3bfa8bf0070682 | Text | 1,115 | 10 | # MICA: A toolkit for Multimodal Image Coupling Analysis
In order to comprehensively reflect the functional states of the brain,
we developed a software based on MATLAB 2014a platform to analyze the across-voxel coupling between multimodal images.
The software mainly included four functions. First, the data rename fun... |
5e3e55525dfa96a4da7816fd6f0843526672e87059b6a33880db5babaa711157 | Text | 1,117 | 29 | # TemporalRegularity_RWD2023
Repo for code for DiTullio et al 2023 Frontiers Manuscript
SFA tools contains primary code for running the analyses of the paper.
SFA_singleexample provides an illustrative example of how the algorithm works.
single_runSFA allows the user to explore different simulation situations and c... |
7730f0b42149fe13b2d1283718873f743b4840cdfafad0c4e5efada32f3748c8 | Text | 1,123 | 66 | # Historia
A set of more or less powerful tools I developed during my PhD for more or less generic scientific computing purposes.
---
## Information
**Status**: `Occasionally developed`
**Type**: `Personal project`
**Development years**: `2018-2021`
**Author**: [stelong](https://github.com/stelong)
---
## Gettin... |
fb02b09a2bf7ed91ef8e6d9dacbe52c9b5cbe27ae61c9e17dd077d96a388ec59 | Text | 1,167 | 31 | # 🦓 CEBRA - Figures and Data
Code and data for reproducing the figures in
[Learnable latent embeddings for joint behavioral and neural analysis (Schneider, Lee and Mathis, 2023)](https://www.nature.com/articles/s41586-023-06031-6).
This repo only contains plotting functions which can be applied to pre-computed resul... |
5ce1ea702fcd48ad5ae5445d8f9e42c6a402f5193078fb8fc2e45d28c394bd77 | Text | 1,177 | 30 | # Graph Neural Network Autoencoders Autoencoder for Jets
[](https://zenodo.org/badge/latestdoi/518371541)
# Overview
A graph autoencoder (GNNAE) for jets in particle physics implemented in PyTorch, mainly used as a baseline for [LGAE](https://github.com/zichunhao/lgn-auto... |
5316747158c1cb06e22c966f40fadd3aafc5065d9973ba6321e05b17da176105 | Text | 1,189 | 13 | # JunaChimp
As a common reference space for the analysis of chimpanzee brain data, we created the Juna.Chimp template, constructed from a large heterogeneous sample of T1-weighted MRI’s from the NCBR (http://www.chimpanzeebrain.org/). The Juna.Chimp template includes a reference T1-template, along with probability map... |
db696c1b13d843ef1e3769eca8936844d5731042de66c9f80fd32d0f891793b1 | Text | 1,192 | 40 | # 2023_CoenSit
Code to replicate the figures from Coen, Sit, et al--2023.
Code comments and examples may be updated compared to the cited version on Zenodo.
The corresponding data is available here: https://doi.org/10.5522/04/22363180.v1
Once you have downloaded, unzip is such that you have a single directory contai... |
844d6a1d3389478672d25ac7eb414231ee6b95c9ec3aebd396a8e78cbd9e591c | Text | 1,198 | 13 | # Multimodal Brain Integration Networks (mBIN)
Multimodal Brain Integration Networks (mBIN) is toolbox for high dimensional analysis of brain networks across multiple imaging modalities. Our goal is to enable high level visualization and interpretation of structual and functional brain data across micro to macro scale... |
59a3c263ecf7953aa68b94d55ecaec0757226914831b331543f4544f47b264ee | Text | 1,202 | 19 | # big_dots
Analysis scripts for Monash/Trinity Big Dots study
##Analysis Pipeline:
###In Matlab, run scripts to process raw eeg files:
(note: In future you can skip steps 1 to 3 because they were just for renaming incorrectly named files and finding noisy eeg channeles, which will already have been found and listed ... |
eef5df3cbeae3398be5e9c231937a539cc0f00ffd66b14358013614b3bebfca6 | Text | 1,205 | 14 | ## Code and scripts
The repo contains:
- MATLAB script for the visualization of Genome-wide association analysis. All GWAS results in txt files are provided.
- MATLAB script for Heat Probe Assay data analysis and visualization. An example excel file (Example.xlsx) is provided.
