sha256 stringlengths 64 64 | language stringclasses 28
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|---|---|---|---|---|
e1c05d77275adc32ed16561a60f603189db61fc722a856897085f132c2da2ef5 | Text | 2,841 | 80 | # Piezo-mediated mechanosensation contributes to stabilizing copulation posture and reproductive success in Drosophila males
[](https://zenodo.org/badge/latestdoi/620594822)
### Figure 2C, D
- DeepLabCut model for tracking the flies position : male_copulation_posture_mod... |
8974a9effcd243b0458966229b23d85557b0f06784f4798873663eb8220d272f | Text | 2,845 | 45 | # Attention based deep learning on EHR data
Replication of recent deep learning models using attention. SARD [1], RETAIN[2] and a Variational GNN [3]. Developed using
the OMOP common data model. The fitted models are stored in /SavedModels
### How to Install
* Install python dependancies from the requirements.t... |
2e561395bf485789a56c1f3120ea350c83bbd1ab6dff36026740ed35d882546e | Text | 2,853 | 53 | # bioseq2seq
## Overview
This is the official repository for the preprint [Improving deep models of protein-coding potential with a Fourier-transform architecture and machine translation task](https://www.biorxiv.org/content/10.1101/2023.04.03.535488v1).
This repository began as a fork of [OpenNMT-py](https://github.... |
8ac7852131b5d904a0aa7a9447a06a649bfde3ef3f2fc86e4f3881372b32c71f | Text | 2,857 | 79 | Code related to the publication:
*The CALIPR framework for highly accelerated myelin water imaging with improved precision and sensitivity*.
# Supporting Data
Supporting data is available at:
[](https://doi.org/10.5281/zenodo.8049179)
and includes bra... |
320d8d867939911ce156a4932b7c00765aeb6031d9351c5d0e58f3c160aba1da | Text | 2,865 | 51 | Code to reproduce spatial proteomic analysis from Davis et al. "Deep topographic proteomics of a human brain tumour"
The analysis is included as an Rmarkdown html file (SpatialAnalysis.html), the corresponding SpatialAnalysis.Rmd file, and the input data.
Installation and running:
1. Download this directory
2. ... |
bdb8bc6acfa2e9b71cd485db45d37cbbfb5a24199bc4fe903448a4f71092906b | Text | 2,872 | 34 | # wormdatamodel
Module implementing a data model for the whole brain recordings (more broadly, of any multichannel volumetric recording - sequence of "hyperstacks"). While there are only a few options to efficiently store an uncompressed sequence of images, so that the issues with uncompatibility of that data with diff... |
ec84e8caf69e8cc9521f60f39d9ae4c44d39c97ceb4e9b9fea7bd50440aa1c89 | Text | 2,903 | 68 | <p align="center">
<img src="https://i.imgur.com/yfXlCYO.png"
alt="deepreg_logo" title="DeepReg" width="300"/>
</p>
<table align="center">
<tr>
<td>
<b>Package</b>
</td>
<td>
<a href="https://pypi.python.org/pypi/stlearn/">
<img src="https://img.shields.io/pypi/v/stlearn.svg" alt=... |
91c3e02a8d0a92bfd4250217317c9fefbaecefa2546fecd4bb3fb5153971f042 | Text | 2,919 | 52 | # A developmental increase of inhibition promotes the emergence of hippocampal ripples
#### Irina Pochinok, Tristan M. Stöber, Jochen Triesch, Mattia Chini, Ileana L. Hanganu-Opatz
Preprint on biorxiv ([here][spwr_biorxiv]).
[spwr_biorxiv]:https://www.biorxiv.org/content/10.1101/2023.08.11.552951v1
Published in Nat... |
ec4cbbf87b228767c69dfc0900fa9de68b429619b67c8ac5f53c763330e940c6 | Text | 2,939 | 67 | # Big-Small Patch (BSP)
Big-small patch is a granularity-guided, data-driven, and parameter-free model for identifying spatial variable genes in 2D and 3D high-throughput spatial transcriptomics data.
