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4f691fbdfa9e13d8e689138127b30163d197d2cdb0995bbf2ee92b004eb6088a | Text | 3,395 | 53 | [](https://anaconda.org/conda-forge/msdnet) [](https://anaconda.org/conda-forge/msdnet) [ imaging of mitochondria and caulobacter. The two main modules are Mito2Drp1.py, NetworkWatchdog.py and NNGui.py.
The overall idea of this project is to adapt the imaging speed of a... |
4cff52b48304c914bedea779261547e4306fa0daa8c8a5e99046a54838670247 | Text | 3,423 | 48 | # Benchmark problems for transcranial ultrasound simulation: Intercomparison library
[](... |
9d9b64c25b758bb69284673a2ab682709bfe4aaaa14e7eec5c84b0db6f46e612 | Text | 3,454 | 109 | # FaceMaskDetection
[中文版](README-zh.md) | English version
### We open source all the popular deep learning frameworks' model and inference code to do face mask detection.
- [x] PyTorch
- [x] TensorFlow（include tflite and pb model）
- [x] Keras
- [x] MXNet
- [x] Caffe
- [x] Paddle
- [x] OpenCV dnn
** Detect faces an... |
7504b19f868b11137fce335d0e63adf61b3f8f88c2abe23002f452b394af4496 | Text | 3,492 | 93 | clustree <img src="man/figures/logo.png" align="right" />
=======================================================
[](https://www.repostatus.org/#active)
[](https://li... |
151aeb5f7009bd225491614bd790d1db3974e390182e810b2c39b0725796fcb1 | Text | 3,524 | 84 | # Splatter
[](http://www.repostatus.org/#active)
[](https://www.tidyverse.org/lifecycle/#stable)
[
<p align="justify"> Spatial transcriptomic studies perform gene expression
profiling on tissues with spatial localization information. With technological
adva... |
61401f0ed26a6b76060eca0f18cfca3fe95215d1157f8344d67393256bf972d2 | Text | 3,682 | 42 | Code to the publication: Neural Networks for self-adjusting Mutation Rate Estimation when the Recombination Rate is unknown.
Cite: `doi: https://doi.org/10.1101/2021.09.02.457550`, bioRxiv.
This directory builds several estimators to predict the scaled mutation rate theta from coalescent simulation and compares them ... |
064960747cb3cd1f81b08f311929bcba8ac077b44aca689a0690c3042f12aa88 | Text | 3,740 | 65 |
# Adera 2.0
Adera2.0 is built using Python and Node.js. It uses Flask and Electron for the front-end.
The purpose of Adera2.0 is to pinpoint drugs that have been already validated for human usage that can be used to treat different diseases. For example, there is a disease (A) with no current effective medication. T... |
0da8dc9be255530d03f4244702cb0d41ae5f04f285ac06b349df62afa9812669 | Text | 3,840 | 84 | fMRIPrediction
==============================
From fMRI data to making predictions
## Installation
1. Clone the repository
```bash
git clone https://github.com/Alirezafathian/fmriprediction.git
cd fmriprediction
```
2. Create a create a python3 virtual-env (Opti... |
5c447e86eec06c3e8fcd3e210599b0d3eafff033a0940baf86433b07bbdda71a | Text | 3,862 | 37 | # Jacobs2022-eLife
Code for Jacobs et al., 2022 Research Advance in eLife
Note the source data for figures can be found through the Dryad repository - doi:10.5061/dryad.9s4mw6mkn. This repo is still in the process of being set up by eLife as of 9/26/22.
