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c23c9f989f09fd278a2abf6751f6cbe083194653ab42202b94b3bb4ea61e144f | Text | 5,968 | 76 | # Wheel tracker
Documentation for behavioral wheel used for head fixed in vivo recordings. It enables precise recordings of wheel movement and enforced motion via a stepper motor. The motor is coupled to the main axle via a one-way clutch. This way the animal can always outrun the (slower) motor movement, but is block... |
1a766853a9286fed76aa868dda9915cd0e97e35b8beb686806e06c578a7bed79 | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (1/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
2e6dd7861076a366d93bc5d4fc7fb91db049ed06a455c933786ea04c33e36141 | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (2/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
92286f40889aa47885f80935128f4c105a32cca372046bbaa3d48fd0a9f4bb0c | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (3/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
a5331b58454e9a9066d29c39dc5951415ce6fa679fcd52b240785869adf603c3 | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (6/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
bab4bc2079dcc88cc0122d844a1f6c6001b93da70e892fe4675493bce9c5b5e1 | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (4/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
ee05f5f19e2df74a33d24553241950d3a4353e7785022128859f65977b263fb3 | Text | 5,983 | 116 | # **A KL Divergence-based Loss for In Vivo Ultrafast Ultrasound Image Enhancement with Deep Learning: Dataset (5/6)**
**Roser Viñals and Jean-Philippe Thiran\
Signal Processing Laboratory 5 (LTS5), École Polytechnique Fédérale de Lausanne (EPFL),
1015 Lausanne, Switzerland**
This dataset contains a collection of ultr... |
8f5e33ab59da27528ea0671ff3e84e0fe5c4055886c954857656b18d18163a59 | Text | 5,986 | 130 | # The webKNOSSOS Wrapper Format
webKNOSSOS wrapper is a file format designed for large-scale,
three-dimensional voxel datasets. It was optimized for high-speed access
to data subvolumes, and supports multi-channel data and dataset
compression.
## Implementations
This repository contains reference implementations for t... |
8bc66846ff9db7646d2d72937078bb30c09170542d73935ee8c3f4a7a9a813b1 | Text | 5,994 | 83 | [](https://doi.org/10.5281/zenodo.7708367)
[PCNportal](https://pcnportal.dccn.nl/) is a website that facilitates access to modelling with finetuned normative models for neuroimaging analysis that are pre-trained and applied with the Python package [PCNtool... |
d6af217e1a5a7aa9da4a6559944fc755efd7a50d0a00a4ba195402d5dbd23f47 | Text | 6,018 | 140 | EIGENSOFT version 9.0.0, 07/20/26 (for Linux only)
## shrinkmode added. 3/15
EIGENSOFT version 8.0.0, 03/30/21 (for Linux only)
The EIGENSOFT package implements methods from the following 2 papers:
Patterson et al. 2006 PLoS Genet 2:e190 (population structure)
Price et al. 2006 Nat Genet 38:904-9 (EIGENSTRAT stratif... |
dc07c8498c36d27ef733cbd7ec60ac0707664746f122b1acdab79ebf31c44464 | Text | 6,033 | 110 | # Automated Deep Learning TM-segmentation project
[](https://doi.org/10.5281/zenodo.8361032)
Link to the centiles web-page: [itmt-icsa.streamlit.app](https://itmt-icsa.streamlit.app/)
We developed an automated deep learning pipeline to accurately measure ... |
9e132ba4437bbbaf7a3eb9c895c1624ff8a1d79316ab5793e492799e55454e41 | Text | 6,059 | 51 | # REAVER
Rapid Editable Analysis of Vessel Elements Routine.