### System Requirements
* Python 3.7+
* scikit-learn
* numpy
* pandas
### Installation
Tested... |
d74da9dfa527cdb1a8cc1d8e9a93b025f478cc4edee1809a1c14a5ae689923cc | Text | 2,943 | 44 | # MATLAB code for 'The medial septum controls hippocampal supra-theta oscillations'
## Description
This repository contains MATLAB code for data analysis on the connection between theta-nested spectral components (tSCs), single unit activities and optogenetic stimulus events. Single unit clusters and hippocampal tSCs... |
c5c6ba2e98d625ba033b84fbbf617fcc18dd73a77da440ed28ad2659bce5ca11 | Text | 2,953 | 23 | Code repository for Talluri, Kang et al. 2022 bioRxiv doi: 10.1101/2022.09.08.507006
If you use the data or the code, please cite: Talluri, B. C., Kang I., Lazere, A., Quinn, K. R., Kaliss, N., Yates, J.L., Butts, D.A., Nienborg, H. (2022). Activity in primate visual cortex is minimally driven by spontaneous movements... |
9f6ce87755e6ff7f98540124f275e40968219e96691218a2bfc23f8cb8a13b55 | Text | 2,961 | 62 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
**This is the legacy repository of BIDSconvertR. Please visit the new repository for LTS: [BIDSconvertR](https://github.com/bidsconvertr/bidsconvertr)**
[](https://doi.org/10.5281/zenodo.5878407)
[**
[](https://zenodo.org/badge/latestdoi/448850893... |
6682f302d04ec959ed0420d8c2bf16783558cd8255f3eb9843252bd508912c61 | Text | 2,980 | 19 | # Project-RRpo-2ndStudy
```
forehead start with 9x_<filename> is the recent code file.
```
기존의 연구인 [Project-RRpo](https://github.com/Noritheyellow/Project-RRpo) 를 참고하라. 기존에 작성했던 논문에서의 주안점은, 서울성모병원 외과중환자실에서 습득한 중환자 50명과 건강한 자원자 50명의 PPG, RR 2분 데이터(**StMary**)와 Bian 이라는 저자가 구성하였던 ResNet 을 독자적으로 구현하고 이용하여 PPG로 RR을 예측하였다... |
c866503a32e839d5cce6c7bd27ed19b60bc8995607f3d0e822bba6aecd9cfdde | Text | 2,982 | 95 | # Introduction
This script allows to do some image preprocessing activities on sonography images.
The actions that can be performed are:
- anonymize;
- crop;
- fill area inside the trace;
- measure area;
- generate trimap images (visible and binary formats).
# Setup Environment
## Linux and MacOS
```sh
$ python -m v... |
eb1053af4c73942bd8782a6267481a57f16cac7ce9e390caeba158f2667e217a | Text | 2,985 | 100 | 
Auryn
=====
Auryn is Simulator for recurrent spiking neural networks with synaptic
plasticity. It comes with the GPLv3 (please see COPYING).
* For examples and documentation visit https://www.fzenke.net/auryn/
* Please ... |
830ecc3dea85e214af814a229a06e1a53fb8fd6a928a06cd8d4740e4a520d32b | Text | 2,994 | 50 | # High-throughput single cell analysis reveals progressive mitochondrial DNA mosaicism throughout life
This repository contains all scripts necessary to reproduce the data analysis and figures presented in Glynos _et al._ (2023).
## Software requirements
### Operating system
This repository was developed and tested... |
c61c9eff4992d23bf7cb2326fe8258ca3fa0aaed852030853ca042020df46feb | Text | 2,994 | 24 | # Manifold discovery and analysis
This code implements the manifold discovery and analysis (MDA) algorithm presented in "Revealing Hidden Patterns in Deep Neural Network Feature Space Continuum via Manifold Learning, in press, Nature Communications, 2023".
Please run demo_MDA.ipynb for analyzing deep learning feature... |
83b1ec891f82316d78f7ff2c121f0ce2b5cbc80d1c8046619d38367edf66c8ad | Text | 3,006 | 68 | # KinomeMETA
The code of "KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling"
Kinase inhibitors are crucial in cancer treatment, but drug resistance and side effects hinder the development of effective drugs. To address these challenges, it is essential to analyze the polypharmacology of kinase ... |
7d05e70b0541a50489a6cecb9796a01e12ff3e3ff634509b77219fc4395bd1c9 | Text | 3,008 | 51 | # Biomimetics Ring Attractors
This repository accompanies the paper "Ring Attractors as the Basis for a Biomimetic Navigation System" by Thomas C. Knowles, Anna Summerton, James G.H. Whiting and Martin J. Pearson.