- MATLAB scripts for Optogenetic behaviora... |
1161729ebc3f4a294bb23c790aa74ee4cf91399f902562f4853246b3221d892a | Text | 1,221 | 32 | # Independent tests
Some scripts to compute the number of independent tests.
## 1. Compute the number of independent tests from a correlation matrix using PCA
This defines N, the internal dimension of the kernel (correlation matrix), as the number of principal components accounting for 99.5% of the variance explained... |
5edcd6477ecb0df0b5e7ba4004a5e7e6ab3c572878d5ff0489de2f367138fb98 | Text | 1,237 | 19 | # TACTiCS
## Cell type matching across species using protein embeddings and transfer learning
<img width="600px" src="overview.png">
### Implementation
To train and evaluate TACTiCS, use the `TACTiCS` class in `tactics.py`. As input, `TACTiCS` requires two scRNA-seq datasets and a distance matrix describing the gene... |
d053d4c20fca13082027c7465314a91b5315afabf4e8631b01867e17bfd3a519 | Text | 1,254 | 41 | # pyelftools
<p align="center">
<a href="https://github.com/eliben/pyelftools/actions">
<img alt="Logo" src="https://github.com/eliben/pyelftools/workflows/pyelftools-tests/badge.svg" />
</a>
</p>
**pyelftools** is a pure-Python library for parsing and analyzing ELF
files and DWARF debugging information... |
4caa3788c480ce257567f52ef366d4507f025683f63c65e1b54a954a66f200b4 | Text | 1,274 | 52 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# SURGE
<!-- badges: start -->
<!-- badges: end -->
The SURGE package streamlines importing of 3D landmark data from
Stratovan Checkpoint into R for analysis.
## Installation
You can install the development version of SURGE from
[GitHub](http... |
14a61554afa23e86b3bd024edd3e41e1e1e47c4058e8434063a6acad3857d55b | Text | 1,276 | 22 | # Attenuated evolution of mammals through the Cenozoic
Data and novel code for Goswami et al. 2022. Attenuated evolution of mammals through the Cenozoic. Science, 378: 377-383.
## Data
- `shape.data.322.csv`: Procrustes coordinates for all specimens
- `csize.322.csv`: Centroid size for all specimens
- `full_species.d... |
bdc471fdf58af8b7b63beddc4bce9e1749e5ce8eb632dcc9f83d9b1c7cb578dd | Text | 1,290 | 11 | # mscca-regression-code
This repository contains an implementation of multiple sparse canonical correlation analysis regression, as described in the paper. Using this method, multiple data-views can be used to stratify a single data-view (Ing et al. 2019).
The code implementing this method is written in MATLAB and is ... |
bb67759ec088e67d189c7656e9dc068e1fd78aaee0490529976e1451ed1807c2 | Text | 1,300 | 37 | ###########################################################################
SMOTE-CD : Synthetic Minority Oversampling TEchnique for Compositional Data
###########################################################################
SMOTE for Compositional Data is an adaptation of the well-known SMOTE algorithm
for the ca... |
9913652e07c14386d1f3a115be41be08a23c4fb473f2ee2f4f2df0cd14d2c229 | Text | 1,305 | 39 | # Install Conda
Install conda at: https://www.anaconda.com/products/distribution
# Install Dependencies
Open a terminal in directory and create the enviroment using the yaml file:
```
conda env create --file environment.yml -n my_env
```
Or enter the following commands:
```
conda config --add channels conda-forge
... |
8808883bdb476be3c4356431eaaae2ac6a383b9799a733cf0d9f010ab39dbd42 | Text | 1,322 | 10 | # JBSI-codes
These are MathCad and MatLab codes to compute the JBSI (Jitter-Based Synchrony Index) of a simultaneously recorded pair of spike trains.
See the original publication (Agmon A (2012) A novel, jitter-based method for detecting and measuring spike synchrony and quantifying temporal firing precision. Neural sy... |
bab9ca2354a920afadcd8e286da41d478eb73c49a5877544d653a3cdcf0531b8 | Text | 1,337 | 25 | # ADC threshold project
Code and data for "A comparison between automated, threshold-based acute ischemic stroke lesion delineation and expert manual delineation" study
Authors: Vitus Gosch, Doctoral Candidate – Center for Stroke Research Berlin, Charité Universitätsmedizin Berlin
## Background
This repository cont... |
ddf829253a7655175a45dc50088f61dee265a8f931373c18cfba6055e0092391 | Text | 1,375 | 18 | # Power spectra scripts
related paper: Kustermann, T., Nguissi, N. A. N., Pfeiffer, C., Haenggi, M., Kurmann, R., Zubler, F., ... & De Lucia, M. (2019). Electroencephalography-based power spectra allow coma outcome prediction within 24 hours of cardiac arrest. Resuscitation. 142 pp. 162-167 https://doi.org/10.1016/j... |
311940e6e1d5a5e37cb9613092c21d4904522a5c80f8a24fef5e711048985587 | Text | 1,376 | 35 | # regionprops3
regionprops3 measures the geometric properties of image objects in 3D space.
