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b2890082ced66d409b764ca68168eb93eb22d45697ecb98435206b7563089717 | Text | 4,705 | 76 | # GeoSPM
## Introduction
GeoSPM allows the spatial analysis of diverse geographic point data. It draws upon differential geometry and random field theory, by leveraging the procedures used in statistical parametric mapping (SPM): a framework for making topological inferences about spatially structured effects, with w... |
64c462f71c3cb3cd9207c4cb427d5416787ead898f0d4416832bb751eef6e03e | Text | 4,713 | 143 | # PyCamcoil (version 1.0.0)
This repository provides a "Python implementation" of the camcoil program
(originally written in C) to estimate the random coil chemical shift values
from a sequence (string) of amino-acids.
There might be updates in the future, but this first version is now fu... |
f31f057613e616934cf21b2a361d0255df4095b5fc66655a47893b2021fa2664 | Text | 4,719 | 76 | # GeoSPM v2.0.3
## Introduction
GeoSPM allows the spatial analysis of diverse geographic point data. It draws upon differential geometry and random field theory, by leveraging the procedures used in statistical parametric mapping (SPM): a framework for making topological inferences about spatially structured effects,... |
1eb50ad5a7630089bc6726b4d473adf3218eaf74ee62f778e50304d3ef06f787 | Text | 4,738 | 111 | # upper-bound-energy-gnn
GNN for predicting an upper bound of the relaxed energy for a given unrelaxed structure
This repo accompanies the paper [Upper-Bound Energy Minimization to Search for Stable Functional Materials with Graph Neural Networks](), _chemRxiv_ 2022.
## Contents
- Pre-trained models: `pretrained_mode... |
a840d3af90560b2b0ec2b125e7ccaa4af1f0baefb41a9c6259c80bdab4c903bf | Text | 4,761 | 145 | =====================
Welcome to pymoten!
=====================
|Zenodo| |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 filters... |
6762c419a46933e2263b380b954baf933d8d4daf3729083a8c759a1c2b0c47a4 | Text | 4,789 | 89 | # FigureFlow
A Python package to allow fast, modular and reproducible generation of publication quality scientific figures and movies with only a few lines of code. <br/>
<br/>
A lot of the code to plot data and add significance information (statannot.py) is from statannot https://github.com/webermarcolivier/statann... |
945181ef225a5b9739ca81d6b25709f006534e6174c470d169aa5d840ae59ffa | Text | 4,797 | 54 | This repository contains a collection of scripts and jupyter notebooks used to perform data processing and analysis for the manuscript ["Merging enzymatic and synthetic chemistry with computational synthesis planning."](https://www.nature.com/articles/s41467-022-35422-y) This repository does not include the code to per... |
e82c86414545cdee727580c7f40b77f673391b141dd820cb5ba9c06597b0b63c | Text | 4,815 | 71 | [](https://github.com/scverse/anndata/actions)
[](https://anaconda.org/conda-forge/anndata)
[](https://img.shields.io/github/v/release/CannyLab/tsne-cuda)
, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.
Please see our [contribution... |
6457fa684a9d28e4a586a92ea8810ba90451cd9c7ed1e7bb495498e7bd3d73ac | Text | 5,040 | 128 | WholeBrain
=========
`WholeBrain` is intended as a software suite, meaning a collection of computer programs sharing a common interface and ability to integrate and exchange data with each other.
The purpose of WholeBrain is to provide a user-friendly and efficient way for scientist with minimal knowledge of computer... |
819c0dcef7b412efaa293e3be7ec8d7382199a4936662926601301d11ed5a154 | Text | 5,046 | 129 | # The Brain Scaffold Builder
[](https://codecov.io/gh/dbbs-lab/bsb)
[](https://doi.org/10.5281/zenodo.7089031)
GNN for predicting an upper bound of the relaxed energy for a given unrelaxed structure
This repo accompanies the paper [Upper-Bound Energy Minimization to Search for Stable Functional M... |
1440b835bf9731ec0150b8a9f27599c252e8c0561f4651b01f13e56074ccd300 | Text | 5,091 | 105 | # rho-HESS-wrapper
The following wrapper was written to allow scaling of local genetic correlation analyses that are reported in **Lam et al : Dissecting Biological Pathways of Psychopathology Using Cognitive Genomics**. <br><br> The wrapper works with rho-HESS version 0.5.4 and LDSC 1.0.1. We assume that users would ... |
01f314aeb6d62ab00290e7d5eb797eb87862845b0a08f58cc6d39c4130f16131 | Text | 5,113 | 96 | This repository contains the datasets and ML models from the research work "Massive Monte Carlo simulations-guided interpretable learning of two-dimensional Curie temperature".