Published in _Biomimetics_ at https://doi.org/10.3390/biomimetics8050399
## The model in action:
](https://doi.org/10.5281/zenodo.5878407)
[](https://bids-specification.readthedocs.io/en/v1.8.0/)
[](https://doi.org/10.5281/zenodo.10903835)
# cellScaleFactors
[<img style="float: right;" src = "inst/figures/cellScaleFactors_hexsticker.png" height="180"/>]
Authors: Sean Maden, Stephanie Hicks
Datasets containing reference tables for cell scale fact... |
3cdb07f73a1bc3132a951508b2ae879445722a08dd0210dac3818d60d63d3c4f | Text | 3,036 | 70 | # Predictive Minisci Late Stage Functionalization with Transfer Learning
Code for the <sup>13</sup>C NMR pretraining and LSF finetuning as described in [King-Smith *et al.*](https://www.nature.com/articles/s41467-023-42145-1?fbclid=IwAR1RnBIirqNfBQUdKE__VOmHBt-yPwn4ilsaX4ZmxzTiBkfHDdR0p82_bX8)
[](https://doi.org/10.5281/zenodo.8049179)
and includes bra... |
b15fd9aa44131b8589b5ffa156f13c8e53fafc799622935e66e9f16c3286e0fb | Text | 3,072 | 24 | # MEAanalysis_ONeill2023
The code in this package was developed to analyze *.mcd files generated during microelectrode array (MEA) recording experiments. It was developed by Kate M. O'Neill (oneill.katem@gmail.com), and all questions should be directed to her and to corresponding author Bonnie L. Firestein (firestein@... |
bb3d398c6be05e229758251da645d9eb736f3ee39301fc17160a3845bce13313 | Text | 3,074 | 86 | .. image:: https://perso.telecom-paristech.fr/bonald/logo_sknetwork.png
:align: right
:width: 150px
:alt: logo sknetwork
.. image:: https://img.shields.io/pypi/v/scikit-network.svg
:target: https://pypi.python.org/pypi/scikit-network
.. image:: https://github.com/sknetwork-team/scikit-network/ac... |
1144e91578e8d4f93b8f13caf4e2e8d4014cbbc75c3c84a931136a92d95df671 | Text | 3,078 | 71 | # Guitar Style Dataset
In this work we present an original, publicly available audiovisible dataset for guitar playing style classification, which is associated with the distinction across 9 types of playing techniques that encompass the vast majority of guitar technique types. We provide two different ways for classi... |
b803c986f8ed2359bb4d9293837640541ce7e0741400ac5e1aecd0d7c134d286 | Text | 3,089 | 35 | # Revisiting a classical theory of sensory specificity: assessing consistency and stability of thermosensitive spots
[Data](data/)
[BioRxiv v2](https://www.biorxiv.org/content/10.1101/2023.07.17.549302v2)
[BioRxiv v1](https://www.biorxiv.org/content/10.1101/2023.07.17.549302v1)
## Highlights
* Our skin's sensitivity t... |
8c265dcafaa0860408de9ed880383a7b6fbdff44263feb52de3282f5cb55ccbd | Text | 3,091 | 68 | # TMS-EMG Kit
*Version 2.1*
### New Feature Update - Plugin Support. Develop and test your own signal processing and analysis algorithms. Community sharing coming soon.
The TMS-EMG Kit is a data analysis application built for researchers working with Transcranial Magnetic Stimulation and electromyography data. It t... |
c2b290c544c0e003fea9d97aa2161364ad79e044f4c54c01c9de0a091e7d11a3 | Text | 3,108 | 48 | [](https://pypi.org/project/bio-past)
[](https://pepy.tech/project/bio-past)
[](https://past.readthedocs.io/en/latest/)
# PAST: a Pr... |
6dbea53115c4df452238561458fd29e816be3a8850c3335af6696af939aec6fb | Text | 3,118 | 57 | # The Glottolog Data Repository
The Glottolog data repository is the place where the data served by the
[Glottolog web application](https://glottolog.org) is curated. This curation workflow includes
- aggregating data from other [sources](SOURCES.md)
- integrating data (e.g. by adding language identifiers to reference... |
da9148cd2251c7b7fa114b46f77e7e2d6e9c3925ef667aba95fedc627a76336b | Text | 3,130 | 70 | This folder contains the processed data and scripts 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
Processed EEG data are found in */eeg_data/*.
* */eeg_data/timelock_dat... |
e6473fca287b58566c170138e1a1b15fa9f3eb5bc1df730a8b79fac49d2ac07e | Text | 3,141 | 80 | # AlphaFold prediction for Drosophila melanogaster CACNA2D3 a2d3 protein structure
This repository provides tools for visualizing the AlphaFold protein structure and pLDDT statistics. We showcase examples for the Drosophila melanogaster CACNA2D3 a2d3 wild-type protein, as well as its two mutant forms: loss-of-function... |
3d2978568652eaecd10bf985b67c4c08c1b97d0efaf79e16c3b47c1ce30bb2ac | Text | 3,153 | 66 | Dataset provided to reproduce figures for the paper
"A unifying method to study Respiratory Sinus Arrhythmia dynamics implemented in a new toolbox"
Jupyter notebooks are available here:
https://github.com/samuelgarcia/physio_benchmark
Human dataset
=============
Contact information : valentin.ghibaudo@inserm.fr ;... |
829770f5efa76cf3dc11146316746a52fc80f4e3314308179b0b5c5391d95c09 | Text | 3,194 | 80 |
<img align="up" src="https://github.com/chunxxc/lokatt/blob/main/lokatt_paint.jpg" alt="drawing" width="400">
# Lokatt: An open source HMM-DNN nanopore DNA basecaller
## Installation
### Install from source (recommended)
It is recommemded to install the lokatt basecaller from source. This only requires the tensorfl... |
bdc78294fa51805ababc6146c919e5c4ed3c5d022f756ad41f96da77e101c13f | Text | 3,194 | 51 | # LMX1A_iPSC_DA
A repository of RMarkdown files used to analyze sc-RNA sequencing data from induced Pluripotent Stem Cell derived dopaminergic neurons of the LMX1A Cre AAVS1 BFP line.