## External Links
1. Preprint of manuscript: .
2. Download vessel network benchmark image data... |
8dff743792abb8e7c8a843f55f4fbe5da8fd18059c1b8b13886802360a18cd25 | Text | 6,076 | 67 | # MsCAVIAR: Identifying Causal Variants by Fine Mapping Across Multiple Studies
MsCAVIAR is a method for fine-mapping (identifying causal variants among GWAS associated variants) by leveraging information from multiple studies. One important application area is trans-ethnic fine mapping. Details on installing and usin... |
3f25dbf572cea6af665f34edd14fd0efb66d2f5c23909467c6392b07f0901c8c | Text | 6,122 | 86 | # Tool recommender system in Galaxy using Transformers
## Published article: [Transformer-based tool recommendation system in Galaxy](https://doi.org/10.1186/s12859-023-05573-w)
## General information
Project name: Galaxy tool recommendation using Transformers
Project home page: https://github.com/anuprulez/galaxy_... |
7fdebe33a1f5c51b21c8c818de0b5eb849dfd16a9087b4d5f90ebdbe17269edd | Text | 6,125 | 72 | # _Please note: SimpleElastix has been integrated in https://github.com/SimpleITK/SimpleITK_
_The current SimpleElastix repository (https://github.com/SuperElastix/SimpleElastix), originally created by [Kasper Marstal](https://github.com/kaspermarstal), is no longer maintained. SimpleElastix has now become a part of [S... |
d49a4c3737811c316e7d9dcfaa9ef5d8d185c7b5608703ff7d77a2fcfbea7e91 | Text | 6,125 | 117 | # ACDC-NN
ACDC-NN is a novel antisymmetric neural network to predict proteins free energy changes upon point variations along the amino acid sequence.
The ACDC-NN model was built so that it can be used to make predictions in two different ways:
1. when both the wild-type and variant structure are available, these ar... |
72856e723c9a543e93ca6a3549e9e961b29a662bb70be2e9fad2ab3fc7add425 | Text | 6,177 | 125 | # MNE-RSA
[](https://github.com/mne-tools/mne-rsa/actions?query=workflow%3A%22unit+tests%22)
[](https://github.com/mne-tools/mne-rsa/actions?query=workflow%3Ab... |
e8aab8daa9d8fbf8935e398e9d4fac876eff6eb2de897eb27bd71929ed713c60 | Text | 6,179 | 133 | # Recognizing protected and anthropogenic patterns in landscapes using interpretable machine learning and satellite imagery
This repository contains the **code** for the experiments of the following research article:
**Citation:** Stomberg TT, Leonhardt J, Weber I and Roscher R (2023) Recognizing protected and anthro... |
f4547fb2304365ec7d7da38caaac58771b93dd4580e758b96022daf958349c33 | Text | 6,241 | 181 |
[](https://pypi.python.org/pypi/pynapple)
[](https://github.com/pynapple-org/pynapple/actions/workflows/main.yml)
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/psf/black)
[](http://creativecommons.org/licenses/by-nc/4.0/)
### [Deep learning for bone a... |
f7b42de44b5ebf8e071a3583656db63b6df4a8e1e01676349ab720ae444ab693 | Text | 6,327 | 158 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# MarkerGenes
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#dormant) [](https://zenodo.org/badge/latestdoi... |
81372d6a3f5408d7df294bdaf568120c52c72068c78b5ca3324ba3dba715c773 | Text | 6,353 | 174 | # CapsNet-Keras
[](https://github.com/XifengGuo/CapsNet-Keras/blob/master/LICENSE)
A Keras (branch [tf2.2](https://github.com/XifengGuo/CapsNet-Keras/tree/tf2.2) supports TensorFlow 2) implementation of CapsNet in the paper:
[Sara... |
fe538c5e0af9088298fe82a37d71fbe21f9a35082af3dff06b1b7b8219e63eee | Text | 6,386 | 140 | # AS-C.Origami
AS-C.Origami applies paternal and maternal ATAC signals obtained from GM12878
dscNanoATAC to [C.Origami](https://github.com/tanjimin/C.Origami), enabling
allele-specific chromatin conformation prediction. Plan A (Default) is the
recommended workflow: it uses bulk DNA and CTCF inputs with paternal or mat... |
ea680f55934ddcb3110a42c10b4a3f909b1644f0809e7e604737ad415356b489 | Text | 6,456 | 125 | # HD-BET
This repository provides easy to use access to our recently published HD-BET brain extraction tool. HD-BET is the result
of a joint project between the Department of Neuroradiology at the Heidelberg University Hospital and the
Division of Medical Image Computing at the German Cancer Research Center (DKFZ).