## Required packages
For *python* (v3+) scripts - many of thes... |
0a38f38978a82ef8a962dfff9d8d729d97382ffb8897a006ea0831653ac23268 | Text | 3,887 | 67 | ____ _ _ _
| _ \ __ _ | |_ __ _ | | __ _ __| |
| | | | / _` || __| / _` || | / _` | / _` |
| |_| || (_| || |_ | (_| || |___ | (_| || (_| |
|____/ \__,_| \__| \__,_||_____| \__,_| \__,_|
Container
[00637-6) is a clustering method design... |
04b82966b99face94a93ef6cc9fa6aac8b3e1f5b3e0291fb0a3fada4f20ddd9a | Text | 4,299 | 57 | ## Graph-based Representation for Identifying Individual Travel Activities with Spatiotemporal Trajectories and POI Data
This repository provides the implementation of the following paper:
> Graph-based Representation for Identifying Individual Travel Activities with Spatiotemporal Trajectories and POI Data <br>
> [Xi... |
9e982512392347fec06fa25258e95e2e0e448e9c2a0b1d646c9eb5a1568abd25 | Text | 4,309 | 99 | <div align="center">
⛑ **Metabolomic profiles predict individual multi-disease outcomes** ⛑
[comment]: <> (<!--)
[](https://colab.research.google.com/github/thbuerg/MetabolomicsCommonDiseases/blob/m... |
4d04c24e20bceb295dbd3f1fe4ba993ea345a94fca00c57ad74c33f3ee340de2 | Text | 4,495 | 49 | # Localized algorithms for controlling network systems
This repository contains MATLAB code for controllability analysis, driver placement, and optimal control design on large-scale dynamical networks using the concept of information neighborhood. The algorithms, underlying theory, and application example details will ... |
34e39aee922e6ff1c6b30d442507f13527a79a4e7eae823614ad547644486170 | Text | 4,526 | 91 | # Stability of motor representations after paralysis
[](https://www.anaconda.com//)
This repository contains the scripts to generate figures for [Stability of motor representations after paralysis](https://doi.org/10.7554/eLife.74478).
## Dataset
The dataset is av... |
5b660a237ff45af7cb8c18193777215a02f8f53cc938bb2e17caa2450f99181f | Text | 4,534 | 53 | # Py_TC-720
Python library for the control of the [TC-720 temperature controller](https://tetech.com/product/tc-720/).
The TC-720 is a peltier based temperature control device made by [TE Technology Inc.](https://tetech.com/) which can control the temperature with high presision and speed. The company provides a grap... |
8bf9e00533146771ca2ca2e6cbe24e0a44c4a53279a7bfdb6f00d34ac70a1949 | Text | 4,640 | 67 |
# cortical-evo
Original scripts for SDS and LDSC partitioned heritability are available here:
https://bitbucket.org/jasonlouisstein/enigmaevolma6/src/master/
We adapted the scripts written by Amanda Tilot and Jason Stein (Tilot et al., 2021) to our own data and research purposes, and written new scripts for the data ... |
fb594079ceb9774743fe09392511b7ffdaec2fbbb2e58074905aba3e3320d68f | Text | 4,800 | 92 | # metagMisc <img src='man/figures/Logo_metagMisc.png' align="right" style="height: 139px;" />
<!-- badges: start -->
[](https://doi.org/10.5281/zenodo.597622)
[](https://cran.r-project.org/... |
599738042bffbf787dfda045ea8292c9bb7dda5b2b75806a87c6f69d3fa1b18f | Text | 4,919 | 61 | SimpleNLG
=========
SimpleNLG is a simple Java API designed to facilitate the generation of Natural Language. It was originally developed by Ehud Reiter, Professor at the [University of Aberdeen's Department of Computing Science](http://www.abdn.ac.uk/ncs/departments/computing-science/index.php) and co-founder of [Arr... |
e725282bdfd82b3c5589bb6c44942e7ce1cee7eee3897d0edb1ceb022fe9f06d | Text | 4,987 | 88 | Denoiser: A nuisance regression tool for fMRI BOLD data
=======================================================
``Denoiser`` is a tool for removing sources of noise from and performing temporal filtering
of functional MRI data. It also provides visualization of the content of nuisance signals
(including *motion* infor... |
27ab3a1193f2b2c951d6bc7023628a96659d1323892ac38bf2a2fc284b770816 | Text | 5,062 | 75 | # PRQ