## Data availability
Raw and processed gene expression data has been deposited in GEO:
+ Time Course experiment [GSE247600](https://ww... |
a2825f0e6600744b24e956630910e0bddf8c2c80eb33b2a2069c281923f1d2e8 | Text | 3,204 | 64 |
# Cell-type-specific expression and regulation in atypical Schinzel Giedion Syndrome (SGS)
__Jordan Whitlock, Tabea Soelter, Timothy Howton, Elizabeth Wilk, Vishal Oza, Brittany Lasseigne 2023__
__The University of Alabama at Birmingham (UAB), Heersink School of Medicine__
## Data Availability
[
### Usage
Clone the... |
b51645325cfc3c0c4ed113ac759d31e2bb1711717ba950c15da5dce23530f98f | Text | 3,233 | 40 | # Welcome to the EUGENe Paper Repo!
This repository contains the code used to generate the results presented in the manuscript "EUGENe: A Python toolkit for predictive analyses of regulatory sequences." You can find the EUGENe documentation pages [here](https://eugene-tools.readthedocs.io/en/latest/index.html) and the ... |
8ea8d5261435b6188eef3c011a284f74c0d1ffeacbb749df8c27cbec2ad019a5 | Text | 3,236 | 74 | <p align="center">
<img src="https://i.imgur.com/yfXlCYO.png"
alt="deepreg_logo" title="DeepReg" width="300"/>
</p>
<table align="center">
<tr>
<td>
<b>Package</b>
</td>
<td>
<a href="https://pypi.python.org/pypi/stlearn/">
<img src="https://img.shields.io/pypi/v/stlearn.svg" alt=... |
0ea8fdfbb624d7ede92b7396f406db3fc47bda9552f1f0edeba339b00e733932 | Text | 3,237 | 56 | # Sampling-based inference in a population of Poisson spiking neurons
[](https://www.biorxiv.org/content/10.1101/2020.11.18.389197v2)
- [Overview](#overview)
- [User guide and system requirements](#User-guide-and-system-requirements)
- [License](#L... |
c1247c847d49f2d55bd5badb87974c837209946591e52b158be76577832827b9 | Text | 3,248 | 26 | # Proteomic-and-transcriptomic-signatures-of-microglia-derived-extracellular-vesicles-
This Repository hosts code that was used in analyzing data for the paper: Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles
Identification of state-specific proteomi... |
976e38579216aa39fd7450a507e83e7529819bc39d700b8ea370ef1be13b0598 | Text | 3,257 | 52 | # Asymmetric RPE paper code repository
This code repository is for all preprocessing, analysis, and plotting scripts related to Hoy, Quiroga-Martinez, et al. "Asymmetric coding of reward prediction errors in human insula and dorsomedial prefrontal cortex" (Nature Communications 2023)
## Data and Experimental Paradigm:... |
59b83104f2fed70e81416f8dc0fadefd339299995ef3ce327ffc681a003fd662 | Text | 3,258 | 68 | # Effects of MRI scanner manufacturers in classification tasks with deep learning models
The paper has been accepted for publication in Nature Scientific Reports (https://www.nature.com/articles/s41598-023-43715-5).
```
@article{kushol2023effects,
title={Effects of MRI scanner manufacturers in classification tasks... |
6c1c4fa0c98935ed339dfa8a5e55fbb5f4827c00ecb22d2b0457d0af56afb8fe | Text | 3,260 | 26 | # wormbrain
This package contains code to handle small point sets representing small brains. It provides a class, Brains, to represent coordinates of a sequence of instances of the same brain, for example the same brain at different time points; functions to to match points in two point sets; and functions geometricall... |
f530d223f4a6de907bc8becff7437121479d065590f39a2ec3619382e72f4cc7 | Text | 3,289 | 74 | controller_validation
==============================
Validation study for the MEG/MRI video games controller developped by the CNeuromod team
To install (assuming you're using conda):
```
git clone git@github.com:courtois-neuromod/controller_validation
conda create -n controller_validation
conda activate controller... |
565b3e08e0591d04bc65a1c3540202098411ec820272b62165d8df24f94a29fd | Text | 3,307 | 98 | RetinalMap
==========
A framework for retinotopic map formation modelling and
evaluation. Currently four models are fully supported (Gierer, Koulakov,
Whitelaw and Willshaw). There is also code to run the Grimbert and
Cang model.