The datasets can be found by unzipping the file "datasets.zip". There would be a total of 10 csv files: train and test data for each lattice ty... |
54bb9349f7557ffbfedbaed518d8f314bfd383c122b3551f24c5ec75651d0d91 | Text | 5,122 | 160 | ## DIANA-DeepTSS - Deep learning computational framework for TSS identification
### Prerequisites
- Unix system
## Installation
##### Install Anaconda python:
Download and install anaconda python [(installation guide)](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)
##### Install conda... |
1c265c70f2386d153b6104f39a3cd05fb4a197118a8e9d195579a53080ee8e59 | Text | 5,144 | 84 | [](https://zenodo.org/badge/latestdoi/424591742)
# README - oct-cbort
This library aims to provide entire processing library (in Python) that is used by the OCT research groups within the Center for Biomedical OCT Research ([CBORT](https://octresearch.org/)) at The Wellma... |
c39fb8d151a9877ee62eb1798730c4c4bb7d516e9424e006d2d4d0808e45936a | Text | 5,224 | 83 | # SPAL — Splicing–Pruning–Activity Loop model of autism
Code, derived data and results for the article
> \*\*Connectivity alterations may precede splicing-factor dysfunction in idiopathic autism: a transcriptomic and biophysical-computational study.\*\*
> \[Author Name], 2026.
The repository formalizes the circular ... |
2cf3151015a3a5af88cb25b261d04a9427e5f44c60ebb2aa82516875e9454450 | Text | 5,264 | 118 | # `pke` - python keyphrase extraction
`pke` is an **open source** python-based **keyphrase extraction** toolkit. It
provides an end-to-end keyphrase extraction pipeline in which each component can
be easily modified or extended to develop new models. `pke` also allows for
easy benchmarking of state-of-the-art keyphra... |
b4ae97bb785292871d9303974d12989376fb1be71d46365451b4e8affd13676c | Text | 5,264 | 72 |
# Réseaux de neurones artificiels et apprentissage machine appliqués à la compréhension de la vision
* Où: Salle PHY51 - Marseille (France)
* Quoi: [Master 1 Neurosciences et Sciences Cognitives](https://ametice.univ-amu.fr/course/view.php?id=89069)
* https://laurentperrinet.github.io/talk/2022-03-23-ue-neuroscienc... |
bdcff9e47c3b8184731f1c579c4bcc45f92c3acdc22295cbe935e1867aa15e53 | Text | 5,280 | 119 | 
## Summary
This is the main code of the project "Interacting Active Surfaces" and follows the ideas in the manuscript:
[https://doi.org/10.1101/2022.03.21.484343](https://doi.org/10.1101/2022.03.21.484343)
... |
3ae489a40183656e76b8a9946b11fec65ae652d15ab65b2774c17c915dd188c7 | Text | 5,361 | 112 | [](https://github.com/dbbs-lab/cerebellum/actions/workflows/integration.yml)
[](https://github.com/psf/black)
[](https://www.codefactor.io/repository/github/gmrukwa/divik)
[](https://codeclimate.com/github/gmrukwa/divik/maintainability)
](https://pypi.org/project/deeptables)
[](https://pypi.org/project/deeptables)
[](https://pepy.tech/projec... |
52ea7837690ecdf41533cf384ed652ccc120d84cfca299a0dddbbeb603ecf9f4 | Text | 5,538 | 34 | This is the repository for the MATLAB and Python codes for generating the results in the manuscript: Exploring the rules of chimeric antigen receptor phenotypic output using combinatorial signaling motif libraries and machine learning, K.G. Daniels, S. Wang, M.S. Simic, H.K. Bhargava, S. Capponi, Y. Tonai, W. Yu, S. Bi... |
e785ad36c00dadd12c474af5862924d9b1736cec4b332be65071ca30b88337ba | Text | 5,557 | 68 |
# Synaptic basis of a sub-second representation of time
This repository contains the c++ code used for carrying out the simulations of the publication: "Synaptic basis of a sub-second representation of time". The code 1) generates instances of cerebellar-cortex networks with the desired statistical properties, as des... |
a45087c8b9133873c5ca0a602cb6a157b12aa73678bb7eb027ad14dae72ffbf9 | Text | 5,560 | 72 | # retinal-contrast-glare
A set of (Python & Matlab) functions for estimating the impact of **glare on the formed retinal image**, derived from **calibrated measurements of scene radiances**, or luminances.
