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5db894f100ce62803e54522c93b54acbeca38271db5d1535159520f745218d74 | Text | 2,556 | 74 | [](https://circleci.com/gh/ionpath/mibilib)
# mibilib
Python client for IONpath MIBItracker API, plus utility functions for working
with MIBItiff images.
https://ionpath.github.io/mibilib/
## Setu... |
8c2f2b49924b82032d94a2c4f59c41996e681671e7997c4cc8c578aa6f8f311d | Text | 2,575 | 30 | <h1 align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/NeuroLang/NeuroLang/master/doc/_static/logo/svg/neurolang-lockup-dark.svg">
<img alt="NeuroLang" src="https://raw.githubusercontent.com/NeuroLang/NeuroLang/master/doc/_static/logo/svg/neurolang... |
1150982548239836871c0b03d145e24218d2387b7d71118900a10c2c52d9af65 | Text | 2,579 | 47 | ### Instructions for Data and Code for Nikolados et al, Accuracy and data efficiency in deep learning models of protein expression, Nature Communications, 2022 ###
To setup the code and data directories using Google Colab:
- open Google Drive
- right-click on the empty space in the directory view and choose 'Conne... |
8539885d947020220362c411dd0978cd0f522315a53e8702bdcaa1188d36ab4a | Text | 2,605 | 59 | # IvCDS: An End-to-end Driver Simulator For Personal In-vehicle Conversational Assistant
This repository is the code for our paper (see this [link](https://www.mdpi.com/1660-4601/19/23/15493)).
## Citation (BibTeX)
If you are interested in our work, please cite it by:
```
@Article{ijerph192315493,
AUTHOR = {Ji, T... |
ed699299310b4fa040fad2a593028bff7d05b01a39fb9965a4a0759b8f5cad30 | Text | 2,607 | 57 |
# SplineDist: Automated Cell Segmentation with Spline Curves
This repository contains the implementation of SplineDist, a machine learning framework for automated cell segmentation with spline curves. The [manuscript](https://www.biorxiv.org/content/10.1101/2020.10.27.357640v1) is accepted at [ISBI 2021](https://bi... |
23c6d5b3d058e0f029ed67c2a50eb5be8442b2538950e211769a5f1ab7eb643c | Text | 2,609 | 45 | # DTGCN
This page shows the original code and data samples of the paper 'Multi-Stage Malaria Parasites Recognition by Deep Transfer Graph Convolutional Network'.
The image samples can be downloaded in [Dataset](https://data.mendeley.com/datasets/2y232dgw36/draft?a=1ab70b62-66c1-4e06-923c-8a86c4deaca0).
The code in ... |
f23aecdcaab03cee1e816205ea515851d981b247190458458b4b0f01dee19da4 | Text | 2,615 | 42 | Blood vessel quantification code for the accepted paper: Neonatal hyperoxia in mice impairs cerebrovascular function, neurogenesis, and behavior into adulthood, The Journal of Clinical Investigation.
The repository contains a single zip file because there are many empty subfolders in the "data" folder, included for fa... |
2f73c89c324cdab661dd72d1491b0a6cd288defc3f78f3b15950b92e4b1f2e5c | Text | 2,619 | 32 | # Comparison Phenotype Prediction
In this repository, we included all simulated phenotypes, precomputed permutation-based GWAS results as well as the
code for conducting the simulations and generate all figures related to the below-mentioned publication.
In this work, we show a systematic comparison of eight phenotyp... |
65246e3279093a116cb34ba3fa7db08cec18ba935126f0dbdac3d7b675903aaf | Text | 2,624 | 59 | # Simulations of giant vacuoles
Repository with all Wolfram Mathematica notebooks developed for simulations of giant vacuoles
## Usage
Follow inline comments.
For the biological meaning of the model parameters, refer to manuscript.