**Step 0:** S0_registration.m : create Info_IX.mat grid structures from input z-stack images.
input: folder path (Go to Registration folder) containing two folders (Basal, TBS (optostim condition)) with TIF z-stack images
after registration using bUnwarpJ ImageJ plugin:
-'XX_XX_c01_pos.tif': TIF file conta... |
18b5baf52fb08098bbd143aaf28bd70c67291ab2ce9fb460600e9b74e86248aa | Text | 5,164 | 150 | # TSAR-2022-Shared-Task Datasets and Evaluation Scripts
TSAR2022 Shared Task on Lexical Simplification for English (en), Spanish (es) and Portuguese (pt) - Datasets and Evaluation scripts
Please look at the website of the Shared Task for more details about the Evaluation Benchmark, Guidelines, Registration Form, etc..... |
f6910a94fa42d342bca2d49e2b7b23de7ee8a2f29f1ff72dada6a5fa77c226c5 | Text | 5,336 | 89 | # H2G-Net
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.3389/fmed.2022.971873)
[](https://github.com/andreped/H2G-Ne... |
31ee5221ef4660500fdd317733f71b6f9d5f921cd832d897b613039db4185963 | Text | 5,420 | 90 | # The NIfTI-MRS data standard repository
This is a repository to store information and code associated with the efforts to define an in vivo magnetic resonance spectroscopy (MRS) NIfTI data format.
[Documentation for the format is available online.](https://wtclarke.github.io/mrs_nifti_standard/)
## Why?
Users of MR... |
457df9e9e97cd7de5cf2043520d1ff0798c9d8e34a6ed06025ebc0a44a52180b | Text | 5,424 | 95 | README
Emo-Fibro: dataset of woman with fibromyalgia
Balducci, T., Garza-Villarreal, E. A., van Tol, MJ. & Aleman, A. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6554869
For MRI data related to this dataset refer to https://openneuro.org/datasets/ds004144/versions/1.0.2
A behavioral, clinical and brain i... |
6eb82b1961fec286f8d0539c3b792fded459289df6aeed07f9496534be42536e | Text | 5,587 | 133 | .. If you read this on hub.docker.com, maybe visit the github page https://github.com/modsim/cellsium
CellSium Readme
===============
.. image:: https://img.shields.io/pypi/v/cellsium.svg
:target: https://pypi.python.org/pypi/cellsium
.. image:: https://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat
... |
ac7b8a045805f28c6d5fd12338b4912fc27183cf933772a5757d2314c24e8db0 | Text | 5,650 | 141 | [](https://zenodo.org/badge/latestdoi/120343858)
# ReproIn
This project is a part of the [ReproNim Center](http://ReproNim.org)
suite of tools and frameworks. Its goal is to provide a
turnkey flexible setup for automatic generation of shareable,
version-controlled BIDS d... |
75bfc25e4409a9150b67476356d65ea4dc9d902be4de8b17927e44bc038a3909 | Text | 5,657 | 140 | # Status
This repository is currently inactive (archived, read only) and serves only as a supplement some of our papers. We have transitioned to using individual repositories for new projects. For our current work, see the [Magenta website](https://g.co/magenta) and [Magenta GitHub Organization](https://github.com/mag... |
44e98b1ad8b29ddd1916741de16f824ef4b38196a360e94f06671f3eb6d33932 | Text | 5,777 | 51 | # App_Spike_Train_Analysis
This code allows to semi-automatically classify spontaneous firing neurones according to regularity, grouping of spikes in bursts and firing frequency inter- and intra-burst
Introduction:
During electrophysiology experiments studying the nervous system some neurones with ongoing activity i... |
c2dd2f5e6eaa84906b96668415af381b18dc163a2741c0f29277a9a90cd431cb | Text | 5,914 | 96 | # Pathology_Adversarial
## Overview
This repository contains the Python version of a general workflow for Adversarial attacks and attack-proof artificial intelligence models in computational pathology.
It is based on workflows which were previously described in [Kather et al., Nature Medicine 2019](https://www.nature... |
3f3a2cd3a98c64667e997b7dcefacb1c1420ff4eb083928c93390072dfc12100 | Text | 6,016 | 96 | # Pathology_Adversarial
## Overview
This repository contains the Python version of a general workflow for Adversarial attacks and attack-proof artificial intelligence models in computational pathology.