The reason for *not* directly using digital camera outputs, is that, **captured camera images do not represe... |
bf112c9cd2d77dc016f45a54aee746831bab67f28b1257d223378f98c8e08740 | Text | 5,590 | 170 | *Our tool is under active development and feedback is very much appreciated.*
# learnMSA2: deep protein multiple alignments with large language and hidden Markov models
<img src="https://github.com/Gaius-Augustus/learnMSA/blob/main/logo/training_loop.gif" alt="" loop=infinite>
## Features
- aligns large numbers of ... |
bf42ea1d137bd82966f5e9139a1772f6f6499e25bd08f1284d0b148d343a5487 | Text | 5,602 | 115 | # Genomic Multiple Kernel Learning methods for Genome Interpretation #
This repo contains the software and the code related to the paper "Genomic Prediction with kinship-based Multiple Kernel Learning produces hypothesis on the underlying inheritance mechanisms of phenotypic traits"
### What is this repository for? #... |
0da7a5be6d22a3fada478b1d7044529777da2a006ae4064df84a786bd275dd5f | Text | 5,660 | 135 | # Covid Predictive Model
A PyTorch Recurrent Neural Network implementation for Covid-19 fatality prediction.
## Characteristics of the RNN
- Daily predictions.
- Attention (static wrt. dynamic(all events),
dynamic(current event) wrt. dynamic(all events) and both mechanisms).
- Custom Loss function.
## RNN Architect... |
4ef7aa737634cf4f6deb01a7417f97fd12968f1fdb1227d234f3b23cf5877436 | Text | 5,699 | 48 | # Brain-Wide Association Study
This repository contains scripts to perform Brain-Wide Association Study (BWAS) to find the association between brain imaging-derived phenotypes and idiopathic pulmonary fibrosis genetic risk, as described in this paper: [A. R. Mohammadi-Nejad, R. J. Allen, L. Kraven, O. C. Leavy, R. G. ... |
be740c78ba1efc88685fc2ebe20ee8358aa1707f0aea17c7f6324d8681677cfb | Text | 5,824 | 107 | # 3D-MASNet
This repository provides the experimental code for our paper "3D-MASNet: 3D Mixed-scale Asymmetric Convolutional Segmentation Network for 6-month-old Infant Brain MR Images".
Created by Zilong Zeng at Beijing Normal University.
**For any questions, please contact zilongzeng@mail.bnu.edu.cn or tengdazhao@... |
c0226708fb563f1527146c9df2764bc17b955d79351040dd69ba53aa283994ad | Text | 5,840 | 207 | UCSC Genomes Downloader
=========================================================================================
|python_version| |pip| |downloads|
Python package to quickly download and process genomes from the UCSC website.
How do I install this package?
----------------------------------------------
As usual, jus... |
0c00ff8bf38d45f6180c971e11170fcce29a66fed5e2e62f76dce36e2bf4647d | Text | 5,843 | 166 | # <a href="http://dataxlab.org/deep-hipo/index.php">HipoMap</a>
[](https://www.dataxlab.org)
[](https://doi.org/10.1038/s41586-020-2649-2)
[
* [Usage](#usage)
* [Data](#data)
* [Data cropping](#data-cropping)
* [Data padding](#data-padding)
* [Data loading, sampling, and page caching](#data-loading-sampling-and-page-caching)
*... |
4627b278a76fadfd528a93616557224eb0b1bb26fd5c5ccf3dad2bc0c28aca18 | Text | 5,922 | 148 | # *ReCSAI:* Recursive Compressed Sensing Artificial Intelligence
is a SMLM (Single Molecule Localisation Microscopy) software to determine the location of sparse fluorescent emitters with subpixel accuracy. The provided trainings are optimized to work with disrupted, nonlinear or varying PSF's occuring in confocal *d*S... |
c23015ae175b45f7c71a35af9c290403f9b98018c4ce99e84c4b4793bcd3f357 | Text | 6,040 | 130 | CILDS (Calcium Imaging Linear Dynamical System)
=================
Code accompanying the paper "[Dimensionality reduction of calcium-imaged neuronal population activity](https://www.biorxiv.org/content/10.1101/2022.03.11.480682v1)". Runs on MATLAB2018a. Note that this code is currently still in preliminary form.
CILDS ... |
4e1653c51d2f1b2f523be5d0cf9efa86efcb5a0feba4069f505520a3295a47d6 | Text | 6,166 | 149 | # DAPCA
Domain adaptation PCA method first introduced in [Gorban et al, High-Dimensional Separability for One- and Few-Shot Learning. Entropy 2021, 23(8), 1090](https://doi.org/10.3390/e23081090)
and described and benchmarked in details [in this preprint](https://arxiv.org/abs/2208.13290).