## Description
### equilibria.nb
This notebook generates steady-state conf... |
826ab081be57c08bfff36d5372ccdb2e78889cce8b9ac1c6404b30654a21e051 | Text | 2,627 | 33 | # Functional Connections Among Neurons within Single Columns of Macaque V1
## Overview
This repository contains code for analyzing cross-correlations between the spikes trains of pairs of neurons in macaque V1 and generating the figures for the following paper:
Trepka, Zhu et al., (2022) Functional Interactions Among ... |
bd74a49d7d023bff0add553368581aeb76e6873dc33e626e36ac3d65ce41425f | Text | 2,657 | 14 | # AbAgIntPre
AbAgIntPre is a deep learning-assisted web server for fast identification of antibody-antigen interactions that only relies on amino acid sequences. By using a Siamese-like convolutional neural network with the amino acid composition encoding scheme, AbAgIntPre achieved satisfactory performance with the Ar... |
2748ff7a7498988a02cea46a11cb35a3d2cb8b67b9fbf26d15f9583cd49e7364 | Text | 2,681 | 85 | <a href="https://github.com/jumphone/scRef/wiki">
<img src="/source/NewLogo.png" width="200">
</a>
* A reference-based toolkit for single-cell analysis <a href='https://github.com/jumphone/scRef/wiki'>Visit Wiki</a>
* A web resource of references <a href='/Reference/'>Visit dbRef</a>
# Table of content
* [Citation]... |
6ec6a17f95c02481e1bc8d001fc6b57d010964a10e293982669748ba9adcca69 | Text | 2,696 | 46 |
This project aims to investigate the effectiveness of Signature Methods to extract predictive and meaningful time series features from Electronic Healthcare Records (EHR) for heart failure (HF) disease early diagnosis. The project will investigate the task using data from the Clinical Practice Research Datalink (CPRD)... |
6563b8b40c943a4463c2de9a97e9e8bd5614779f5d3916397cc62ffb8639421c | Text | 2,719 | 59 | # **Fi**nd **N**europyhsiological **N**etworks (FiNN)
A Python Toolbox for the analysis of electrophysiological data
The main directory *finn* contains the toolbox itself, while *finn_demo* contains a number of demo files describing end-point functionality of the toolbox. *finn_tests* contains automated tests to perf... |
d3fabd9ba2593c062712839e92a1dde06c3ecc09f5b899af8231fe3e362cf1ad | Text | 2,726 | 55 | 1) Environment and Dependencies:
- Tested on Linux (Debian 9.3)
- Python 3.7
- Uses Python’s virtualenv
- All needed Python packages are installable from dataset-gen/requirements.txt & simulations/requirements.txt as explained below.
- Pacakge dependencies are pretty light, hence, installation should be very fast depen... |
cefc55b767b749c1561ec803c702f792cddd6d8fe0f2385de97a263608a67baa | Text | 2,728 | 56 | # Physics-induced Graph Network for Particle Interaction (PIG'N'PI)
PIG'N'PI learns the pairwise force or pairwise potential energy from the trajectories of interacting particles.
Authors: Zhichao Han, David S. Kammer and Olga Fink.
(MIT license)
### Requirements
Python dependencies:
-- Python>=3.6.12
-... |
d6bf9d5f059a81a2800885770c6391be43a44837f0e34dd26ee075016b51c716 | Text | 2,740 | 37 | Code to execute:
Fase1L %in the folder with the videos to be analyzed
Fase2newLuin %in the folder with the output files from Fase1L
Fase3Lnew %in the folder with the videos to be analyzed
%load file "Info", e.g. by "load('Info')"
DomenicaFase4
Classifytraj
-------------------------------------------... |
bb4f945bdc003a813d4cf1c1299b2585e337304fc7798070dc0ad694a969e379 | Text | 2,741 | 52 | <p align="center">
<img height="420" width="593" src="/images/philosopher.png">
</p>
[](https://github.com/Nesvilab/philosopher/releases/latest)
* Neural Processes (NPs)
* Attentive Neural Processes (ANPs)
The code for CNPs can be found in `conditional_neural_process.ipynb` while the
code for both... |
7a0a3e05e343d1aaa30ef73d768fd4ffe2e51966078182913d3b7f2ed352e16f | Text | 2,785 | 42 | ## 1) Environment and Dependencies:
- Tested on Linux (Debian 9.3)
- Python 3.7
- Uses Python's virtualenv
- All needed Python packages are installable from dataset-gen/requirements.txt & simulations/requirements.txt as explained below.
- Pacakge dependencies are pretty light, hence, installation should be very fast de... |
d3e0c0e97b1b6b4487e0a2a24c24bab3e0bdb28bcd0b3905330d335cda8aa4bc | Text | 2,798 | 35 | # subset-bam
`subset-bam` is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag. The latest version is `v1.1.0` and can be found [on the releases page](https://github.com/10XGenomics/subset-bam/releases).
## Overview of how it works
`subset-bam` is a simple tool implemented in... |
5885b0f6dea4f41677b9305cc161f882bfc0490654028c80e3b1772ee41c689d | Text | 2,802 | 75 | > [!NOTE]
>
> This repository has moved and is now maintained as a part of the [BSB monorepository](https://github.com/dbbs-lab/bsb).
_*No ducks were punched during the construction of this monkey patch._
# Installation
```
pip install nrn-patch
```
## Minimal requirements
* Pyt... |
a39ccd29cb54f78a5fdbefd9304bcbd8e4322650d8cf55e1ad78671d2209960f | Text | 2,854 | 40 | # TrackFluoNGFvesicles
Scripts in MatLab to track single vesicles containing fluoNGF
Code to execute:
-----------------------------------------------------------------
Fase1L %in the folder with the videos to be analyzed
Fase2newLuin %in the folder with the output files from Fase1L
Fase3Lnew %in the folder with the ... |
d16028fe72833dfcbf7420498edabe947857b5ff59b199644e924fac27aeafd5 | Text | 2,882 | 70 | # Symmetry perception by deep networks
This is the code to reproduce the results in our paper titled ["Recurrent connections facilitate symmetry perception in deep networks"](https://www.nature.com/articles/s41598-022-25219-w) (_Scientific Reports, 2022_)
## Authors
* [Shobhita Sundaram](https://ssundaram21.github.io... |
d8bffaef72d58c71257b5de5db758ed0a0a94452033c16d97ae8c29238ef8ad4 | Text | 2,883 | 92 | # Image Weighing
This code is the original experimental setu... |
c21bfa5a34f60ddc3d823bb79aa2ee36f876ee5719de10bfddac2eb2f44c297e | Text | 2,903 | 72 | # MEDNet
This repository contains the Implementation details of the paper "Edge detection networks inspired by neural mechanisms of selective attention in biological visual cortex".