It is based on workflows which were previously described in [Kather et al., Nature Medicine 2019](https://www.nature... |
589ba4e36932ab6dcf2a2874aa9fad0289d6ad544a725d261220c90c26372b2b | Text | 6,025 | 73 | # IVIMNET
For more deep learning qMRI code and latest updates, see: https://mriresearch.amsterdam/software/ivim-net-and-dce-net/
Now installed by "pip install ivimnet"
This repository contains the code regarding the publication: Improved unsupervised physics-informed deep learning for intravoxel-incoherent motion mod... |
3cc2d60aba6c44bcabfab688b5d98ded3699daff957fdaca6008c194d18acf53 | Text | 6,026 | 168 | [](https://travis-ci.org/BlueBrain/eFEL)
[](http://codecov.io/github/BlueBrain/eFEL?branch=master)
[](https://travis-ci.org/DmitryUlyanov/Multicore-TSNE)
This is a multicore modification of [Barnes-Hut t-SNE](https://github.com/lvdmaaten/bhtsne) by L. Van der Maaten with Python CFFI-based wrappers. This code also ... |
1b037dd73de6aa86c886f545ac64c786041be4a90f3f38b164512984ef1a1661 | Text | 6,181 | 94 | # Introduction
HFNILM is a tool for solving the energy dissagregation problem using high-frequency (HF) data.
It aims to provide a baseline systems for both new and experienced researchers within
the area of energy disaggregation and Non-Intrusive Load Monitoring using HF data.
# Publication
The HFNILM toolkit is pa... |
8867217f0970220324de4db86f2f668e162db5c48fa6e369ded6c39bc30bbe35 | Text | 6,268 | 125 | # Visualizing the Loss Landscape of Neural Nets
This repository is a fork of the [original repository](https://github.com/tomgoldstein/loss-landscape) by the authors of the paper
> Hao Li, Zheng Xu, Gavin Taylor, Christoph Studer and Tom Goldstein. [*Visualizing the Loss Landscape of Neural Nets*](https://arxiv.org/ab... |
95a9fe657cb8eeae87b09dc62ca084d41ee2c100e7df0811d7c0b61a6e73e731 | Text | 6,429 | 168 | .. -*- rest -*-
.. vim:syntax=rst
.. Use raw location to ensure image shows up on PyPI
.. image:: https://raw.githubusercontent.com/nipy/nibabel/master/doc/pics/logo.png
:target: https://nipy.org/nibabel
:alt: NiBabel logo
.. list-table::
:widths: 20 80
:header-rows: 0
* - Code
-
.. image::... |
d3c44ed56545da31a61bf6b6750b1a9b202c449473cad9adedaf04652c546e25 | Text | 6,474 | 161 | # How to run CMIC
1. splitDNA2vec
When you use your own CGI methylation data,
a csv file is needed with headers,
'beta_2' (target methylation rate),
'seq' (DNA sequence),
and optionally
'chrom' (chromosome ID),
'startpos' (start position).
Our input dataset and Bock2006 dataset are in the data direc... |
45b0e76a2ca67a4075300d59a076d38ff8e1af0d23070265969e7d36863f9871 | Text | 6,493 | 157 | # [vsi2tif](https://github.com/andreped/vsi2tif#vsi2tif)
[](https://opensource.org/licenses/MIT)
[](https://pypi.org/project/vsi2tif/)
[, by Ka... |
bb5b0130390e3896d43a10271e096a09adf39ce05e9c9aa3b1477f3ff3040315 | Text | 6,620 | 77 | ## Two-channel motion artifact correction (TMAC)
### Installation:
Navigate to the python project directory
```
git clone https://github.com/Nondairy-Creamer/tmac
cd tmac
pip install -e .
```
### General description:
For a full description please consult the paper:
https://doi.org/10.1371/journal.pcbi.1010421
Modifi... |
96afefa1d8987775233ef4df62ee3fc6926e6335fc096fe2bec70fd7b19aa8be | Text | 6,641 | 160 | #### ARA-CNN
This repository contains an implementation of ARA-CNN - a Bayesian deep learning model intended for histopathological
image classification.