URL for github repository, this will create a RetinalMap directory:
https://github.com/H... |
7a53232cba2f4b1dfa673ea4f134846bcfcc54d92f13db97b5d42cda42979df8 | Text | 3,309 | 82 | This is the data and code to accompany the paper "Classification of Neurons in the Adult Mouse Cochlear Nucleus: Linear Discriminant Analysis" by Paul B. Manis, Michael R. Kasten, and Ruili Xie
File Manifest
-------------
1. NWB\_files_.zip : A zipped archive of NWB (Neuroscience Without Borders; https://neurodatawit... |
28c28eed7b7320cfd7fda8323c806c8c0e7594c13bddec38d18985796f998cb1 | Text | 3,314 | 72 | # Categorical Scatter plot (Box Whisker plots with data points)
A replacement for the traditional box and whisker plots provided in MATLAB (command boxplot). The categorical scatter plots additionally shows the data points, which is useful the visualize the underlying distribution (similar to violin plots).
## Example... |
4b6e36f6a11c48de227b0c38fb4e76eacba501eb41d75e4fe356108658e3221f | Text | 3,319 | 80 | # PyCoBi
[](https://github.com/pyrates-neuroscience/PyCoBi)
[](https://badge.fury.io/py/pycobi)
[](https://badge... |
a4cc1ec937f6f74fd06d476b798305c9074186236e68df7703ef37bd7e8d7f81 | Text | 3,324 | 12 | # SemiSeg
Code for Semi-Automated Segmentation of Microscopic Video Data. Created for Widefield Fluorescent Calcium Imaging data formatted as tiff stacks in Mice. Nothing too novel used, as many techniques are used in commercial packages, but I needed something I could get under the hood with and alter things as nece... |
997f345b8f27c9c7019b314ec00275f58c7e388bd3c3204f97282b56329ac04a | Text | 3,327 | 51 | # From Proteins to Ligands: Decoding Deep Learning Methods for Binding Affinity Prediction
This repository contains all code, data, instructions and model weights necessary to run or to retrain a model.
## Project Abstract
Accurate *in silico* predictions of protein-ligand binding affinity can significantly acceler... |
70d6212bc02a8f89e06f2644268a2d91609317466fc489d9b2f6da7485a9f77f | Text | 3,329 | 61 | # ptltsne
Parametric time-lagged tSNE. The code fits the input trajectory to a reference PDB
file. Next, it introduces a time lag in the spirit of time-lagged independent component
analysis (TICA) method. Finally, it optimizes parameters of an artificial neural
network to provide tSNE representation as the output. It ... |
0821d97aa7f982786f21461443a6febdeaae99e0efbdba4c1a63c2df090cfe09 | Text | 3,347 | 90 | DOI Citation
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, https://doi.org/10.3389/frai.2023.1230383
Introduction
Facial characterization and imag... |
f8e56ed892b5d0e306cd6ef520b1cfb2fca4e01189dd5caa280bc9cc51f5c373 | Text | 3,349 | 74 | # causal-optoconnectics
Causal inference of connectivity between neurons
# Introduction
When estimating connectivity between neurons, confounders are your enemy when
you desire an estimate that reflects the causal (mechanistic) influence
between neurons.
Confounding arises when there is a common drive that
influences ... |
ef639eea80dcc5a7a3ea1d55b59e877e59929d756a209003089e229178549db1 | Text | 3,352 | 62 | # TorchRBM
Basic implementation in Pytorch of the Restricted Boltzmann Machine with binary hidden units.