... |
64ca04d4b2a3bfe9c5d7ee9033eec84ae225fa986c3b35cadeabbf94ec0356ce | Text | 6,460 | 128 | # DASA
Differential ATAC-Seq Analysis
DASA is a complete tool for differential ATAC-Seq analysis. Starting from the output
of a peak caller like MACS2, it combines peaks from replicates of the same condition,
and it finds a set of comparable peaks between the two conditions. These peaks are then
quantified, using appr... |
d2ef078c1f1e34610aa4333cc47fb92e9329d0f7fad13a62bf30dff18ea72aa4 | Text | 6,488 | 88 | # **Dataset Description**
## **Introduction**
The dataset is composed of four sub-datasets, and the load category name contained in each sub-dataset is saved in the ‘labels.txt’ document under each sub-dataset folder. The data of each type of load are relatively ideal and pure operating environment to avoid the i... |
8cb715de999b704214e4a0ef273ddb7cb0bf8c4046e0b21674abdeb7a92e4f39 | Text | 6,491 | 172 | 
[](https://www.biorxiv.org/content/10.64898/2026.01.06.697909v1)
An interactive web application for simulating somatic CAG repeat expansion in Huntington's disease and modeling the potential therapeutic ... |
e338bba01ccbf6ccf40fc2e70544dca9478e620b97c0f4a09c73e20629fac4b7 | Text | 6,699 | 111 | # 📄 [*Improving reduced-order models through nonlinear decoding of projection-dependent outputs*](https://doi.org/10.1016/j.patter.2023.100859)
[](https://zenodo.org/badge/latestdoi/603501121)
This repository contains code, datasets, and results from the paper:
> K. Zdy... |
d18de9b84be646175c889ad56e7e0c57aad5e2907adfee8400ceb7719a0959b3 | Text | 6,776 | 105 | # OpenScope Credit Assignment Project Code
## 1. Description
This repository contains the code for analyzing the data from the Credit Assignment project, an [**Allen Institute for Brain Science**](https://alleninstitute.org/what-we-do/brain-science/) [**OpenScope**](https://alleninstitute.org/division/mindscope/opensc... |
0af178002dcdefbb51f55212ce9cd886f267d5613cfb0a207dcc86d2e4c301ea | Text | 6,800 | 148 | # Unified Super-Resolution in PyTorch
This repository implements an algorithm based on a unified model for super-resolving medical images (MR images and CT scans).
<img style="float: right;" src="https://github.com/brudfors/UniRes/blob/master/figures/example_2.png" width="100%" height="100%">
The algorithm combines:... |
0ced50c0d0088ecd9cf0818ce644183a2c82fd9a77e0d496bebccbee56e703bd | Text | 6,830 | 207 | # COCO FROC analysis
FROC analysis for COCO annotations and Detectron(2) detection results. The COCO annotation style is defined [here](https://cocodataset.org/).
### Installation
```bash
pip install coco-froc-analysis
```
### About
A single annotation record in the ground-truth file might look like this:
```json... |
a073f42f12be1db3c607fd2b303c8897fff52f85ced0a3c93ee31c7846adfd3e | Text | 6,834 | 175 | # Welcome to face-rhythm
[](https://badge.fury.io/py/face-rhythm)
[](https://pepy.tech/project/face-rhythm)
[](https://pypi.org/project/fac... |
e49e5af2a5af80179dc5808e4b7d85a41af9da49433d53da135ad091d4f29b31 | Text | 6,840 | 141 | # Complex-Valued Neural Networks (CVNN)
Done by @NEGU93 - J. Agustin Barrachina
<a href='https://arxiv.org/abs/2302.08286'><img src='https://img.shields.io/badge/Paper-Arxiv-red'></a>
[](https://complex-valued... |
938a5b0c1bdb6189d0708024c53813106ba31dfdad66291a6872e634f478b766 | Text | 6,842 | 134 | # Contractile ring closure analysis
This repository contains ImageJ macros and Jupyter notebooks used for the analysis of embryo cleavage in a research project.
## Prerequisites
1. Fiji
2. Jupyter notebook
3. Morpholib J plug-in for Image J (https://imagej.net/plugins/morpholibj)
4. Attenuation correction plug-in for... |
5219ee40b128ca806d8954da6b3b346002bb96bd56fd59dd186cf250a6efc6d8 | Text | 6,860 | 114 | # CarsiDock
**A deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training**
Official repo of CarsiDock proposed by CarbonSilicon AI.