ARA stands for Accurate, Reliable and Active. Any method that works on patient data needs to be accurate and reliable,
meaning that in addition to very high classi... |
27e7c82f591a32681c698746bae2475090778366ff847c0f4423e88660bec214 | Text | 6,656 | 45 | # Interactive thresholding with ImageJ/Fiji
[](https://opensource.org/licenses/MIT)
[Image segmentation](https://en.wikipedia.org/wiki/Image_segmentation) and [thresholding](https://en.wikipedia.org/wiki/Thresholding_(image_processing)) plays an importa... |
92dd6a102832b27f1cb250ea9644a871328fb84e53d626af52661bb2ce5f4db0 | Text | 6,873 | 69 | # Interpretable machine learning model for DNA aptamer design and analysis
This repository allows to reproduce most figures in this [paper](https://www.biorxiv.org/content/10.1101/2022.03.12.484094v1).
This repository also contains the DNN and traditional ML models used for comparison with the RBM. No explicit script... |
6e9e2c8f5e310e516a2584997099aca5cc01f7cf594313d6ceaf2612e26ec2cc | Text | 6,916 | 81 | # asm-map
## Project description
This script is dedicated to the **detection of Artisanal and Small-Scale Mines (ASM) in Africa**.
In practice, this project makes use of satellite hyperspectral imagery, combined with Deep Learning model training, in order to detect and map the ASM activities.
The images we use are pr... |
b35bb258f9248907cca9f146e42c14afa8810f2e292b5a792dc34f6fe3bd8038 | Text | 6,972 | 119 | # 3D human pose estimation in video with temporal convolutions and semi-supervised training
<p align="center"><img src="images/convolutions_anim.gif" width="50%" alt="" /></p>
This is the implementation of the approach described in the paper:
> Dario Pavllo, Christoph Feichtenhofer, David Grangier, and Michael Auli. [... |
be121774f95f419171d057186945573b230bf41010d104dbecc65ee07897ac67 | Text | 6,994 | 127 |
# LDpred #
LDpred is a Python based software package that adjusts GWAS summary statistics
for the effects of linkage disequilibrium (LD). The details of the method is
described in Vilhjalmsson et al. (AJHG 2015) [http://www.cell.com/ajhg/abstract/S0002-9297(15)00365-1]
* The current version is 1.0.11
##... |
47536fd6d2836e8ba7a60f4592fe8dc2c2518f16fae034261a407845616a1efa | Text | 7,116 | 179 |
# Gnocis
Bjørn André Bredesen-Aa, 2018-
#### Stability
/badge.svg)
 MRI.
It creates synthetic raw ASL data according to set acquisition and data format parameters, based
on input ground truth maps for:
* Perfusion rate
* Transit time
* Intrinsic MRI parameters: M0, T1, T2... |
605b4db571c24c9c5f62bdf4a0a37142da0c425efb35c6f868b3da0a8373d4e5 | Text | 7,379 | 150 | # Common Robot Interface
>A Python library for controlling various robot arms using a common interface.
The Common Robot Interface (CRI) library currently supports the following robot arms:
- ABB Robotics IRB 120
- Universal Robots UR3/5/10 - using the [Real-Time Data Exchange (RTDE)](https://www.universal-robots.com... |
62fa330204e8346b45a2f7a067e9e364bac1d9f7cf625fdf7c9a6306299aeb6c | Text | 7,560 | 219 | # WCNN3D
This repo demonstrates how to reproduce the results from
[WCNN3D: Wavelet Convolutional Neural Network-Based 3D Object Detection for Autonomous Driving](https://www.mdpi.com/1424-8220/22/18/7010) (Published in MDPI Sensors journal, 2022) on the
[KITTI dataset](http://www.cvlibs.net/datasets/kitti/). The codeb... |
0a20a11488385b3d34a3999b9f6d234dee12cb4365a75169d26543c8a92be4a2 | Text | 7,586 | 118 | # Deep mutational scanning of SARS-CoV-2 RBD
Analysis of deep mutational scanning of barcoded codon variants of SARS-CoV-2 RBD
Study and analysis by Tyler Starr, Allie Greaney, [Jesse Bloom](https://research.fhcrc.org/bloom/en.html), and co-authors.