The address of the paper is at (https://www.frontiersin.org/articles/10.3389/fnins.2022.1073484/full)
## Citations
If you are using the ... |
dff9357072ac17d4774a78bb3b2d0e359f2b0325b75f04c050d162e3fbd12423 | Text | 2,960 | 42 | # High-Dimensional-Neural-Network-Potential
Fortran implementation of a high dimensional neural network potential.
This is a simple implementation of the prediction step for a high dimensional neural network potential (HDNNP)[1].
The calculation of analytical derivatives of the energy with respect to the atomic posit... |
f437309d99f5d72a71ff69b844561ac70bb68c68eb296ff4ec0063e9d53b6c4f | Text | 2,971 | 91 | NetworkX
========
.. image::
https://github.com/networkx/networkx/actions/workflows/test.yml/badge.svg?branch=main
:target: https://github.com/networkx/networkx/actions/workflows/test.yml
.. image::
https://img.shields.io/pypi/v/networkx.svg?
:target: https://pypi.python.org/pypi/networkx
.. image::... |
fbf7f02238ca53a920af1ee04fbd03605934d5cbaeb8291253d6672a6e1dbf6d | Text | 2,982 | 74 | [](https://github.com/sappelhoff/ecomp_experiment/actions/workflows/build.yml)
[](https://github.com/sappelhoff/ecomp_... |
f9c9b1c59b4ba57f97a11b0d656ec9f2e95c92b1dfdc2ddc38e01f6c532d9ac8 | Text | 3,042 | 67 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# Background
This repository contains scripts used to perform a colocalisation analysis using the REM sleep behavior disorder (RBD) GWAS and two eQTL datasets:
- [eQTLGen](https://pubmed.ncbi.nlm.nih.gov/34475573/)
- [PsychENCODE](https://www... |
8286a66b44b517e451f8edca704a977e89eac77e69ad0c0d6bffd67bcbbaca39 | Text | 3,052 | 73 | # GPU-enabled docker container with Jupyterlab for artificial intelligence
[](https://bio.tools/gpu-enabled_docker_container_with_jupyterlab_for_ai) [
## How does it work?
- DeepFPC was implemented... |
3cdc4686832896f56505bccbb74ad4e2847cdfb6995ad021f441d9dfd575b34f | Text | 3,155 | 49 | # MAsP, R Shiny-based web application
Micro-scaffold Assisted Spatial Proteomics (MASP) is a novel method for spatial proteomic studies. MASP precisely procures spatial information by precise tissue spatial compartmentalization using a 3D-printed micro-scaffold, and accurately/sensitively quantifies thousands of prote... |
6beaea2cf3542e4977bdb0853b227cda9bd9d71cca15594036b8dd567f3fe730 | Text | 3,174 | 46 | # ML-based cloud cover parameterization for ICON
A neural network based cloud cover parameterization for the ICON-A model. <br>
This repository contains the neural network and analysis code, and an extract from the training data.
It is part of our paper published in JAMES:
> Grundner, A., Beucler, T., Gentine, P., Igl... |
079fd3b343e222d82f7bd8669cac41bb89b1c3d97de8682febe5f9381ac9a72e | Text | 3,185 | 66 | # VE-ICANS
## Published on bdsp.io
- **Project:** https://bdsp.io/content/5n52dv55u1r47qlm0t3h/1.0.0/
- **DOIs:** [10.60508/67tw-zc72](https://doi.org/10.60508/67tw-zc72) (v1.0.0) · [10.60508/7c23-zj08](https://doi.org/10.60508/7c23-zj08) (core)
- **Paper:** Jones DK, et al. *EEG-based grading of ICANS.* Sci Rep 2022;... |
5e44da3f96e2441c1e3bdc02cc37d3f3d10d95fc508ae86704e271f11e0ef0fd | Text | 3,200 | 41 | Description
ProFitFun-Meta is successor of ProFitFun for assessing the quality of predicted model structures by
an effective combination structural information of various backbone dihedral angle and residue surface
accessibility preferences of amino acid residues with other spatial properties of protein structures.... |
43842a56b684e3552e54676c174ff1a7bcd94d8d80689c3e1354296b7471f661 | Text | 3,209 | 69 | # chemoenzymatic-askcos
[](https://github.com/itai-levin/chemoenzymatic-askcos)
[](https://github.com/ASKCOS/askcos-data)
[](https://github.com/usegalaxy-eu/gpu-jupyterlab-docker/actions/workflows/release.yml)
## GPU-enabled docker container with Jupyterlab for artificial intelligence
[](https://travis-ci.org/hachmannlab/chemlg)
[](https://codecov.io/gh/hachmannlab/chemlg)
[](h... |
4b47f903ce3023519c94aedad2695b7434b07a6dfd2ba6c8b1ec26a08426cf25 | Text | 3,236 | 77 | # Graph‐generative neural network for EEG‐based epileptic seizure detection via discovery of dynamic brain functional connectivity
- [paper link](https://www.nature.com/articles/s41598-022-23656-1)
GGN is a generative deep learning model for epilepsy seizure classification and detecting the abnormal functional connect... |
3ce8934e6fb5db7e4996ff9cbce9487d6759a47058d86d66004ef86c0270b29b | Text | 3,259 | 74 | [](https://github.com/sappelhoff/ecomp_experiment/actions/workflows/build.yml)
[](https://github.com/sappelhoff/ecomp_... |
c5dbad54dcb93cc179676059a71a0701b4e3b2f715af9f6c2f5a99dbe61457fc | Text | 3,317 | 45 | # Saluki: Predicting mRNA half-life from mRNA sequence
This repository is intended to accompany our publication, primarily to enhance the reproducibility of our results. For more information please refer to:
Agarwal V, Kelley D. The genetic and biochemical determinants of mRNA degradation rates in mammals. 2022. **_b... |
5dde0283bf21e759043fada3e08016f46ad4519eede37ecc83a4c839ee76ac1c | Text | 3,327 | 35 | # MaPbI3-HDNNP
High dimensional neural network potential [1,2] for MaPbI3.