Objects are defined as connected pixels in 3D. This function
uses regionprops to get pixellist from the binary image. If you'd like
to define objects connectivity on our own, use bwlabeln first.
output = regionprops3(img,pro... |
a095452133d043a4e42cb35821e487167308d306aa6584dd8a0a871425012145 | Text | 1,381 | 18 | # Representational drift in the mouse visual cortex
This repository includes analyses and processed data presented in Deitch et al., 2021.
## Usage and documentation
Scripts are provided in the *scripts* directory. Data sets are provided in the *data* directory.</br>
Note that the provided data sets are a processed v... |
04171902ae0dfc0b5898d93a2867b8adff3a79d1ab1ffd25fc47d89ad1846f84 | Text | 1,388 | 25 | The included MATLAB scripts were used in the study: Seitzman et al., 2019.
Trait-like variants in human functional brain networks. PNAS. These scripts
will allow users to create network variants, assign them to network
templates, and find subgroups/sub-types of individuals on the basis of
network variants. The order i... |
e30a6a9bb25d3c9cd6b4bca014d7ef35cfd436b892f6db80dab61caffa95731c | Text | 1,428 | 27 | # binorg_decoding
Bin-Organized Decoding (J. Neuro: Bae&Luck, 2018).
Here you will find an updated version of Bae & Luck (2018) analysis scripts. We have updated the scripts to allow the use of bin-organized decoding, therefore allowing users to use EEGlab/ERPlab* to format and decode their own data more seamles... |
6394f73780e8737a8d9374b9a305414d7c73c2ecde9b889d8469fa14c43116ed | Text | 1,433 | 41 | ## SS-GNN
> This is a Pytorch implementation of `SS-GNN`, a simple-structured GNN model for drug-target binding affinity (DTBA) prediction as described in the following paper:
The `SS-GNN` defines the prediction of DTBA as a regression task, in which the model’s input is the drug-target representation, and the outpu... |
004cc2fc7eb9b8dd37f58b0f687aba8a40a1105837be2bc963b3b6f9ee9d0819 | Text | 1,449 | 24 | # PICUNeuroPrediction
Admission predictive modeling for PICU patients with suspected acute neurological injury
## Data Source
Trichotomous Outcomes in Pediatric Critical Care (TOPICC, https://www.cpccrn.org/study-datasets/topicc/). Due to data use restrictions with our agreement with the NICHD, we are unable to shar... |
bdc67f3c4c4ee8decdc379ff919c9cbf8b82efa88114fa3a40786d31a1b93919 | Text | 1,449 | 32 | # Overview
This repo contains the accompanying code for our paper [Motion Extrapolation for Video Object Detection](https://arxiv.org/pdf/2104.08918.pdf)
Best Paper Runner Up at the [Robust Video Scene Understanding: Tracking and Video Segmentation](https://eval.vision.rwth-aachen.de/rvsu-workshop21/) CVPR 2021 worksh... |
0d9f9eea0975427cf49685da432ce0464b1eba6d194c5f6135ce1970e7eca9b5 | Text | 1,469 | 18 | # Modelling novelty detection in the thalamocortical loop
Here we provide the Matlab code to reproduce the results of the paper "Modelling novelty detection in the thalamocortical loop".
1. download this repository into your local directory <local_path> and unzip it.
2. create two folders named `Simulation Results` a... |
fda9cce0782408fe9fa1de1362700f32a071f54f45aff994a208994dc7d814a3 | Text | 1,478 | 31 | # CRISPR-ONT & CRISPR-OFFT
## Overview
CRISPR-ONT and CRISPR-OFFT are attention-based convolution neural networks (CNNs) frameworks to accurately predict CRISPR/Cas9 sgRNA on- and off-target activities, respectively. By integrating CNNs with attention mechanism, both CRISPR-ONT and CRISPR-OFFT are able to capture the ... |
510e6a7c7c9f2cf212277fb7a81511e1d39ed5fa0f2021f35175cf35bf7377e0 | Text | 1,489 | 34 | # Description
This protocol is used to calculate the moving speed and turning frequency from the crawling trajectories of the larva. There is no need to install and you could just copy the script and run it directly.