*Example of samples obtained for a RBM trained on CelebA in black and white:*
## Installation
Install the package
```bash
... |
1723167b73a1ebb5c4e3af989d1872b5c74dcd01107666d8c56e422a4a365768 | Text | 3,369 | 40 | # CEST-Generator
#### **Introduction:**
This repository contains the MATLAB implementation for generating synthetic 2D CEST datasets and in silico phantoms. It is designed to simulate Chemical Exchange Saturation Transfer (CEST) MRI datasets and serves as a reference standard for improving neural net... |
6ac83b159a4e79ccfc9c524810de7f42291ffe44160e2d305f3205c8e20d7357 | Text | 3,378 | 69 | <div align="center">
<h1>Apnea of Prematurity and transcriptional cerebellar changes</h1>
<h3><i>Main branch</i></h3>
[](/LICENSE)
[](https://zenodo.org/badge/latestdoi/665567093)
<a href = "https://ma-... |
3194e9763cf9de699a5c71cdc03511b157512692baf125717ae14a57f9887d22 | Text | 3,379 | 53 | # Matrix Product Belief Propagation
[](https://github.com/stecrotti/MatrixProductBP/actions/workflows/ci.yml)
[](https://codecov.io/gh/... |
9bc23a2cd0dab278796333bbb357c2edc2b856429a7ab03052321e3f10c7e554 | Text | 3,393 | 59 | # [**Common infections and neuroimaging markers of dementia in three UK cohort studies - Green et al., 2024**](https://doi.org/10.1002/alz.13613)
_Rebecca E Green, Carole H Sudre, Charlotte Warren-Gash, Julia Butt, Tim Waterboer, Alun D Hughes, Jonathan M Schott, Marcus Richards, Nish Chaturvedi, Dylan M Williams_
--... |
da4307d07801f1f1d47af1af9f12426837de7e03484b9032ac0d1c73be27a3bf | Text | 3,413 | 95 | [](https://zenodo.org/badge/latestdoi/265101910)
# idtrees_competition_evaluation
Evaluation metrics for 2020 IDTreeS competition using NEON remote sensing data
<h2> IDTreeS Data Science competition for identifying trees from remote sensing </h2>
This repo hosts the cod... |
6a9ac9f4b078b142950d65ce23edb7d2ea1ae5c5becd5aa32fd4a1977fa97ea5 | Text | 3,441 | 89 | "Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models"
Koji Ooka(1,2) and Munehito Arai(1,2,3)
1 Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
2 Komaba Organization for Educational Excellence,... |
47617888e8d113585c75e1114909d1f0dd9412c2a31cdbc7f34c5599776101c8 | Text | 3,442 | 85 | # PyCoBi
[](https://github.com/pyrates-neuroscience/PyCoBi)
[](https://badge.fury.io/py/pycobi)
[](https://badge... |
bb4ea8ef21cb63940d2fcb1fe3cb01e0f4723e337883b59725f4a2b04a90e287 | Text | 3,454 | 35 | # Code and datasets for C.elegans connectome analysis
This is a connected open-source repository for the publication "Communities in C.elegans connectome through the prism of non-backtracking walks" published in ... |
adb0c4de58aa4123381b92859fa646131aca0102334d7ee4e082b66f8b1625cc | Text | 3,462 | 83 | 
[](https://app.codspeed.io/ML4GLand/SeqPro?utm_source=badge)
# SeqPro (Sequence processing toolkit)
```python
im... |
ffcc6b1fe93bf960fb0effc584e2c1e0b83cc1b9be2789da3e0d18e649e6ce9d | Text | 3,462 | 43 | # omop-learn
## What is omop-learn?
This library was developed in order to facilitate rapid prototyping in Python of predictive machine-learning models using longitudinal medical data from an OMOP CDM-standard database. omop-learn supports the easy definition of predictive clinical tasks, featurizations of OMOP data,... |
b0cf1e23c9b4fc81cad2553d6e190397f7eae467caba85d9e3f59bdbb30757a0 | Text | 3,465 | 102 | # ST Spot Detector
A web tool for automatic spot detection and positional adjustments for ST datasets.
The arrays used to generate ST datasets may contain positional variations due to printing artifacts. This web tool aims to detect correct spot positions using the images generated from the ST protocol.
In order to ob... |
c3acb20050f0a483bca44eea5bf480761df5ee239296d91ae14d85452b7b38f7 | Text | 3,476 | 69 | # dsRID: Double-Stranded RNA Identifier
dsRID (Double-Stranded RNA Identifier) is a machine learning-based method designed to predict dsRNA regions in silico by leveraging the power of long-read RNA sequencing (RNA-seq) and molecular traits of dsRNAs. dsRNAs are potent triggers of innate immune responses upon recognit... |
c23f0066e6956bd3f9516c968ee2803612f1d15f57b7b34414f1efa2c184344f | Text | 3,490 | 70 |
# PMF-CPI：Assessing drug selectivity with a pretrained multi-functional model for compound-protein interactions
## Brief introduction
Here we present a sequence-only and pretrained multi-functional model for compound-protein interaction prediction (PMF-CPI) and fine-tune it to assess drug selectivity. PMF-CPI can ... |
d1fc9858923e3e54bb2f9bb4b985dbc7e581cc089affde5f75b5db28a91e1050 | Text | 3,527 | 70 | # [conST: an interpretable multi-modal contrastive learning framework for spatial transcriptomics](https://www.biorxiv.org/content/10.1101/2022.01.14.476408v1)
We are actively updating this repository! More features/examples/experiments coming soon!