The potential was developed for Funnel Hopping Monte Carlo study of MaPbI3 [9].
Please cite this reference if you use this potential or the dataset.
The potential was trained with the RuNNer software [3] using energy and forces of structur... |
7cadc8e653928883eff6397813cb2f9a95ea970c5aa32ffbf2883b14bf42fd2b | Text | 3,392 | 98 | <!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
<a name="readme-top"></a>
<!--
*** Thanks for checking out the Best-README-Template. If you have a suggestion
*** that would make this better, please fork the repo and create a pull request
*** or simpl... |
a1cf717ae4125d5fe578f8a9ace1bebfc21b9175f8f4fc9fa3c9963ff1a82fd9 | Text | 3,396 | 113 | =====================
Welcome to pymoten!
=====================
|Build Status| |Github| |codecov| |Python|
What is pymoten?
================
``pymoten`` is a python package that provides a convenient way to extract motion energy
features from video using a pyramid of spatio-temporal Gabor filters [1]_ [2]_. The f... |
b33f071b101bb1b127ac0d29c0eb601c6226d60ffb8dc70bc581c7b6cec40599 | Text | 3,400 | 33 | <img src="./RAVEN2.png" width="200px">
[](https://GitHub.com/SysBioChalmers/RAVEN/releases/)
[](http... |
3faa59674307c08e2888124398c3218f5afb7c524fb439fe2bda077c1b02716a | Text | 3,402 | 20 | # De novo discovery of traits co-occurring with chronic obstructive pulmonary disease.
This repository contains scripts, data, results, figures and reproducibility report for "De novo discovery of traits co-occurring with chronic obstructive pulmonary disease" study published in [Life Science Alliance](https://www.lif... |
c8d4fa2b9889d1adc94e27e77331fa54d3222500f7e963e6e81ba348e07323d0 | Text | 3,428 | 84 | # Database of Bimodal Detection Task
Experimental details can be consulted in the main paper,
https://www.biorxiv.org/content/10.1101/2022.08.12.503802v1
Data is organized by day experiment. In database you should find the following files:
* List_files.csv
* Data
## List_files
This csv file contains a recopilati... |
5d57b5937d23457b9fdd484de1ea8aee07a588dd6ac504d40272e5c2b3dc665e | Text | 3,453 | 103 | [](https://github.com/psf/black)
[](https://bsb.readthedocs.io/en/latest/?badge=latest)
[![Build Status](https://travis-ci.com/dbbs-lab/bsb.svg?branch=master... |
bc2b9aee2d507c9bc37fc3e394d79b4b63fff5883faca108f29b7bbb993b264a | Text | 3,457 | 110 | <div align="center">
<img src="https://raw.githubusercontent.com/zarr-developers/community/main/logos/logo2.png"><br>
</div>
# Zarr
<table>
<tr>
<td>Latest Release</td>
<td>
<a href="https://pypi.org/project/zarr/">
<img src="https://badge.fury.io/py/zarr.svg" alt="latest release" />
</a>
</td>
</... |
831d0732806fd1161a367292bcc9e10672eaf6776cc6ff6dfa3fc89caa954e98 | Text | 3,498 | 66 | # Welcome to NetChar!
NetChar is a developing package of functions I have used in my network analyses to process and format correlation matrices for subsequent analysis using the SVINet package by Prem Gopalan (https://github.com/premgopalan/svinet).