# Package versions
The version of softwares and packages for testing codes:
Python: 3.8.8
pandas: 1.... |
96c9c8ad831871aba8858df671decb9095399546f37ed21eb53f45d33832907d | Text | 1,520 | 50 | # Snapshot-Ensemble-Colorectal-Cancer
Implementation of our paper **[SnapEnsemFS: A Snapshot Ensembling-based Deep Feature Selection Model for Colorectal Cancer Histological Analysis](https://www.nature.com/articles/s41598-023-36921-8)** published in **_Scientific Reports_, Nature (2023).**
## Overall Workflow
<img sr... |
3deab3e1aee8014f6049d3a907f28b0f8cd3859bf6497e2e5168c9686e58d057 | Text | 1,554 | 26 | # Code for "Differentiation of white matter histopathology using b-tensor encoding and machine learning"
Code for the Machine learning pipeline used in "Differentiation of white matter histopathology using b-tensor encoding and machine learning" by
Ricardo Rios-Carrillo, Alonso Ramírez-Manzanares, Hiram Luna-Munguía, M... |
ad4816d9c83e20996b39e88223880732a103ef8010cbd233571fb6c74645a47b | Text | 1,566 | 18 | # AuReTim
Open-source portable psychomotor vigilance test for the Raspberry Pi
AuReTim uses Apache Maven as the software project management tool. After installing Maven, the program can be built using the command mvn install in the root directory of the source code. The command will download all required dependencies ... |
a755bc2ce956c43f3be5baabe301ad4b80ef8b4572c9552eebf5b51d03cdedc1 | Text | 1,567 | 56 | # NHGNN-DTA
NHGNN-DTA: A Node-adaptive Hybrid Graph Neural Network for Interpretable Drug-target Binding Affinity Prediction
## File list
- Data：It contains the data files for training.
- Vocab: It contains the vocab files for protein and drug tokenizer.
- Code: It contains code files.
## Generation of... |
2ff087a4c9f54c10933296868d788685ee1893982edb0ac39220569d438cdea7 | Text | 1,658 | 60 | iScience-2023
================
This is the repository for the article: *Probabilistic integration of
preceding responses explains response bias in perceputal decision
making* by Schlunegger & Mast (2023) in *iScience* **(under review)**.
## Reproduce results and figures
To replicate the results and figures reported ... |
a25b4926dd0208a04c7e440c46ce086d135165c8bd2fa2db8417d62e802cad06 | Text | 1,659 | 37 | # CRISPRedict
CRISPRedict is an interpretable gRNA efficiency prediction model for CRISPR-Cas9 gene editing.
## Requirements
The scripts are written in Python 3.7.12 (Anaconda version: 4.8.5) and run on Windows OS:
```
Windows-10: 10.0.19041-SP0
```
- The versions of Python packages which we used are, specifically:... |
b6ee034a0dc6989599e9abf1ec7d01fee60e1754822708835a675827e72513e3 | Text | 1,661 | 22 | # GraphGPT
### Natural Language → Knowledge Graph
*Note: this is a toy project I built out over a weekend. If you want to use knowledge graphs in your project, check out [GPT Index](https://github.com/jerryjliu/gpt_index).*
GraphGPT converts unstructured natural language into a knowledge graph. Pas... |
521ecb49cd00c6ab9575a3cd8a665bf0baeea426b49dbc577d174a054334231c | Text | 1,663 | 50 | # OSTEO_MODELS
UNIMODAL and MULTIMODAL CNN MODELS TO PREDICT OSTEOPOROSIS
Multimodal.ipynb, UNIMODAL_CT.ipynb and UNIMODAL_MRI.ipynb are the saved models in Jupyter Notebook and can be used for TESTING OSTEOPOROSIS.