【[paper](https://pubs.rsc.org/en/content/articlelanding/2024/SC/D3SC05552C)】
## Abstract
The expertis... |
b09c200f608a95aaf19668082c21092f29a281140a10fb64d85f740d2ffbdd38 | Text | 6,904 | 112 | # Self-Supervised Pre-Training with Contrastive and Masked Autoencoder Methods for Dealing with Small Datasets in Deep Learning for Medical Imaging
Publication about self-supervised pre-training in medical imaging accepted in Nature Scientific Reports. \
Nature: https://doi.org/10.1038/s41598-023-46433-0 \
ArXiv: <htt... |
e469a7dc83ed72952d7e27dbdee9228377fc7963a147f1383332f4a041fb698b | Text | 6,929 | 210 | # ADOL-C
## An Algorithmic Differentiation package based on Operator-Overloading in C++
[](https://coin-or.github.io/ADOL-C/)
[](https://github.com/coin-... |
5adc332b93c1783dec2a1747bbc7eb2093b9de8715208cd42f4c7a7877b9363f | Text | 6,930 | 186 | # pyRiemann
[](https://img.shields.io/badge/python-3.7%20%7C%203.8%20%7C%203.9-blue)
[](https://badge.fury.io/py/pyriemann)
[![Build Status](https://github.com/pyRiemann/pyR... |
4f82694884f7b0d8d977ab3728fff000ac5630894f4f6c21700de0a5040a1960 | Text | 6,961 | 53 | # Code_Kannegieser_et_al_2024
Analysis files for the publication "Visual guidance fine-tunes probing movements of an insect appendage" , https://doi.org/10.1073/pnas.230693712. Processes body and proboscis positions of hawkmoths probing artificial flower patterns.
The raw data for this publication is deposited at htt... |
5b9dab25f40c0e1fd5bd65973c0ccb8687c0cb8d011693fbc70b4234b9677aa5 | Text | 6,970 | 120 | # CETYGO (CEll TYpe deconvolution GOodness)
The majority of epigenetic epidemiology studies to date have generated genome-wide profiles from bulk tissues (e.g. whole blood) however these are vulnerable to confounding from variation in cellular composition. Proxies for cellular composition can be mathematically derived... |
0fb20d317caa5ffcfb3d9e03f4bec7290337a331212e8c1bf85d5ba54104d97e | Text | 6,977 | 176 | # Deep learning using computed tomography to identify high-risk patients for acute small bowel obstruction: development and validation of a prediction model
PyTorch implementation and pretrained models for DBA+DRP. For details, see the paper: [Deep learning using computed tomography to identify high-risk patients for ... |
029e47a0694feae0078c35e74bf32d1ad4e99d4b97e72e686380c8e6f5e4d71d | Text | 6,981 | 98 | # mini-world (minimir)
A small artificial-life world for preregistered experiments on the evolution of learning. Creatures on a 128 by 128 torus look for food, burn energy, reproduce and die; each one is driven by a tiny neural network that passes to its offspring with mutations. No rewards, no goals. Every experiment... |
69071789e3c6d3aef42d2b86bd5567992484afe408f553309fd26045195ef645 | Text | 7,023 | 184 | [](https://github.com/tseemann/barrnap/actions)
[](https://github.com/tseemann/barrnap/releases)
[](http... |
3d229d9c5195bb96d9d42ec205921ba4afd87171e19227ff9e543104ec869238 | Text | 7,041 | 98 | [](#python)
[](https://opensource.org/licenses/MIT)
# Explainable Multilayer Graph Neural Network for Cancer Gene Prediction
<strong>Published at UOC Bioinformatics</strong>... |
b92a6acd7b1ebcaf431b64b798f774cc246e0c946db56f1fbae846d2ca4c9932 | Text | 7,041 | 169 |
# Meliad
***This is not an officially supported Google product.***
_This code is provided "as-is" to the broader research community. Google
does not promise to maintain or otherwise support this code in any way._
## Introduction
The Meliad library is collection of models which are being developed as part
of ongoi... |
748a3c29a7e49256e30a246b93b80b751f329c3b524fab8477584a6ece3a383a | Text | 7,088 | 85 | Nearest neighbor suspect spectral library
=========================================
For more information:
* [Official code website](https://github.com/bittremieux/gnps_suspect_library)
The nearest neighbor suspect spectral library is a spectral library that was created in a data-driven fashion by propagating annotat... |
27212eb5ef705165ad8cc1d843d77574c547e664c107fcb387dc33e3c1541e03 | Text | 7,118 | 148 | # Metabolic spiking
## Tutorial
Please see the folder tutorial for getting started.