## API
### Entropy Analysis
runEntropy: Wrapper that sets up ent... |
ea2f307187437893158e7b3e8f8a82c1d2c70ad7d2b07ea3cc4c25069c3cffc4 | Text | 3,508 | 94 | 
[](https://pyqmc.readthedocs.io/en/latest/?badge=latest)
# PyQMC
PyQMC is a Python package for real-space quantum Monte Carlo (QMC) electron... |
800d92400b8ba974a4237b67b47ddd871984ec9ae946ea47fe98b5eadb48da9a | Text | 3,538 | 44 | # Readme for deamidation
This is a command-line script to calculate deamidation rates of peptides to estimate the deamidation of Asparagine to Aspartic acid and Glutamine to Glutamic acid per RawFile.
The program expects an "evidence.txt" file from <a href="http://www.biochem.mpg.de/5111795/maxquant">MaxQuant</a> as in... |
d46cba479beffd1b2c14e149665230c78b245540c23d29ccbb58ad7a7573c4bc | Text | 3,565 | 63 | # VAMPIRE (Visually Aided Morpho-Phenotyping Image Recognition)
**A robust method to quantify cell morphological heterogeneity**
**1. System requirements**\
OS : Windows 10 (64 bit) Version 1909\
Software is not compatible with older versions of Windows.\
Mac OS is not officially supported, but it may work... |
69b81d16d7a8cd040b566e9b339b5b4bdbdd21191f0ef77f6eee0501f9637cdc | Text | 3,594 | 66 | # Building and evaluating encoding models of EEG visual responses using DNNs
Here we provide the code to reproduce the results of our data resource paper:</br>
"[A large and rich EEG dataset for modeling human visual object recognition][paper_link]".</br>
Alessandro T. Gifford, Kshitij Dwivedi, Gemma Roig, Radoslaw M.... |
dbf35a7a0751232250085e900e7acbc9c570f02cfef7dd1039556762845577c4 | Text | 3,599 | 24 | # Spinal_premotor_interneurons_controlling_antagonistic_muscles_are_spatially_intermingled
MATLAB live scripts to run an executable version of Ronzano et al 2022 eLife and its associated supplementary materials.
The code has been tested on Matlab version 2022a.
In order to run the code, download to your local compute... |
619ca4325d87f41ca647193ab1c6bc3f89eb2f747d710bd5a1801b76b2c52072 | Text | 3,614 | 66 | Archived
========
This project is no longer maintained. Consider using [ImageNet training in PyTorch](https://github.com/pytorch/examples/tree/master/imagenet) instead.
ResNet training in Torch
============================
This implements training of residual networks from [Deep Residual Learning for Image Recognitio... |
a13ff25a5dd84d4a2f69ca6be88e9436bc2efe6105a6112f9cdbdcc22771f34f | Text | 3,629 | 112 | # NapShift (version 1.0.1)
This repository provides a standalone Python3 implementation of the (full atomistic)
NapShift program to estimate the backbone atoms' chemical shift values from NMR protein
PBD files. For the new version of the coarse grain (Martini PBD files) model please che... |
b16d1c3550fc404ce51e14080314424c655de791f056b6969893a3dd674f75fe | Text | 3,657 | 81 | # TimeAwarePC: A Python Package for Finding Causal Connectivity from Time Series Data [](https://pypi.python.org/pypi/timeawarepc) [](https://timeawarepc.readthedocs.io/en/la... |
149781f9b1fe2f478a6eca8fd1dae95adadb86c1349da03c46fcef81670b5b6d | Text | 3,704 | 44 | # deep-network-orthobiologics
This repository contains MATLAB m-files with code that trains various deep networks on orthobiologics data.
It also contains an Excel file that holds all the orthobiologics data in our dataset: OrthobioDatasetV4.xlsx
The code, and further code derived from it, were used for the project... |
c075c4b48e7cf877c029e3aa8a156e323da78dc615ce89b0944f7361f90b7879 | Text | 3,715 | 48 | # Synthetic-Brain-Aging
## Source code
The source code for the paper [1] can be found in the directory ```code```.
## Data sharing
In this repo, we publish a synthetic collection of three datasets generated by our proposed methodology (the following paper [1]). More details are shown in the corresponding subsection. ... |
1d7d29f80d71719d4aad22036288417634de494f65062839cbb204fe3670c2e4 | Text | 3,747 | 71 | Attention-based Deep Multiple Instance Learning
================================================
by Maximilian Ilse (<ilse.maximilian@gmail.com>), Jakub M. Tomczak (<jakubmkt@gmail.com>) and Max Welling
Overview
--------
PyTorch implementation of our paper "Attention-based Deep Multiple Instance Learning":
* Ilse, M... |
956041e04054c61e5559d05559f5d2fddfe12d165bf18bd86ec9299accf949a9 | Text | 3,771 | 80 | # Mice dFI
## AI for unsupervised learning of aging principles from longitudinal data
This repository contains the proposed model in the paper
[https://www.biorxiv.org/content/10.1101/2020.01.23.917286v1](https://www.biorxiv.org/content/10.1101/2020.01.23.917286v1).