UNIMODAL_CT.html and UNIMODAL_MRI.html are the saved models in Jupyter Notebook as html.
trainable_un... |
eefd9fef181e90907dfc084ca1440ff6f3b50dd51556d1e3c408db761cc8ef65 | Text | 1,663 | 34 | # *linc-mipep* and *linc-wrb* encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
- This repository contains R scripts and codes for various analyses of scRNA-seq and scATAC-seq data in the following preprint by Tornini et al.:
<https://www.biorxiv.org/content/10.1101/2022.07... |
a08794cb9d1138d344359b23fe5434885a8220713de93bb8af83dfa0d45bdf6a | Text | 1,678 | 26 | # SpikeShip: A method for fast, unsupervised discovery of high-dimensional neural spiking patterns.
The Python 3 module `spikeship` which implements the fast, unsupervised dissimilarity measure described in Sotomayor-Gómez, B., L., Battaglia, F. and Vinck, M. (2023). "SpikeShip: A method for fast, unsupervised discove... |
36052d1b853ed67ca749eedb6ebf77ccebba2950302d2442b1ea3b5615269707 | Text | 1,708 | 30 | # INRF-IQA-VQA
This repository contains the Matlab code to run the INRF-IQA and INRF-VQA algorithms in "Luna, R., Zabaleta, I., & Bertalmío, M. (2023). State-of-the-art image and video quality assessment with a metric based on an intrinsically non-linear neural summation model. Frontiers in Neuroscience, 17."
Folder ... |
9e1c5c77d7bc6a40e027a635cd2e67413835cf14079f8c5a4810da1cd1cb6bee | Text | 1,708 | 61 | # EVOLVE
A genetic algorithm tool to mutate protein structures based on Richardson's Rotamer library and to
fitness evaluations
## Citations
Please cite the following work if you use and modify EVOLVE to add your own evaluators.
`EVOLVE citation`
## Getting Started
These instructions will get you a copy of the p... |
e5c8fb4e0483f28f3420fd3939cdc7042aad37be81f823b3d074364523d9bae2 | Text | 1,708 | 38 | """"""""""""
SNS-Toolbox
""""""""""""
Documentation is available on `ReadTheDocs <https://sns-toolbox.readthedocs.io/en/latest/index.html>`_:
.. image:: https://readthedocs.org/projects/sns-toolbox/badge/?version=latest
:target: https://sns-toolbox.readthedocs.io/en/latest/?badge=latest
:alt: Documentation St... |
539d7e7b6a5c8c1b425dba3467df0ddd12ffec9bac0cbe73f5ff76dadbdd5d36 | Text | 1,714 | 39 | # Temporal Mapper
This repository hosts code related to the Temporal Mapper project written by Mengsen Zhang. The associated paper is the following:
> Zhang, M., Chowdhury, S., & Saggar, M. (2022). [Temporal Mapper: transition networks in simulated and real neural dynamics](https://braindynamicslab.github.io/papers/t... |
d7dd78639821fabe4a9742e14f10830ee55a949e8b6fc876a5953667ab382072 | Text | 1,725 | 25 | # Pause-And-Play
Source code for the upcoming Nature Neuroscience paper entitled "Pedunculopontine Chx10+ neurons control global motor arrest in mice", [Goñi-Erro et al. 2023](https://doi.org/10.1038/s41593-023-01396-3)
**Chr2 Grooming behaviour**
### Abstract
Arrest of ongoing movements is a... |
60ad6cb63e003b7c3eebb7ef5220dea5f92f70b3b895c9e53188cc806d731703 | Text | 1,730 | 38 | # Mutate and Observe
This repository contains the code and some materials used in the experimental work presented in the following paper:
[1] [Mutate and Observe: Utilizing Deep Neural Networks to Investigate the Impact of Mutations on Translation Initiation](https://academic.oup.com/bioinformatics/advance-article/do... |
081a2b4115e8f9b9aba0554a58bd41bc7e2d81f7322f4c7a45a412fd20a13c2c | Text | 1,731 | 56 | <img src="FRmatch-sticker-2.png" width="110" height="125">
# FR-Match v2.1
__Citation:__ Hu et al. (2026) *bioRxiv* https://pmc.ncbi.nlm.nih.gov/articles/PMC12190912/
__*To contribute, please open an [issue](https://github.com/NLM-DIR/FRmatch/issues) on this Github repository.*__
## Prerequisites
* R
* S4 class da... |
cc5a11145d16cf3491d62b2c94f1c6c8e5d71cc95876b4d563ffba91d18f614a | Text | 1,733 | 29 | Cardiac Electromechanics Research Group App
-------------------------------------------
[](https://github.com/CemrgDevelopers/CemrgApp/actions/workflows/build.yml)
[![Tests](https://github.com/CemrgDevelopers/CemrgApp/actions/wor... |
ac728737ecac689f915798b73fd5ed88965bf48c3e010d1c5df5c891200b0fa0 | Text | 1,746 | 27 | # ZebrafishAquaticVisualStatsCode
This repository contains Matlab code for running the analyses described in the manuscript "Spatiotemporal visual statistics of aquatic environments in the natural habitats of zebrafish" By Cai et al.