For the full paper, see [Deep mutational scanning of SARS-CoV-2 rece... |
155c2b52c1c97a9d5454e5f1780647299b99fa181cbda2ea1d9e0228c8fc3676 | Text | 7,666 | 187 | # TGN: Temporal Graph Networks [[arXiv](https://arxiv.org/abs/2006.10637), [YouTube](https://www.youtube.com/watch?v=W1GvX2ZcUmY), [Blog Post](https://towardsdatascience.com/temporal-graph-networks-ab8f327f2efe)]
Dynamic Graph | TGN
:-------------------------:|:-------------------------:
](https://travis-ci.com/anirban6908/All-active-Workflow)
[](https://alleninstitute.org/legal/terms-use/)
# Workflow f... |
999da210e7b3077676a5375c629965a1b066a745cd10067f8db12c9241839dec | Text | 8,203 | 135 | # Visualizing the Loss Landscape of Neural Nets
This repository contains the PyTorch code for the paper
> Hao Li, Zheng Xu, Gavin Taylor, Christoph Studer and Tom Goldstein. [*Visualizing the Loss Landscape of Neural Nets*](https://arxiv.org/abs/1712.09913). NIPS, 2018.
An [interactive 3D visualizer](http://www.tele... |
9cb96e1d2f984915cda6943910e1bc03bf4bda63c5c08c56d18e200867205565 | Text | 8,282 | 214 | # boruta_py #
[](https://github.com/scikit-learn-contrib/boruta_py/blob/master/LICENSE)
[](https://badge.fury.io/py/Boruta)
[: e0272386.... |
d8434edbf53a818d712efdafa4666fb9a692bb09b4b6a01df5ec059d5be2330d | Text | 8,644 | 101 | # Transformer Models for MATLAB
[](https://app.circleci.com/pipelines/github/matlab-deep-learning/transformer-models)
[, with the following main
differences:
* More compact data structures are used, so memory requirements are much
lower (by orders of magnitude).
* The estimation of alignment variable m... |
b4c4ec4a7c5e1744991446c7c95ecb1c210ec200180bfd71c656ddb76a584938 | Text | 8,823 | 1 | #####################
Data and R script for:
Andreassen, A. H., Hall, P., Khatibzadeh, P., Jutfelt, F., & Kermen, F. (2022). Brain dysfunction during warming is linked to oxygen limitation in larval zebrafish
Please refer to the paper and supplements for data collection methods and analysis. For questi... |
cd5fbe0c0c4d18d0f3f527dad031f4c8148efce787342e6565b83b60869ee3af | Text | 8,924 | 19 | # EZT2022SA
Jupyter Notebooks for Science Advances paper
ZampeseSA2022 README (8 AUG 2022):
This repository contains five Jupyter Notebooks (Python 3.0) created or modified for specific use with action potential analysis for the Zampese, et.al. 2022 Science Advances paper. APandFRatio4Dplots.ipynb was created to gener... |
f3d813ffc0351a7e45220b71962b06e4487bf4d73ed2ee72fa740df81a77f19d | Text | 8,965 | 115 | # Optical Chemical Structure Recognition - Benchmark
[](https://GitHub.com/Kohulan/OCSR_Review/releases/)
[](https://zenodo.org/badge/latestdoi/277765775)
[![License](https://img.shields.io/badg... |
870bfa9b136815c36ae80f6dd1ba0351d7d285bb74a90d2b30eae1680c52b9cb | Text | 9,095 | 201 | # MIrROR: Microbial Identification using rRNA Operon Region
<img src="https://user-images.githubusercontent.com/31500750/100863170-817d0800-34d7-11eb-9928-8a19502762d0.png" height="180">
**Analysis tool for metataxonomics using 16S-ITS-23S rRNA operon region.**</br>
With the advancement of long-read sequencing technol... |
f6b0da5336220f62fc679c535fc3406c70d17555b863d3a07b4ae1e6c0fcf390 | Text | 9,307 | 219 | * [SpikeNet](#spikenet)
* [Getting Started](#getting-started)