It also contains notebooks and data to reproduce th... |
0f28779097de8e2840abcf9e3ac1c855e65b6759d2685342219efe2b5c663201 | Text | 3,775 | 120 | .. -*- mode: rst -*-
`NICE Tools`
=======================================================
Get the latest code
^^^^^^^^^^^^^^^^^^^
To get the latest code using git, simply type::
git clone git://github.com/nice-tools/nice.git
If you don't have git installed, you can download a zip or tarball
of the latest code:... |
688b1a384fd17fb2edf1bcd293e3ac787634d718bd3234f8e2b1ca3547ae97ce | Text | 3,783 | 110 | # PreprocEEG
This code is related to the work presented in the EMBC 2022:
[La Fisca and Gosselin, "A Hybrid Framework for ERP Preprocessing in EEG Experiments", 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), July 2022.](https://hdl.handle.net/20.500.12907/43258)
... |
8cc2cf48d1b045656d1218ef8842c40ef4c1e19474f31a07b7a272858f43c34f | Text | 3,789 | 101 |
# BlotIt - Optimal alignment of western blot and qPCR experiments
The present package bases on [blotIt2](https://github.com/dkaschek/blotIt2) by Daniel Kaschek. The aim of this toolbox is to align biological replicate data to a common scale, making the quantitative data of different experiments comparable.
## System... |
16700856d02a54578c1167e61cacaa0b3375f620de028aaa54c7ec864e2a009d | Text | 3,871 | 77 | **Note**: This package is no longer maintained as I no longer actively use it myself.
For gene set enrichment analysis in R, please check out instead [`fgsea`](https://bioconductor.org/packages/release/bioc/html/fgsea.html) or [`clusterProfiler`](https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html... |
572b0f753d6c8f1ad2e25d343cd51b96b4809ef919f14d21be7aed5ad561eda4 | Text | 3,888 | 76 | # Update
We have fully migrated the application and all of its interfaces, underlying models, etc. to Gitlab. Please see https://gitlab.com/mlpds_mit/askcosv2/askcos2_core for instructions on deployment; components in their own repositories will be automatically pulled during setup based on the provided config file in ... |
410ebe2216c9284358f17e56f746e046d7003c353f29cceeed35b6cb3bc327f5 | Text | 3,917 | 80 | # Classification of SARS-CoV-2 sequences using FCGR and CNN
Frequence Chaos Game Representation with Deep Learning
## Try the trained models
A [web app](https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr) is available with all the trained models, you just need to upload a fasta file with your sequenc... |
692f0e5e9e572f9c8e6317f1384b8d03824652f63e2ec6b91d993496d2b1bf2a | Text | 3,939 | 136 | # Volumetric Segmentation Pipeline
Contact: Mika Rubinov, `mika.rubinov at vanderbilt.edu`
## Run from Docker Container
Instructions [here](https://github.com/mikarubi/voluseg/blob/master/README-docker.md).
## Dependencies
- `h5py`, `dask`, `scipy`, `scikit-image`, `scikit-learn`, `matplotlib`, `nibabel`, `request... |
e761ce44763e740ade4404bce21a9a4d2d015c1f2b7f394903fe6eb113ef60d5 | Text | 3,971 | 56 | [](https://www.zenodo.org/badge/latestdoi/357736760)
# APARENT2
This repository contains the code for training and running APARENT2, a deep residual neural network t... |
25ac17d8a43ed6d7a1e48ceba854dbd786aef9d4e5d94b2cdc96562ee5084821 | Text | 3,973 | 100 |
# speckle
<!-- badges: start -->
<!-- badges: end -->
**Please note that the speckle package has moved to the following repository:
https://github.com/phipsonlab. Version 0.0.3 of
the package will remain here but will no longer be actively updated/maintained.
This version of the package contains the propeller and c... |
31a945e0b37bae50f8240edc3cab05c78843a9c44a077366e93d29711352e2e4 | Text | 4,009 | 47 | # Welcome to the Transdiagnostic Gradients Project!
### Here you can find the code and data that was used and generated for the manuscript „COORDINATED CORTICAL THICKNESS ALTERATIONS ACROSS PSYCHIATRIC CONDITIONS: A TRANSDIAGNOSTIC ENIGMA STUDY“ (https://www.medrxiv.org/content/10.1101/2022.02.03.22270326v1.full)
## ... |
e8a5faa6112da6cf266093e49c48dd4cbcd51a868db90d58966dbd0303d4ac06 | Text | 4,026 | 50 | # MP2RAGE EPG Simulations
Extended Phase Graph (EPG) Simulations of the MP2RAGE Sequence including T2 relaxation, diffusion, radio frequency spoiling, and B1+ variability.
Transverse magnetization is not assumed to be zero but is fed into the next run as an input.
The main file **MP2RAGE_sd.m** provides simulations of... |
af801066f000981744c85f716855f1fa8a1e076af64f02cde28b40dea0386bbb | Text | 4,032 | 75 | # SupervisedPCA
Classification supervised PCA inspired by Yehuda Koren and Liran Carmel and essentially developed by E.M. Mirkes, S.V. Stasenko, A.N. Gorban and A. Yu. Zinoviev.