## Overview
Framework... |
dca7d2b983b9afe4c036a0eeea9e691eccc54f29cbb3e06430b56bfd6dcbab12 | Text | 3,532 | 90 | # Analysis tools for split-seq
## Requirements
Requires python 3.
Additional software needed:
- [STAR](https://github.com/alexdobin/STAR)
- [samtools](https://github.com/samtools/samtools)
To install all dependencies, try running `install_dependencies.sh`, which installs dependencies to `~/split_seq_reqs/`.
To in... |
d1360521c2dc1a0e918f6e1e33c801b0e321eca442dc39a51bc4b7d5f359931c | Text | 3,559 | 65 | # Preserved neural dynamics across animals performing similar behaviour
By: Mostafa Safaie<sup>\*</sup>, Joanna C. Chang<sup>\*</sup>, Junchol Park, Lee E. Miller, Joshua T. Dudman, Matthew G. Perich and Juan A. Gallego.
This repository includes code to reproduce the figures in [Safaie & Chang et. al., Nature, 2023](... |
510e8029ccfc48fcbecab05f2c405a287de268b95634c0cb33231e894bd8c7f2 | Text | 3,580 | 53 | # InvivoBrainHSI-Benchmark
## Overview
This GitHub repository contains the MATLAB code of the research paper titled "Hyperspectral Imaging Benchmark based on Machine Learning for Intraoperative Brain Tumour Detection" published in npj Precision Oncology in 2023. The paper presents a robust k-fold cross-validation appr... |
085e1ac9e2d00793b5fa16eb81f0e02cb38d994fc6ac8bc36f13a1bf544a1628 | Text | 3,582 | 37 | # ptychoStainedTissue
Brain tissue ultrastructure resolved with synchrotron X-ray ptychography.
The code in this repo supports the plots and findings presented in this study:
> **Non-destructive X-ray tomography of brain tissue ultrastructure**
>
> Carles Bosch, Tomas Aidukas, Mirko Holler, Alexandra Pacureanu, Eli... |
b0cdeb5202bebe84ac144cbf99f1ef4d86263f27fa10a748568323b4e59574bb | Text | 3,595 | 107 | scripts for downloading previously published snATAC-seq kidney datasets from downloads folder
```
# url accessions for downloading accession files
70M control snATAC-seq kidney
GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172008
Accession: SRX10595439
Biosample: SAMN18736215
Sample: GSM5239694
https://w... |
e0aa71ad255df66530451026f7c7421aad128e5f8c3d2ef160843f88838ce642 | Text | 3,601 | 99 | # OrgCrystGNN
This repository provides codes for OrgCrytGNN.
It is possible to compare prediction accuracy using molecular and crystal graphs.
When you use or refer this repository, please cite the published paper (https://doi.org/10.1021/acsomega.3c05224).
, [arXiv:1401.0080 \[hep-ph\]](http://arxiv.org/abs/1401.0080). It contains tools to apply the discussed methods to new models and contains a... |
7038e42781a11adb109ab1651044fdabb8357d1d875f23056722c60fa9f3ada7 | Text | 3,614 | 17 | # NeuropsychBrainAge
BrainAge models based on neuroimaging data have shown good accuracy for diagnostic classification. However, they have replicability issues due to site and patient variability intrinsic to neuroimaging techniques. We developped a BrainAge model trained on neuropsychological tests to identify a biom... |
41408b2e3788e4b7c75e8ca410609a9e7d74593dcf7123be2e7aa9daa5f04cfb | Text | 3,620 | 90 | ## Spaco: a comprehensive tool for coloring spatial data at single-cell resolution
[](https://www.python.org/)
[](https://opensource.org/license/gpl-3-0/)
[
<img src='./utils/figs/seqdiff_anim_720p.gif' width='600' style="horizontal-align:middle">
## Getting Started
The easiest way to ge... |
e9c1d3cca7c62d205ecbcdc5c8e0218c9d7148dfcaae20cb224a7a0672236b46 | Text | 3,646 | 128 | # Python -> R bridge
[](https://pypi.python.org/pypi/rpy2)
[](https://codecov.io/gh/rpy2/rpy2)
[]... |
092818fbdebeecac74768f3c211924417e3bb61261eea3e2b83ee623a41bce74 | Text | 3,669 | 96 | # cermep-bids-retro
> Brain Imaging Data Structure p**r**e-clinical P**ET**-M**R**I f**o**rmatter
This project is hosted and maintained by the [CERMEP](https://www.cermep.fr/) Imaging Platform in Lyon, France.