The dataset of terrestrial and aquatic videos should be downloaded separately from:... |
a6545017fead688032952087c182d9c22f56976dd01ca9156c6dc8fc5b6c9c09 | Text | 1,759 | 35 | # PLS COVID-19 emotions
Code to compute partial least square (PLS) correlation results and figure for the publication : Thomasson, M., et al. (2023) _Markers of limbic system damage following SARS-CoV-2 infection_
The code includes two parts: the first part runs in Matlab (folder MATLAB) and is taken from the _myPLS... |
4deae2e7cc3732781997d3f6afa2168ea472cd8d37646a0e2a0cb3f6cdd65ef5 | Text | 1,770 | 50 | ## Interneuron evolution
Analysing the evolution of cortical interneurons using single cell RNA sequencing data. This code accompanies the paper [Cortical interneurons: fit for function and fit to function?](https://doi.org/10.1101/2023.02.23.529671), in which we constrast a functional (or optimisation) view of interne... |
8ad76beb95dfce4bd604abbb8206f410bb878a43ba3db248c5556797325c17b7 | Text | 1,781 | 59 | Coding Potential Calculator
===========================
Introduction
------------
Coding Potential Calculator (CPC) is a Support Vector Machine-based
classifier to assess the protein-coding potential of a transcript (i.e
whether a cDNA/RNA transcript could encode a peptide or not) based on
six biologically meaningful... |
6d0a6437c36d46ef7b4084cda74d4c51958c089f79aee209fac8737520bae0da | Text | 1,807 | 38 | # KCF tracker in Python
Python implementation of
> [High-Speed Tracking with Kernelized Correlation Filters](http://www.robots.ox.ac.uk/~joao/publications/henriques_tpami2015.pdf)<br>
> J. F. Henriques, R. Caseiro, P. Martins, J. Batista<br>
> TPAMI 2015
It is translated from [KCFcpp](https://github.com/joaofaro/KCFc... |
e8908c86851315a9f7edaeffa37b840d4be9339ecb652959344d4fc7b3711453 | Text | 1,817 | 19 | # Mouse Brain Cell Counting
This repository contains Jupyter Notebook and Streamlit app that allow working with the data that accompanies the article. Click the button below to execute the Brain Data Explorer application.
[](https://d... |
f1875706159876b8a4d80f6bff0b541e10b1c2412430c01127af8b04abf0407e | Text | 1,834 | 36 | ## A model of cue integration as vector summation in the insect brain
This repository accompanies the manuscript "A model of cue integration as vector summation in the insect brain". All relevant data and sofware are included in this repository.
## Software
All python code used for simulations and plotting can by fou... |
81cfedbb287d84749edd2c719832c635ad86732f9d5914fcfe6c098dd6220e85 | Text | 1,880 | 52 | # multiunit-cluster
Python code for "A multi-level account of hippocampal function from behavior to neurons".
## Software and packages
Python version: 3.8.2
Python packages:
- pytorch 1.7.1
- numpy
- matplotlib
- scipy
- pandas
- itertools
- imageio (optional: plotting gifs)
## Scripts
Models
- MultiUnitCluster.p... |
7104502af6a407abee195856612c04b94979ca7e0faa7b14809de6483e04e3a3 | Text | 1,886 | 35 | # Parieto-occipital ERP indicators of gut mechanosensation in humans
## Introduction
This repo contains codes and scripts used to analyze data from minimally invasive probe targeting perceptions of the gastrointestinal system via capsule vibration. Please refer to ... |
02ffc81afbc6b67024fd5196e4d47e35db4156c12b4cff9917e9d275e180120a | Text | 1,901 | 58 | # EvoAug Analysis
This repository performs the analysis from "Evolution-inspired augmentations improve deep learning for regulatory genomics" by Nicholas Keone Lee, Ziqi (Amber) Tang, Shushan Toneyan, and Peter K Koo. Code in this repository is shared under the MIT License. For additional information, see the [EvoAug ... |
b1d867415c13fad6bdf1af64967e514a2810438955e959f691457e80ea2ffbf1 | Text | 1,903 | 53 | # AcrNET: Predicting Anti-CRISPR with Deep Learning
Pytorch implementation and trained model for *AcrNET: Predicting Anti-CRISPR with Deep Learning*.