Google collaboratory based
Explore the basic spiking with metabolism: [Tutorial1](https://colab.research.google.com/drive/1z3FlVweGB9Q4xz9FIDcE4ftLDeQAANQa?usp=sharing)
Explore how spiking can provide RETROS protection: [Tutorial2](... |
f48cab97f273f521b25ff3718862697349e6cb24c6043ea36acdf1dcb247032d | Text | 7,118 | 166 | [](https://doi.org/10.21105/joss.00925)
[](https://badge.fury.io/py/ripser)
[](https://pypi.python.org/pypi/ripser/)
[](https://doi.org/10.5281/zenodo.7996403)
Contains relevant DOI information and README instructions for use of the BREEZE-mappi... |
e0c04d68f1f634d1f4b8e57d10b8465416238ccf261b21f6f96cef92c4fc805b | Text | 7,134 | 45 | # Clinimetric assessment of the Therapy Intensity Level (TIL) scale for traumatic brain injury
The Therapy Intensity Level scale for traumatic brain injury: clinimetric assessment on neuro-monitored patients across 52 European intensive care units
## Contents
- [Overview](#overview)
- [Abstract](#abstract)
- [Code](#... |
15a19fe2cc15ff2ac9e8443682496272fa3026e22c2749ff7c10b13da033cd5f | Text | 7,200 | 126 | [](https://travis-ci.org/bgruening/galaxytools)
[](https://zenodo.org/badge/latestdoi/5466/bgruening/galaxytools)
Galaxy Tool wrappers
====================
This repository con... |
767cdf418427a64eb20d575a3564e204d693b4f6c7779aa83753ec6b7e6e4417 | Text | 7,215 | 145 | # <center> [](https://twitter.com/Knoblich_lab)   </center>
ventral mi... |
47eb8e10ccf90b120c848101fafaf83e62079262a2dbe8e2883622d4430c8b3a | Text | 7,222 | 141 | ## <a name="start"></a>Getting Started
```sh
git clone https://github.com/ruanjue/wtdbg2
cd wtdbg2 && make
#quick start with wtdbg2.pl
./wtdbg2.pl -t 16 -x rs -g 4.6m -o dbg reads.fa.gz
# Step by step commandlines
# assemble long reads
./wtdbg2 -x rs -g 4.6m -i reads.fa.gz -t 16 -fo dbg
# derive consensus
./wtpoa-cns... |
74a55a4a4c05b2287928559f4fefb822b10c1e067c10b47b8b0d3a9de3464b16 | Text | 7,234 | 79 | # Human BNST volume analysis
Analysis code for *Substantial evidence against sex differences in bed nucleus of the stria terminalis volume in the human brain*.
This repository contains the analysis code, the [literature-prior inputs](data/prior_sources/README.md), and our [BNST segmentation guide](docs/BNST_Segmentat... |
81c4c493b8bed6342afbce592ab5b9f41cf1040c54456cee0b52a7fb6ebb82e1 | Text | 7,241 | 137 | # SeqPredNN
Deep feed-forward neural network for predicting amino acid sequences from protein conformations.
## Table of Contents
1. [Requirements](https://github.com/falategan/SeqPredNN/blob/main/README.md#requirements)
2. [Usage](https://github.com/falategan/SeqPredNN/blob/main/README.md#Usage)
1. [Installi... |
d4dab5826f17328f82aeca4369bcbf585bd836bba17bfe94e3649e438218aa56 | Text | 7,306 | 206 | # Michigan Image Reconstruction Toolbox (MIRT) - Matlab Version
https://github.com/JeffFessler/mirt
This directory contains various algorithms for image reconstruction and
other inverse problems such as image restoration and image registration.
It also contains code for related applications including MRI pulse design... |
de2361225a0abc05d1ab24efb09cbd467018ed8d8033f354d03618f4c35070e0 | Text | 7,349 | 91 |     for machine learning benchmarks
Meta-Learning for Compositionality (MLC) is an optimization procedure that encourages systematicity through a series of few-shot compositional tasks. This repository shows how to apply MLC to the [SCAN](https://github.com/brendenlake/SCAN) and ... |
720fa4d9cef5c0ecb2cf7dfc7109a566322d30b2529eef2c06ae03df4f49314a | Text | 7,431 | 108 | # PG is all you need!