Domain Adaptation Principal... |
d5a03120ca94d3d95f02e243193a693d7ae3b91556286687b558b7d1ae920c56 | Text | 6,169 | 71 | README for PatSep, created 12/2018
This code is associated with the article "Temporal pattern separation in hippocampal neurons through multiplexed neural codes", by A. Madar, L. Ewell and M. Jones (2018) available on BioRxiv: https://www.biorxiv.org/content/early/2018/09/19/421479
For questions, please contact An... |
bf0bfce122458102564b34ef3775083f9cc0767cd0b8a94d96d726f4a8fc4df4 | Text | 6,306 | 92 | # self-consistent-expression-recovery-machine (SERM)
SERM is a data-driven gene expression recovery framework. Using deep learning, SERM first learns from a subset of the noisy gene expression data to estimate the underlying data distribution. SERM then recovers the overall gene expression data by analytically imposing... |
b8dc5517e5503f1a7dffb64e6bed9f535cd1c404cea4d39855f6245ce629aaaa | Text | 6,334 | 102 | # MELD classifier
Neural network lesion classifier for the MELD project.
The manuscript describing the classifier can be found here https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awac224/6659752
*Code Authors : Hannah Spitzer, Mathilde Ripart, Sophie Adler, Konrad Wagstyl*
[](https://github.com/nf-core/nanoseq/actions)
[](https://g... |
971c2fd67032016e003c0627e4c387c46364d77db47dd378eae692fd36a3a9de | Text | 6,490 | 88 | # qPCR-Biomark
**R scripts to process and analyze qPCR data from Fluidigm Biomark HD**
---
**Creation : 2016/01/06**
**Last update : 2023/04/03**
---
## Motivation
qPCR-Biomark contains different R scripts developed to analyze high-throughput qPCR data from Fluidigm Biomark HD.
Normalization to a reference gene i... |
5c27f19c70dd68d6ff03a1f9d5386e05f3e38578130c7d143e571769da4cdf68 | Text | 6,506 | 136 | # README
Magellan is an R package to identify locations within a spatial transcriptomics experiment that are undergoing a biological response to a perturbation.
Magellan builds on our [Augur](https://github.com/neurorestore/Augur) package for cell type prioritization within single-cell transcriptomics data.
The intui... |
d7bf9d1c84e87a1bf0c378589f752907224d133039ffd99f88a79cc0cbda8961 | Text | 6,509 | 101 | # Music Transformer
[](https://colab.research.google.com/github/asigalov61/SuperPiano/blob/master/Super_Piano_3.ipynb)
Currently supports Pytorch >= 1.2.0 with Python >= 3.6
There is now a much friendlier [Google Colab version](https://github... |
7c585e4f8a0caf0a61cba7c7e216f1afe90ef861dac30515cbf4747e6dfbf79b | Text | 6,542 | 56 | # 3D brain plot
Create three-dimensional plots of scores on the brain surface.<br/>
<br/>
3D brain plots of the left hemisphere of a neonatal brain with random scores. The figure shows the brain of a neonatal subject of the developing Human Connectome Project [DHCP](http://www.develop... |
94bac0071c72768c6f67d24c4ca9e2607c9ab62ed7570d7fbffa5267515274f0 | Text | 6,589 | 166 | # Cere-MEG-Bellum (CMB)
[](https://pypi.org/project/cmb/)
[](https://github.com/ceremegbellum/ceremegbellum/blob/main/LICENSE)
[](h... |
6f017ab6835c92e136b61f9f7ba945cc1bd9e81fec36edf61b969c86f92e2444 | Text | 6,687 | 172 | Tools for Gene Ontology
========================
.. image:: https://img.shields.io/pypi/v/goatools.svg
:target: https://crate.io/packages/goatools/
:alt: Latest PyPI version
.. image:: https://img.shields.io/pypi/dm/goatools.svg
:target: https://crate.io/packages/goatools/
:alt: Number of PyPI downloa... |
54a61ff5dfea9de466043b0fb1bd2b6dfebd4ef763c83e60751b45e989311102 | Text | 6,748 | 104 | # PREPAIR - Unsupervised Physiological Regressor Estimation from Phase and mAgnItude sub-tR
We created an unsupervised physiological noise removal tool -- PREPAIR -- using magnitude and phase data to identify respiration and cardiac fluctuations in the brain without the need of external recordings. PREPAIR was tested ... |