Yehuda Koren and Liran Carmel introduced supervised PCA for classification problem in their paper
Koren, Y., & Carmel, L. (2004). Robust li... |
c5021f5c044d9e715603a2fb6f6010cb9ed5180378ec0ce93bd5b38687a135b6 | Text | 4,032 | 81 | # Brian2Lava
> **NOTE**
>
> Intel has officially ended the support for the Lava framework (also see their statement in the [Lava repository](https://github.com/lava-nc/lava)).
>
> Therefore, the development of Brian2Lava is finally discontinued as well. The latest code and release are archived here in this repository... |
f45803614e3b663bf7bbe273b546ca1309f66cfe5b40c8dee79abebf2c82fbe5 | Text | 4,078 | 91 | # Resting state HRF estimation and deconvolution
[](https://pypi.org/project/rshrf/)
Please refer to https://github.com/compneuro-da/rsHRF for MATLAB version
## The basic idea
This t... |
bd12075dc0d3d225626519bc50e2cbb65fe90ec9f5fe7aeaba10ba245816b8e6 | Text | 4,083 | 53 | # DrMZ
[](https://brekmeuris.github.io/DrMZ.jl/stable)
[](https://brekmeuris.github.io/DrMZ.jl/dev)
[](https://github.com/brekme... |
730f6f5a8c9282fbdb54b9f898d4b7590f47e8403e712aec148ed88be9d6c06d | Text | 4,094 | 87 | # Adaptively-thresholded Low Rank Approximation (ALRA)
## Introduction
ALRA is a method for imputation of missing values in single cell RNA-sequencing data, described in the preprint, "Zero-preserving imputation of scRNA-seq data using low-rank approximation" available [here](https://www.biorxiv.org/content/early/2018... |
dfccd22931d797370e38ebe4b3665209dafdaab3017aaa82a97685f57e8b1249 | Text | 4,095 | 132 | .. -*- mode: rst -*-
.. _scikit-learn: http://scikit-learn.org/stable/
.. _scikit-learn-contrib: https://github.com/scikit-learn-contrib
|Travis|_ |Pypi|_ |PythonVersion|_ |Coveralls|_ |Downloads|_
.. |Travis| image:: https://travis-ci.com/dmbee/seglearn.svg?branch=master
.. _Travis: https://app.travis-ci.com/githu... |
bedc0ccdbd0f6159cdc18a489564f7c998d052cf84125c25d2443814dc03a433 | Text | 4,135 | 96 | # textureSynth
This package contains MatLab code for analyzing and synthesizing digital
image of visual texture. The algorithm is described in the references
given at the bottom of this document. Further information, as well the
most recent versions of the code, are available at
http://www.cns.nyu.edu/~lcv/textur... |
22985fa6cad413c656d7842df7560551712a042eadd70963da456fbee4e82cd7 | Text | 4,145 | 74 | WARNING: We just noticed that the newest version of Juicer Tools (v1.22) interacts with SIPMeta in weird ways. Please use Juicer Tools v1.13 instead.
# SIP
<img src="https://github.com/PouletAxel/SIPImage/blob/master/guiSIP.jpeg" width="600">
# What is SIP?
SIP (Significant Interaction Peak caller) is a tool to ide... |
4b01006dbe8fd9dce9272df7298314fcf85253495f4cedd0792465731f18342f | Text | 4,190 | 67 | [](https://zenodo.org/badge/latestdoi/90018285)
[](https://www.python.org/downloads/release/python-360/)
# Computing functional maps of zebrafish brain
This code processes light-sheet data in several steps:
* pa... |
dcc14278d8f330f165aec14420dd873276881126b7383d99fbc874e2fc97416b | Text | 4,200 | 113 | # Graphene
Pre-trained graph neural network and downstream tasks
## Download files
Download the following files respectively
`gtex_js.csv`: https://doi.org/10.6084/m9.figshare.19550818.v1 to `./fig3-b/` folder;
`network.npy`: https://doi.org/10.6084/m9.figshare.19550902.v1 to `./network_data/` folder；
`label.npy... |
1841dfbac2e89c31e993dfda0800325e1411f4777255eeb233bcb1c11159ecc7 | Text | 4,205 | 70 | %%%file organization
Data file:
-IM-[rat#]_[RecordingDate]_[Tetrode#]_SNr.mat
-Each file includes SNr units from one tetrode from a single session with trial information.
-See below Data file organization for more information.
Analysis file:
-Behavior_ValuesForPlot.m : generate analyzed behavioral data
-Su... |
0040792b307711002ce79d17911a6aaccc943625023f1407669cbb3e0680ab5c | Text | 4,269 | 128 | # DeepSolid
An implementation of the algorithm given in
["Ab initio calculation of real solids via neural network ansatz"](https://rdcu.be/c4rNI).