## Project description
cermep-bids-retro enables the formatting of retrospective PET and MRI data to BIDS st... |
4168beca7ff1401e469dabc67dc76d1a8e61995c38117240b6d348c6cb6ffb22 | Text | 3,672 | 65 | # Measuring Neuronal Avalanches to inform Brain-Computer Interfaces
---
This repository contains the code and supporting documents associated with the following manuscript:
M.-C. Corsi*, P. Sorrentino*, D. Schwartz, N. George, L. Hugueville, A. E. Kahn, S. Dupont, D. S. Bassett, V. Jirsa, F. De Vico Fallani (2023). M... |
fae58f8eef9c590c957ad5dd49ead735d068c61b26fb18a1a3de05ecf1ae4960 | Text | 3,685 | 70 | # ORN-Optogenetics
ORN-Optogenetics contains the MATLAB code that accompanies the paper: "Sensorimotor transformation underlying odor-modulated locomotion in walking Drosophila."
## Getting Started
This code was made on MATLAB 2019b and tested on 2022 versions.
To get started, please download or clone the GitHub re... |
05ac83dcf5dd7fb2714bdbefd56fb4caf169dd1be79bca1a15df99d597590580 | Text | 3,703 | 68 | # Phenexplain — Official PyTorch implementation
## Requirements
* Python libraries: pip install -r requirements.txt
(Main requirements are pytorch, opencv-python, mako. StyleGAN2 currently does not work with the latest PyTorch version.)
* The official[ StyleGAN2 repositor... |
492a343c3f96384efeb65c00f2fd9dc5e796f131d5200a3f17655bfc609dfcdc | Text | 3,706 | 69 | # dsRID: Double-Stranded RNA Identifier
dsRID (Double-Stranded RNA Identifier) is a machine learning-based method designed to predict dsRNA regions in silico by leveraging the power of long-read RNA sequencing (RNA-seq) and molecular traits of dsRNAs. dsRNAs are potent triggers of innate immune responses upon recognit... |
506738d65c926b87b2fb5a9e5182ee926df4a46c650040c53d08e3b3af3fd1d8 | Text | 3,709 | 96 | # Human few-shot object learning benchmarks
[](https://github.com/himjl/hobj/actions/workflows/ci.yml)
This repository contains the few-shot object learning benchmarks described in ["How well do rudimentary plasticity rules predict adult visual ob... |
6e76d9d2044e01de673865a1fbb0bb2da0e374bcb3625d402c2a11ec64e0cfd0 | Text | 3,721 | 129 | # SAR2Opt-Heterogeneous-Dataset
This is an overview of our proposed heterogeneous remote sensing images "SAR2Opt" dataset.
SAR2Opt dataset can be used as a benchmark in __change detection__ and __image translation__ on remote sensing images.
 — accompanies Paper 7 v3 (concept DOI 10.5281/zenodo.19857662).
Reproducibility and deployment package for Paper 7: *HC-Anchored Rank
Normalization for Cross-Cohort EEG Classification of Alzheimer's Disease:... |
5306494b3f7e6158c69c2fcea016179ac0a5d2eeb0218aa4bb46b12135204668 | Text | 3,786 | 75 | # CAP–HRV: an automated EEG–ECG framework for CAP–HRV analysis
Open-source MATLAB pipeline for integrated analysis of the cyclic alternating
pattern (CAP) of NREM sleep EEG and heart-rate variability (HRV) from overnight
polysomnography. Companion code for the *Frontiers in Physiology* (Technology
and Code) manuscript... |
2647f3d1843569ba869c7b91c4fd83febd78768220d8af5d674acb52f3c8683c | Text | 3,823 | 38 | # Methylation-free E.coli nanopore sequencing (ONT R9.4) data set
This dataset contains the necessary files to reproduce the experiments and evaluate the performance of the Lokatt basecaller, as described in [the accompanying paper](https://www.biorxiv.org/content/10.1101/2022.07.13.499873v2), available in [the Github... |
b121c9c1aab2565e864372ae427a8816ef4b03f9c0e4273a747d037706a9de5f | Text | 3,829 | 92 | # Working Memory (WM) with Self Repairing (SR) in a Spiking Neuron-Astrocyte Network (SNAN)
Some parts of the code are from: https://github.com/altergot/neuro-astro-network
The self-repairing capability and some modifications in the working memory model are added in this work.
This repository is the MATLAB codes for... |
c51e31de34625e84048f0650272dcd9586c8d2b2cf68fddc01f883fd83f72a7f | Text | 3,843 | 81 | ## **CellGO: A novel deep learning-based framework and webserver for cell type-specific gene function interpretation**
## **What is CellGO?**
CellGO is a method designed to discover cell type-specific active pathways of a single gene or a gene set by modeling the propagation of cell type-specific signals through the ... |
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