40f7e0cf1e8c5f494a220e7b335460781105b92cff92b636ae2783110e8488ac | Text | 6,757 | 160 | .. Following contents should be from LONG_DESCRIPTION in abagen/info.py
abagen: A toolbox for the Allen Brain Atlas genetics data
=========================================================
This package provides a Python interface for fetching and working with the
`Allen Human Brain Atlas`_ (AHBA) microarray expressio... |
72706b5dfd0157139c487edcafb4ddd53d3768444f720e96b2d0af668390c38c | Text | 6,891 | 75 | # _CardioFitness_ — VO2max prediction with wearables
### 📖 Longitudinal cardio-respiratory fitness prediction through wearables in free-living environments
code for Nature Digital Medicine '22 paper
<details><summary>Abstra... |
160c1e728a018ee1b0f39b4aa25da0e7373c47425dc3b9c3197ce023c78de40a | Text | 6,928 | 82 | # Nonnegative spatial factorization for multivariate count data
This repository contains supporting code to facilitate reproducible analysis. For details see the [preprint](https://arxiv.org/abs/2110.06122). If you find bugs please create a github issue. An [installable python package](https://github.com/willtownes/sp... |
9377315af4e2fb23d282c408b2851015fc2eb1dcafd426b2ced184cbd2aa2e53 | Text | 7,024 | 84 | # Nonnegative spatial factorization for multivariate count data
[](https://zenodo.org/badge/latestdoi/415147174)
This repository contains supporting code to facilitate reproducible analysis. For details see the [preprint](https://arxiv.org/abs/2110.06122). If you find bug... |
20af3d80602d005e887a35049243dd7c1eef57eb12448918a05572bee3a65915 | Text | 7,107 | 145 |
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/spm/
%
% R E A D M E
%
%__________________________________________________________________________
%
% This README gives a b... |
aa790631ff27a9a93afea000f774f296a692b2fa201efeb1a7960589fffb36b0 | Text | 7,158 | 213 | 
[](https://badge.fury.io/py/pysnirf2)
# pysnirf2
Dynamically generated Python library for rea... |
a6e7d9795265631920df2352b029942ba3f9ec04298a9527d6c9e8f4d800d6f4 | Text | 7,160 | 122 | # TULIP - TUmor CLassIfication Predictor <img src = "images/tulip.svg" alt = "tulip" width = "50" height = "50">
TULIP (the TUmor cLassIfication Predictor) classifies RNA-Seq samples into tumor types.
## Description
TULIP is a 1D convolutional neural network for classifying RNA-Seq data with [60K genes](https://gith... |
198603fc6a2cee81b5b98b727c11b09d30b6340c373bef430d506965e27fb1bc | Text | 7,202 | 138 | # KUL_VBG
KUL_VBG or "KULeuven - Virtual brain grafting" enables whole brain parcellation in the presence of large lesions.
Whole brain parcellation means labeling the brain in parts, gyri, etc...
Many parcellation software packages fail in the presence of large brain lesions.
The approach taken here is to:
- Extra... |
34c0888c7ea982e2dcc298c9645f9a613297b56c3522634b62375d00d13768e7 | Text | 7,238 | 112 | <h1 align="center">
LightPropagation.jl
</h1>
<p align="center">Fast and accurate numerical routines for simulating light transport in scattering media.
<div align="center">
 [ electric-field
simulation in which the white- and gray-matter conductivity tensor is derived from b-tensor-encoded
multidimensional diffusion MRI (MD-dMRI / QTI) rather than conventional single-shell D... |
c6a9c9c09db9ac95a5e4b2e0aa639751dc86f21345303fbd002ebb38ebdd42c0 | Text | 7,458 | 165 | CILDS (Calcium Imaging Linear Dynamical System)
=================
Code accompanying the paper "[Dimensionality reduction of calcium-imaged neuronal population activity](https://www.nature.com/articles/s43588-022-00390-2)"[[1]](#1). Runs on MATLAB2019a. Note that this code is currently still in preliminary form.