<!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
[](#contributors-)
<!-- ALL-CONTRIBUTORS-BADGE:END -->
This is a step-by-step tutorial for Policy Gradient algorithms from A... |
c7df9bb0336c166cabf146379f7e3afb70f583a6ddf4c4c2382840a4f2a05a26 | Text | 7,453 | 124 | SVIM - Structural variant identification using long reads
=========================================================
.. image:: https://img.shields.io/pypi/v/svim?style=flat
:target: https://pypi.org/project/svim/
.. image:: https://img.shields.io/conda/vn/bioconda/svim?style=flat
:target: https://anaconda.org... |
249247e3ef669b734100ca6262b52aa06eefc55fe0746c89f97c59a02e326d40 | Text | 7,455 | 136 | # Meta-Learning for Compositionality (MLC) for machine learning benchmarks
Meta-Learning for Compositionality (MLC) is an optimization procedure that encourages systematicity through a series of few-shot compositional tasks. This repository shows how to apply MLC to the [SCAN](https://github.com/brendenlake/SCAN) and ... |
872be4ea39a5e8241ff261f55dd2de9c6d773a4fd8dc66a48a665194f9e738be | Text | 7,474 | 52 | # Field-Induced Recursively embedded atom neural network
## Introduction
Field-induced Recursively embedded atom neural network (FIREANN) is a PyTorch-based end-to-end multi-functional Deep Neural Network Package for Molecular, Reactive and Periodic Systems under the presence of the external field with rigorous rotati... |
69642ffd089c9505a3602ddd5c505e642f4ed4d0f78a24d8b84867ad1dcd8ed4 | Text | 7,498 | 144 | # MATLAB code to replicate main results from "Decoding Motor Plans Using a Closed-Loop Ultrasonic Brain-Machine Interface"
==============================
## Project Organization
------------
├── README.md <- The top-level README for developers using this project
├── setup.m <- Used to se... |
14628a58444a1c6af6aeaa16a8a65ff94246cfe1a9c674315a766f09daa931d9 | Text | 7,511 | 152 | # CEFCON
[](https://zenodo.org/doi/10.5281/zenodo.10101434)
CEFCON is a computational tool for deciphering driver regulators of cell fate decisions from single-cell RNA-seq data.
It takes a prior gene interaction network and expression profiles from scRNA-seq data as... |
5758946bfbe4600a590522e86957dde3b03688d667248ce0718af069059a431e | Text | 7,512 | 112 | graph_ensemble
==============
by Shuting Han, Apr. 2017, Sep. 2018; Jonathan Shor, June 2018.
Overview
--------
This project applies conditional random field models in _in vivo_ two-photon calcium imaging data in mouse V1 cortex. We built CRFs on such imaging data to identify representative neuronal ensembles corresp... |
fa10a11e290791bfc5ae243ec4290ebc595b243d8ac7ef18ae1d2995a7ca6fdf | Text | 7,514 | 105 | # User-directed unsupervised identification of cell populations
## DAFi: User-directed unsupervised filtering and identification of cell populations from flow cytometry data
### Authors:
Yu "Max" Qian, Ph.D., mqian@jcvi.org or qianyu.cs@gmail.com, Ivan Chang, Ph.D., ichang@jcvi.org, and Bob Sinkovits, Ph.D., sinkov... |
ae29dc16e4b73ddd23bb6bd35ec4d7d6c7c342ce7d1eb2ce2808ab32367a63e3 | Text | 7,555 | 149 | 
[](https://www.python.org/)
[](http... |
3ae4242eae960879737a1207c43bf8c0c7a2f7cbeede912ee5637c149400bcf2 | Text | 7,578 | 78 | # [Brain tumour genetic network signatures of survival](https://doi.org/10.1093/brain/awad199)
# Article codebase
## Table of Contents
- [What is this repository for?](#what-is-this-repository-for)
- [Code](#code)
- [Usage queries](#usage-queries)
- [Citation](#citation)
- [Fundi... |
ae20090e1bb99c6ec2dc9d0d0091e67e462538c91749369c291d8c657d47b0d4 | Text | 7,581 | 106 | [](https://doi.org/10.5281/zenodo.1201320)
[](https://javadoc.io/doc/io.github.mianalysis)
[![Sonatype Central](https://maven-badges.sml.io/sonatype-central/io.github.mianalysis... |
f4702c4b0435cf081e0a83acd0f13769af8a5803a7b4bc588aa8bbbdd41c4365 | Text | 7,593 | 223 | # Information-Restrited-NLMs
Code of the paper: "Information-Restricted Neural Language Models Reveal Different Brain Regions' Sensitivity to Semantics, Syntax and Context"
# Installation & Set up
First, install the requirements.
```shell
git clone git@github.com:AlexandrePsq/Information-Restrited-NLMs.git
cd Inform... |
206b556aed93ae46fac10842d3fefacac0031900ce03fac7f24e9d1c5445e715 | Text | 7,597 | 127 | # InferSent
*InferSent* is a *sentence embeddings* method that provides semantic representations for English sentences. It is trained on natural language inference data and generalizes well to many different tasks.