## Environment Setup
- Download the repository.
```python
git clone https://github.com/banma12956/AcrNET.git
cd AcrNET
```
- Install [anaconda](https://www.anaconda.com... |
cf52ec8a6c994d3d0df1827caf1cb01377e5b49a35be990b1e7d3e51e40cf642 | Text | 1,903 | 19 | # Nova Proteins Direct Synaptic Integration of Somatostatin Interneurons Through Activity-Dependent Alternative Splicing
## Abstract
Somatostatin interneurons are the earliest born population of cortical inhibitory cells. They are crucial to support normal brain development and function; however, the mechanisms under... |
21197fe5148233e26c6c56372ce6a814a4f7be8eed3f16df361cb81dae83bca0 | Text | 1,929 | 37 | [](https://zenodo.org/badge/latestdoi/621232437)
## A model of cue integration as vector summation in the insect brain
This repository accompanies the manuscript "A model of cue integration as vector summation in the insect brain". All relevant data and sofware are include... |
56b40a3da24188f1fd91fcdb321dadb96557aff9f16ebc8b418d959ff83fab59 | Text | 1,952 | 63 | AA-TransUNet: [Attention Augmented TransUNet For Nowcasting Tasks](https://arxiv.org/abs/2202.04996)
---
[AA_TransUNet](https://github.com/YangYimin98/AA-TransUNet/blob/main/model.eps) Architecture.
---
Datasets & Pre-trained Mode... |
61cbbb266202577f77dc4cea9c27c7b377b7a2ee6ce9486647ef726a84e380a2 | Text | 1,959 | 77 | colorednoise.py
===============
Generate Gaussian distributed noise with a power law spectrum with arbitrary
exponents.
An exponent of two corresponds to brownian noise. Smaller exponents
yield long-range correlations, i.e. pink noise for an exponent of 1 (also
called 1/f noise or flicker noise).
Based on the al... |
c5e5274b82f8b587d825fb3d37f6ded0f2c28ee9ce53dc28b72f01fd15ca75e8 | Text | 1,991 | 57 | # Overview
Contact: ryan.dale@nih.gov
Given the position of variants and protein domains within a cDNA, this tool
will run many permutations and calculate empirical p-values for the geometric
mean of pairwise distances be... |
68188ea0c24436a7384ec60a09c58e0f85fca77e3395872e02384ada043874af | Text | 2,002 | 55 | # qupath-spot-utils
Scripts for processing microarray spots in QuPath
### Citation
If you use this package in your work, please cite:
Geras, A., Darvish Shafighi, S., Domżał, K. et al. Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data. Genome Biol 24, 120... |
b91580aeea7ba071e601f78cd758021e1cce0c4b7973adc273c7ed6dc968d4fd | Text | 2,003 | 45 | ### [Wearable based monitoring and self-supervised contrastive learning detect clinical complications during treatment of Hematologic malignancies](https://www.nature.com/articles/s41746-023-00847-2#additional-information)
## 1. Data Preparation
Let's start with the data preparation.
By runing [`data_alignment.py`]... |
081f82d16ea4a236c332102afd4dcf432c3c5a0b6e6cb5252228edeb6d703ff9 | Text | 2,012 | 35 | # Single-frame super-resolution microscopy（SFSRM）
Example data and demo of SFSRM for single-frame super resolution of microscopy images.<br>
## Requirements
SFSRM is built with Python and pytorch.
* Python >= 3.7
* PyTorch >= 1.7
## Install
1. Clone repo<br>
```
git clone https://github.com/crrayna/SFSRM.git
... |
6480bcfb3397ba499006236f4aea5b142c47e87b8b910552d4cd9c3dc3ebc584 | Text | 2,059 | 48 | ################ ACRIMA project ################
The images of this database come from the ACRIMA project (TIN2013-46751-R) founded by the Ministerio de Economía y Competitividad of Spain, which aims to the development of automatic algorithms for retinal disease assessment.
In this folder, the images of t... |
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