CILDS ... |
c154e25fa738c363fdf7de4f3356e733af9c32107b02e4320910a8fbb1e95be3 | Text | 7,517 | 119 | # TF-MoDISco
TF-MoDISco (**T**ranscription **F**actor **Mo**tif **D**iscovery from **I**mportance **Sco**res) is an algorithm for discovering sequence motifs from machine-learning-model-derived importance scores. Unlike traditional motif discovery methods that rely solely on sequence enrichment, TF-MoDISco leverages c... |
60cd0b7410200b0a02e22306f6219b3decd5a135cc3ed02bbcd7110942117a91 | Text | 7,564 | 120 | # Self-Supervised Graph Neural Networks for Improved Electroencephalographic Seizure Analysis
Siyi Tang, Jared A. Dunnmon, Khaled Saab, Xuan Zhang, Qianying Huang, Florian Dubost, Daniel L. Rubin, Christopher Lee-Messer. *International Conference on Learning Representations, 2022*. https://openreview.net/pdf?id=k9bx1E... |
e8dddcc104cb9423cdf5830083adc77bff296a7e57219425d08b7f7cdf73bbdd | Text | 7,650 | 245 | <h1 style="text-align:center">
pysnirf2
`pip install snirf`
</h1>
[](https://badge.fury.io/py/... |
7e19656c2433145b3495c9c6c8f311a9d415b2961709a6ae6ee6d731df89aad1 | Text | 7,846 | 198 | <img width="300" src="https://ax.dev/img/ax_logo_lockup.svg" alt="Ax Logo" />
<hr/>
[](https://pypi.org/project/ax-platform/)
[](https://pypi.org/project/ax-platform/)
[](https://github.com/sappelhoff/sp_experiment/actions?query=workflow%3A%22Python+tests%22)
[](https://codecov.io/gh/sappelhoff/sp_experi... |
19a764c403019ab2442e45ecaa87ac7b914b420398279e01523c1b5e38f72c6f | Text | 8,008 | 170 | # MiraikanDrawing
Code for analysing children's drawings, replicating results for:
Philippsen, Tsuji, and Nagai:
"Quantifying developmental and individual differences of spontaneous drawing completion in children" (under review)
An OSF preregistration of this study has been performed for part 1 of the analysis, cove... |
0d155f479b4b50fb758172cd2631b42a79f0044d2e4ae95123efa8f711c915d5 | Text | 8,018 | 234 | # [tf-keras-vis](https://keisen.github.io/tf-keras-vis-docs/)
<!-- sec.0 -->
[](https://pepy.tech/project/tf-keras-vis)
[](https://badge.fury.io/py/tf-keras-vis)
[![PyPI version](https://b... |
2d0a3aab29c6f7a8b0ef26098c2685193cdecadd8f913c66c9105dded18e9f06 | Text | 8,054 | 188 |
# Experimentally unsupervised deconvolution for light-sheet microscopy
This repository contains code for experimentally unsupervised deconvolution for light-sheet microscopy with propagation-invariant beams.
This work was first presented in:
*Wijesinghe P., Corsetti S., Chow D.J.X., Sakata S., Dunning K.R., Dholaki... |
d7c1ce7a6ba14846ab59c53a1fd6ee3bfe2853beac0b529f9831a9c29e4c55d3 | Text | 8,097 | 232 | # _CNV-espresso_
A tool designed for confirming ***C***opy ***N***umber ***V***ariants from ***E***xome ***S***equencing ***Pre***diction***s*** in ***S***ilic***o***
<img src="https://shenlab.github.io/images/cnv_espresso.png?raw=true" style="float:right;width:150px" alt="cnv-espresso">
## Dependencies
Python with ... |
0365cd6432919d28fc9011635c5c38ad2248a031a0f1f5e7dbdd0b28e070e8fc | Text | 8,216 | 177 | # Continual Learning
This is a PyTorch implementation of the continual learning experiments with deep neural networks described in the
following article:
* Three types of incremental learning (under review; a presentation of a workshop verion is available here:
[link](https://virtual.lifelong-ml.cc/poster_67.html))
Th... |
4a53f6d288c859fc5302c070dbf38fcedfdea52849b40fd2b031db6fd7689c71 | Text | 8,306 | 158 | # ML4ML
### Machine Learning Analysis for MATLAB
_A MATLAB Wrapper for Machine Learning, with another wrapper for neuroimaging data analysis_
## Requirements
These functions require the following packages:
* [LibSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) (for `ML_SVC` and `ML_SVR`) for MATLAB
* [SPM](https:... |
157f0fea7fdca5c053c51707752ad2a48697285f023d4f82f04d349423f85675 | Text | 8,444 | 245 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# sigminer.prediction
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#experimental)
<!-- badges: end -->
Mutational signatures represent mu... |
382cf4d8e74fd1b480dc7ee7fd5d3346e2355bfbb233a787c471f9a7f743c2ec | Text | 8,518 | 222 | # BCBToolKit
Created by Michel Thiebaut de Schotten and Chris Foulon.
> **BCBtoolkit is not approved for clinical use.**
> BCBtoolkit is the property of Chris Foulon and Michel Thiebaut de Schotten.