We provide our pre-trained English sentence encoder from [our paper](https://arxiv.org/abs/1705.02364) ... |
08c040f2a7873d334ddeda2c1cf807d7762c7a5b29f7f23535209e12543af109 | Text | 7,606 | 52 | # Field-Induced Recursively embedded atom neural network
## Introduction
Field-induced Recursively embedded atom neural network (FIREANN) is a PyTorch-based end-to-end multi-functional Deep Neural Network Package for Molecular, Reactive and Periodic Systems under the presence of the external field with rigorous rotati... |
e3f2341b709e50b7e5f6ed824151bd968183ded673301ccae81b2ab203a519e6 | Text | 7,613 | 150 | # MATLAB code to replicate main results from "Decoding Motor Plans Using a Closed-Loop Ultrasonic Brain-Machine Interface"
==============================
## Project Organization
------------
├── README.md <- The top-level README for developers using this project
├── setup.m <- Used to s... |
01458b77e94edcd31c4ac7aba7c62e187a9e4ba2337e4d4ef9d1317874cc113d | Text | 7,684 | 107 | <p align="center">
<img height="150" src="https://raw.githubusercontent.com/aristoteleo/spateo-release/main/docs/_static/logo.png" />
</p
[](https://spateo-release.readthedocs.io/en/latest/)
[Installation](https://spateo-release.... |
2a529ecbf95e690471244bd7885879e2ea904d97ffd92317f64ba7c84adb8ed8 | Text | 7,730 | 211 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Symphony <img src="man/figures/symphony_logo.png" alt="logo" width="181" align="right"/>
<!-- badges: start -->
<!-- badges: end -->
Efficient and precise single-cell reference atlas mapping with Symphony
[Kang et al. (Nat Comm,
2021)](https:... |
cc644b5fa6fa508d878027edb701acccc1b9ef7d08df8bc31f5ba0c10d8d2e6e | Text | 7,778 | 81 | # Evaluating the Effectiveness of Stain Normalization Techniques in Automated Grading of Invasive Ductal Carcinoma Histopathological Images
## Abstract
**Background and Objective**: Debates persist regarding the impact of Stain Normalization (SN) on recent breast cancer histopathological studies. While some studies pro... |
f06661ae9a36b62975829fe5d2e21c24f764ac8d17353aefd912c082acbb5e9d | Text | 7,795 | 148 | # DFEI dataset
_This dataset is hosted on ZENODO under the DOI 10.5281/zenodo.7799170. Please consider citing if you use it_.
The dataset was used in the paper "GNN for Deep Full Event Interpretation and hierarchical
reconstruction of heavy-hadron decays in proton-proton
collisions".
The project describes a full even... |
dd43966f7c619638de032d434fb776e7f8eec09cb88aff91c82a034c393aa470 | Text | 7,927 | 126 | # Installation
Works on most modern Linux distributions. Matching pursuit implementation empi (github.com/develancer/empi) is compiled for Linux, statically; currently (2022.11) there are no recent builds for Windows or Mac.
- Install Python3.10
pyenv and virtualenv useage is strongly advised.
- Install requirement... |
ea32eba01bf231d7af0e5db8a22f4606e10f53a4a973ecfe08076f48945df280 | Text | 7,943 | 62 | # GPR_fMRI
This code belongs to the paper *"Encoding of continuous perceptual choices in human early visual cortex"* by Barbieri, Töpfer et al. (2023), published in Frontiers In Human Neuroscience. It consists of a collection MATLAB scripts and functions for reproducing the main analyses described in the paper. The ne... |
dd8d936e91ff314db1b14568bb94860d22d5904ffcdb788590ea57d0a0ea150b | Text | 7,993 | 182 | ### Quick start
Download [binary](https://github.com/philres/ngmlr/releases/tag/v0.2.6) from github and unzip or [](http://bioconda.github.io/recipes/ngmlr/README.html) or pull docker [![Docker Automated bui... |
280fada1d9f7f7f94fad0d97433e4c3b285ffc50c596cf529259400d8e81b13b | Text | 8,042 | 208 | > [!IMPORTANT]
> Please go to [here](https://github.com/Neuroesc/rate_mapper) for the latest version. This repository will no longer be updated.