A periodic neural network is proposed as wavefunction ansatz for solid quantum Monte Carlo and achieves
unprecedented accuracy compared with other state-of-the-art metho... |
a3d9082e4303b5b0a3c111f027ce5036bad3c0f867fc89808ce3c4221dd9f814 | Text | 4,272 | 74 |
# README file for the following manuscript:
Rumetshofer, T., Inglese, F., de Bresser, J. et al. Tract-based white matter hyperintensity patterns in patients with systemic lupus erythematosus using an unsupervised machine learning approach. Sci Rep 12, 21376 (2022). https://doi.org/10.1038/s41598-022-25990-w
Under Ge... |
fccebcd3e39de333f281b7d9cd3295113b0980e54b578eb645bd44cc6bb078be | Text | 4,291 | 80 | # HER2-overexpression
Prediction of HER2 overexpression status and IHC score as seen in "Predicting the HER2 status in esophageal cancer from tissue microarrays using convolutional neural networks".
## Usage:
### Quick intro
To train a resnet on example images available in _data/example_images_ run:
```console
$... |
05a2c17fe420d51c02766c5c5bf119b1a3bfc122e663cb33e6faa3dd46054a4a | Text | 4,292 | 58 | # FriendlyClearMap-scripts
This is the collection of scripts to build your own Dockerfiles for ClearMap1 and ClearMap2's CellMap component, as outlined in our 2022 GigaScience publication:
Negwer, M., Bosch, B., Bormann, M., Hesen, R., Lütje, L., Aarts, L., Rossing, C., Nadif Kasri, N., & Schubert, D. (2022).
Friend... |
21602c97ab58403c90e8fa0958d90682511ea7c4053c418f382459790d0b1588 | Text | 4,314 | 116 | # seqeval
seqeval is a Python framework for sequence labeling evaluation.
seqeval can evaluate the performance of chunking tasks such as named-entity recognition, part-of-speech tagging, semantic role labeling and so on.
This is well-tested by using the Perl script [conlleval](https://www.clips.uantwerpen.be/conll200... |
e137833a512eee0b448755c9b60f0e47e39d944ebaf425799b514fb8d3c2fdd9 | Text | 4,370 | 69 | # DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage through Deep Learning
## Overview
<div align="center">
<img src="./resources/DeeReCT-APA.png" width="600" height="450">
</div>
This repository contains the implementation of DeeReCT-APA from
Li,Zhongxiao, et al. "DeeReCT-APA: Prediction of Alternat... |
e8d94995966c1b44e5c8de8c07a72fd1f15c117c6287b358a1858d07e15a1a17 | Text | 4,448 | 124 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# dabestr <img src="man/figures/logo.png" align="right" height="139" /></a>
<!-- badges: start -->
[](https://cran.r-project.org/)
[![CRAN Download
Count](https://cranlogs... |
b367e6682c4cc095cb96d3981fb41cd093b901a8a0404e77f6a92ad0778f002d | Text | 4,494 | 68 | # BR-project
# Data analyses for the project: "Perturbation or Function? Intrinsic brain dynamics in the Default Mode Network predict involuntary fluctuations of visual awareness"
## Data repository: https://datadryad.org/stash/dataset/doi:10.5061/dryad.bf1b1
The original neuroimaging data accessible to the public ha... |
b332b9b697e5a9a16818088f4322ee080dc3489ab1c9f4de23497cd65f91bf55 | Text | 4,508 | 99 | klustakwik2
-----------
.. image:: https://travis-ci.org/kwikteam/klustakwik2.svg?branch=master
:target: https://travis-ci.org/kwikteam/klustakwik2
**NOTE: please follow the instructions for the klusta package https://github.com/kwikteam/klusta : the instructions below should not be used.**
Installation inst... |
87a1bab4ae1e560e1f0a10040e4301f8a617b522a4a79c751533508790c7b913 | Text | 4,566 | 107 | # prostatecancer.ai [![MIT License][license-image]][license-url]
__prostatecancer.ai__ is an [OHIF-based](http://ohif.org/), zero-footprint [DICOMweb](https://www.dicomstandard.org/dicomweb/) medical image viewer that utilizes artificial intelligence technologies to identify clinically significant prostate cancer.
[R... |
04adc8b14c59c8b5cee8f62409eea5f94710217a63ccbf0305511ea183098ca2 | Text | 4,616 | 51 | # Retention Index based on Cocamide Diethanolamine homologous series (C(n)-DEA)
<img
src= https://github.com/raalizadeh/RIdea/raw/main/v1.0/Win/doc/toc_DEA.png width=450 />
This repository contains the models and codes for generating experimental and predicted liquid chromatographic retention index values for eme... |
00a71beeb2efdabcd2c0c6018b795372faf4918498acc7a398d83ec71306ea05 | Text | 4,631 | 129 | # Metex - Maximum Entropy TEXtures
[](https://www.gnu.org/licenses/gpl-3.0.txt)
[](https://pypi.python.org/pypi/metex/)
[](https://doi.org/10.5281/... |
731b4c1b5735b503b39fedb7e611868dc8273ba93e6a48f7b0e73de2c2f6717c | Text | 4,693 | 40 | # Tonic Survey
This data set belongs to a joint project carried out by three neuroscientific Collaborative Research Centres (CRC/TRR 135, CRC 1315 and CRC 1158) with the support of the NFDI Neuroscience initiative with the aim of creating a homogeneous project structure. Two initial templates that had been created a... |
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