> Contact: hd.chrisfoulon@gmail.com or michel.thiebaut@gmail.com
Compatible with Mac OSX 10.7–10.10 and Linux (ArchLin... |
edccc50cd9405ff80ee505c81a1bbf74941f3dd7a952753c7fcdd73db47ef7dc | Text | 8,847 | 123 | # MolRep: A Deep Representation Learning Library for Molecular Property Prediction
## Summary
MolRep is a Python package for fairly measuring algorithmic progress on chemical property datasets. It currently provides a complete re-evaluation of 16 state-of-the-art deep representation models over 16 benchmark proper... |
8c3f2bc4da99072cfdc07e06510c93910808e83f73848dde870cb2d861b07738 | Text | 8,911 | 317 | **Nanom6A**
**Quantitative profiling of N6-methyladenosine at single-base resolution using Nanopore direct RNA sequencing**
**The default model is applicable only to "MinION or GridION R9.4.1 flowcells".**
Gao, Y., Liu, X., Wu, B., Wang, H., Xi, F., Kohnen, M. V., ... & Gu, L. (2021). Quantitative profiling of N 6-m... |
d51d7b8db04090b0b911d75dd1d027fcc0a0f06f4183b56048929b9101c7b313 | Text | 9,103 | 190 | # Neural Inverse Design of Nanostructures (NIDN)
[](https://nidn.readthedocs.io/en/latest/?badge=latest) [](https://github.com/esa/NIDN/actions/workflows/ru... |
58866ae0df8a2497c08ebfa3d13eb8ebf6f63bbe49ccec59e0d2ab68b7b745d0 | Text | 9,150 | 251 | [](https://zenodo.org/badge/latestdoi/423527863)
# ecomp_analysis
This repository contains the analysis code for the eComp project.
The archived version can be found on Zenodo:
- doi: [10.5281/zenodo.6411287](https://doi.org/10.5281/zenodo.6411287)
All important detail... |
f3ed4af76af7cc5926b2165c963f05fc116a74b2aa88ba428dfa48e379d8b8f4 | Text | 9,221 | 110 | # 
[](https://github.com/nf-core/chipseq/actions)
[](https://... |
54f4dfa8528df312c559fcd759ea1842820beaf864a3ff0181a33aa153c1bde9 | Text | 9,259 | 203 | # Covariates_Analysis
This repository is linked to the publication:
[La Fisca et. al., "Biases in BCI Experiments: Do we really need to balance stimulus properties across categories?", Frontiers in Computational Neuroscience, Volume 16, Pages 153-172, 22 November 2022](https://www.frontiersin.org/articles/10.3389/fn... |
547a0ea79ca41954e7e604ffdef00dd96fa84d3d28df4da8875296895e7f75df | Text | 9,271 | 171 | 
# CDPred
## Function of CDPred
CDPred is a deep transformer tool for predicting interchain residue-residue distances of protein dimers or any two interacting chains in protein complexes. For a homodimer consiting of two identical chains, it takes the tertiary structure and multiple sequenc... |
494bafd39e550ac39bd14293e7a45534aec54329bf7dceed8544f74c69f3a349 | Text | 9,273 | 204 | # A Loihi emulator based on Brian2
The package extends *Brian2* classes such that they match Loihi simulations. While the neuron and synapse model results in an exact match to *Loihi*, the pre- and post-synaptic traces have very small variations from the *Loihi* chip due to stochastic rounding.
Further details are ex... |
4ab9ebbe4ba90baacb33325cec0db94fb5908f5f2bdc906a258f4503d58c8b05 | Text | 9,374 | 251 | [](https://zenodo.org/badge/latestdoi/423527863)
# ecomp_analysis
This repository contains the analysis code for the eComp project.
The archived version can be found on Zenodo:
- doi: [10.5281/zenodo.6411287](https://doi.org/10.5281/zenodo.6411287)
All important detail... |
80120cc375b71b3f04389fdffbc15a784362a369b25b45b818d03b122f418204 | Text | 9,580 | 82 | # gc_segment
Annotation-based organelle segmentation using graph cuts
## Getting started
1. Install some version of anaconda, e.g. [miniconda](https://docs.conda.io/en/latest/miniconda.html).
1. Open the terminal.
1. Create a new conda environment: `conda create -n gc_segment python` and activate it: `conda activate ... |
dce9cd714f65d62fe20b422bbec79c1993cacc827f3d9f87ace72c693d01cd3c | Text | 9,610 | 180 | # ANLS_STDP
anls_stdp implements the model for the coupling of astrocyte-neuron lactate shuttle (ANLS) with spike-timing dependent plasticity (STDP) published in
Yulia DEMBITSKAYA, Sylvie PEREZ, Charlotte PIETTE, Hugues BERRY, Pierre J MAGISTRETTI, and Laurent VENANCE. Lactate supply overtakes glucose when neural co... |
f9d444a3044af41b8c5d858f4578cafbbfd2b19fe169af978f2c025b517bc01d | Text | 9,616 | 192 | # Continual Learning
[](https://zenodo.org/badge/latestdoi/150479999)
This is a PyTorch implementation of the continual learning experiments with deep neural networks described in the
following article:
* [Three types of incremental learning](https://www.nature.com/article... |
db4cb27c86ebf8ad91300502c4b7f3fc11de0ad291796eec70b12edf86b674d4 | Text | 9,732 | 107 | # Meisler_Reading_FBA
To cite:
Steven Lee Meisler and John D.E. Gabrieli (2022). Fiber-specific structural properties relate to reading skills in children and adolescents. _eLife_ 11:e82088.