# rate_mapper - map spike and position data in 2D
This is Matlab code which can be used to generate 2D firing rate maps
for spatial analyses. This code can create maps usi... |
c644f1150a08caa047cff13cc8c258eb1da719a54f7d744d6d89362c64aac35f | Text | 8,055 | 94 |    ](https://github.com/gilestrolab/ethoscope/actions/workflows/ci.yml)
[](https://github.com/g... |
2c788436aa4070e20eedc12899db066ddd879de9b4458297969750a5592ffa7b | Text | 8,127 | 150 | # Echo from noise: synthetic ultrasound image generation using diffusion models for real image segmentation · [](http://makeapullrequest.com) [
[ and Average
Silhouette Width (ASW) metrics from Harmony and kBET, respectively, as
well as the Adjusted Rand Index... |
adccd14bdc483c7ddd891da3e17adaf5666aa9dda765f4779b99d426fdb38649 | Text | 8,196 | 104 | # Survival_plus_x: Multitask approaches for outcome modelling of head and neck cancer
This is the source code accompanying our manuscript entitled "Multitask learning with convolutional neural networks and vision transformers can improve
outcome prediction for head and neck cancer patients" (submitted to Cancers).
##... |
37a75e172c2849a676bedc2955140b8089fee86405104b469ab9037683ca369b | Text | 8,245 | 210 | # pyRiemann
[](https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13-blue)
[](https://badge.fury.io/py/pyriemann)
[![Build Status](https://github.com/pyRiema... |
c9ac3be883b577e3940f47ec61984c8a07f5ddfe1ae25104484bedb1a6aa48d8 | Text | 8,274 | 171 | # Toolbox-Romano-et-al
## Computational toolbox for analysis of calcium imaging data of neuronal populations
See the preprint **A computational toolbox and step-by-step tutorial for the analysis of neuronal population dynamics in calcium imaging data** by Romano et al for tutorial and full description (doi.org/10.110... |
4ed2d89f6b39d36834916a305590ed60603858c85707a090e8c576a5388079e5 | Text | 8,332 | 138 | # DeepMicro
DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation.
## Quick Setup Guide
**Step 1:** Change the current working directory to ... |
934a651911e8bb1cc65eead5b4297a7c9785b545c583d5952d2a800e5a2a0d3d | Text | 8,374 | 153 | <h1 align="center">🔬<ins>ToMoDL</ins>🔬<br>Model-Based Deep Learning Architecture for Optical Tomography Projection 3D Reconstruction</h1>
<p align="center">
<a href="https://www.linkedin.com/in/marcos-obando-22a816170">Marcos Obando</a>
·
<a href="https://www.creatis.insa-lyon.fr/~ducros/WebPage/">Nicolas Ducro... |
268ce68cb2fde797ca208b881eda1ad9e44a5e992c5eae48a3785e96172da2b8 | Text | 8,396 | 125 | <div align="center">
<img src="assets/accum_grad_v5_reduced.png" width="35%" alt='gradient-accumulator'>
<h1 align="center">GradientAccumulator</h1>
<h3 align="center">Seemless gradient accumulation for TensorFlow 2</h3>
[
[](https://doi.org/10.5281/zenodo.23729180)
A small artificial-life world for preregistered experiments on the evolution of learning. Creatures on a 128 by 128 torus look for food, burn energy, reproduce and die; each one is driven... |
9b9027275ccf1afa07e522e63d26ece045d9486e162c427652877ab4f242a47a | Text | 8,427 | 104 | # mini-world (minimir)
[](https://doi.org/10.5281/zenodo.23713553)
A small artificial-life world for preregistered experiments on the evolution of learning. Creatures on a 128 by 128 torus look for food, burn energy, reproduce and die; each one is driven... |
f8add8c20a2ac0bc5dd260062d1916f1c0d3d1e1d174b74846e553cbb485b582 | Text | 8,439 | 202 | # 3DTV-CNN: Deep learning on 3D CAD shape classification
This repo contains source code and preprocessed data for the paper:
[Qingfeng Xia](https://www.researchgate.net/profile/Qingfeng_Xia),
[DTV-CNN: deep learning on fusion of depth and thickness views for 3D shape classification](https://www.sciencedirect.com/s... |
95ea3652d0467364d20f46feb02f536d40470cff06d686968dcbd8914e32ea11 | Text | 8,479 | 300 | pyEcoHAB package
=====================
pyEcoHAB is a Python library for loading and analyzing behavioral data obtained in experiments performed with the Eco-HAB. Eco-HAB is a system for fully automated and ecologically relevant assessment of social impairments in mice.
pyEcoHAB supports Python3.
pyEcoHAB allows for ... |
cd8f58bde371753753e0b63663e2af2e8e8d7fc909da6ce86c2e5b1a7cdbc6ca | Text | 8,491 | 116 | Deblur
======
[](https://github.com/biocore/deblur/actions/workflows/main.yml)
[](https://coveralls.io/github/biocore/deblur?branch=master)
... |
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