[](https://doi.org/10.7554/eLife.82088)
Code used in the Meisler an... |
74efa68a8fe96d76e47150c262e5288d96bc8dd13b171a5406a31438a3316b2b | Text | 10,396 | 196 | # NIST Randomness Testsuit
This is a Python implementation of **NIST SP 800-22** – A Statistical Test Suite for Random and Pseudorandom Number Generators for Cryptographic Applications
## Getting Started
### Prerequisite:
You need the following software and packages for this application:
1. Python 3.6 and above (Tes... |
c0ca22550bff64fa8ee99a75d4736c3abd01fd2048deef90ffc033b828a61198 | Text | 11,134 | 189 | 
# maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
[](https://github.com/JuliaMath/Bessels.jl/actions/workflows/CI.yml?query=branch%3Amaster)
[](https://juliamath.github.io/Bessels.jl/st... |
73c5240e9e7e861aa06e972a0ab41ddfd44b060da6aa762a9a362e19700bb2fa | Text | 11,184 | 105 | # CanineGliomaManuscript
This page provides the analysis code used for the paper entitled, "Reprogramming the Canine Glioma Microenvironment with Tumor Vaccination plus Oral Losartan and Propranolol Induces Objective Responses."
[](https://zenodo.org/badge/latestdoi/520531... |
fc53f2217b20114e8d2a324ee9622163f32719d6c074264c32949245e69eb904 | Text | 11,623 | 233 | # M4Depth
This is the reference TensorFlow implementation for training and testing M4Depth, the depth estimation method described in
> **Parallax Inference for Robust Temporal Monocular Depth Estimation in Unstructured Environments**
>
> [Michaël Fonder](https://www.uliege.be/cms/c_9054334/fr/repertoire?uid=u225873),... |
2561eebb0f3d264e957b2dbe3d3160f2e00e7b571c4503c6d9ab52399b33a446 | Text | 11,957 | 113 | #  
[](https://github.com/nf-core/nanoseq/actions?query=workflo... |
90bf23ef42830f34bf09d4bcd3ab7246313f78eb5e01dd7afa1d8d62edf963ec | Text | 12,026 | 319 | Audio Super Resolution Using Neural Networks
============================================
This repository implements the audio super-resolution model proposed in:
```
S. Birnbaum, V. Kuleshov, Z. Enam, P. W.. Koh, and S. Ermon. Temporal FiLM: Capturing Long-Range Sequence Dependencies with Feature-Wise Modulations. N... |
b25f17435f8f0efb3e3576d06c44874fc9e6f25a8ec0a8d1517ea1878a06d2c3 | Text | 12,151 | 198 | # FigureFlow
[](https://figureflow.readthedocs.io/en/latest/?badge=latest)
A Python package to allow fast, modular and reproducible generation of publication quality scientific figures and movies with only a few lines of code. <b... |
53bac43c231216635b23bb4a1e2e6d2cf5c228e69ced5ba17f8b4266c330d1d1 | Text | 12,719 | 184 | [][license]
# Morphological atlas of neonatal brain development
Spatio-temporal neonatal brain atlas constructed as part of the [Developing Human Connectome Project (dHCP)][dhcp].
The methodolo... |
d311f1ee01fc08b52dac9cf4b27f2e8d75f315dc8421dadd9939a1b96cb4465e | Text | 12,830 | 267 | # SpikingJelly
[中文](./README_cn.md) | English
[](https://pypi.org/project/spikingjelly)
[](https://pypi.org/project/spikingjelly)
[](https://zenodo.org/badge/latestdoi/369565611)
# Code for the `mpib_sp_eeg` dataset
The code in this repository was used to analyze the data from the `mpib_sp_eeg` dataset
(see "Download the data" below).
Below, we describe how to setup the environment necessary to rep... |
073788d128dc0d428a529e20519f7bf2bcfde74d013c4e87ca3212977ac21c9a | Text | 12,952 | 158 | [](https://circleci.com/gh/miykael/fmriflows/tree/master)
[](https://github.com/miykael/fmriflows/issues/)
[![GitHub pull-requests](https://img.shields.io/github/issues-pr/m... |
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