* [Prerequisites](#prerequisites)
* [FAQ](#faq)
* [Installing](#installing)
* [Run the demo](#run-the-demo)
* [High performance computing](#high-performance-computing)
* [The workflow](#the-workflow)
* [More details](#more-detai... |
d60a2f4f2c8144eacc3786e8e65aca331d8ece27b139ccfd8831c805d4b0ebb9 | Text | 9,447 | 221 | * [SpikeNet](#spikenet)
* [Getting Started](#getting-started)
* [Prerequisites](#prerequisites)
* [FAQ](#faq)
* [Installing](#installing)
* [Run the demo](#run-the-demo)
* [High performance computing](#high-performance-computing)
* [The workflow](#the-workflow)
* [More details](#more-detai... |
cca96037ba1aeeba4c821da82b3ed1321bb27b8a226718f3fbdb6c220bd0b9b4 | Text | 9,610 | 186 | <div align="center">
<img src="data/Icons/fastpathology_logo.png" width="128">
<h1 align="center">FastPathology</h1>
<h3 align="center">Open-source software for deep learning-based digital pathology</h3>
[](https://opensource.org/licenses/BSD-2... |
61149b8af65384ac123daf6c3cfebf2aecf14fe83e6d1935d90d2888a6a7d25e | Text | 9,785 | 209 | ## Implementation of the SIFT-CNN method
This repo implements the following paper:
<em>
Tsourounis, D.; Kastaniotis, D.; Theoharatos, C.; Kazantzidis, A.; Economou, G. [SIFT-CNN: When Convolutional Neural
Networks Meet Dense SIFT Descriptors for Image and Sequence Classification](https://www.mdpi.com/2313-433X/8/10... |
b9b94957754d94fdf171e08b7dbdef6db3f465dd6e43699acf94e22e107d829b | Text | 9,967 | 64 | # The Turing Way
[](https://gitter.im/alan-turing-institute/the-turing-way) [](https://github.com/libvips/libvips/actions)
[](https://issues.oss-fuzz.com/issues?q=is:open%20project:libvips)
[![Gitter](htt... |
80273d561ecba7dfdf4912689098f821661f359983f7ad7659fa612647959b01 | Text | 10,125 | 241 | # Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks
Codes used in the following paper:
Takaki Yamamoto, Katie Cockburn, Valentina Greco, Kyogo Kawaguchi
"Probing the rules of cell coordination in live tissues by interpretable machine learning base... |
9ebd46b1b1a690f7cf3242e2807d88f2e203d97fd5bb22632f6d3abb3f911af3 | Text | 10,204 | 252 | This README.txt file was generated on 01-Jun-2022 14:26:18 by Emilio Salinas
GENERAL INFORMATION
1. Title of Dataset:
Dataset: A conflict between spatial selection and evidence accumulation in area LIP
2. Author Information:
Author 1
Name: Joshua A Seideman
Institution: Wake Forest School of Medicin... |
97787717d6c16ed2c7cbdfebb5d7989d23847cfb3999dbaed5ea9c4e6c91e325 | Text | 10,347 | 149 | SpecSeg: Cross spectral power-based segmentation of neurons and neurites in chronic calcium imaging datasets
[](https://doi.org/10.5281/zenodo.7113362)
[](https://zenodo.org/badge/latestdoi/256322811)
[](https://github.com/ClearAnatomics/ClearMap)
[](https://github.com/cYoren/SC-FC_coupling/actions/workflows/ci.yml)
[]... |
6cb7c7f8418265c55322f021af046a99715fae968d06666af62ea69f3656d183 | Text | 11,313 | 174 | # scfc — calibrating regional structure–function coupling estimators against spatial geometry
[](https://github.com/cYoren/SC-FC_coupling/actions/workflows/ci.yml)
[]... |
bbb766376c6751652a6cf260a432858ae94d05c6235fb40b7188ffebb341dc24 | Text | 11,535 | 164 | # TreeNetAI
<p align="center">
<img src="images/logo.png" width=auto, height=300px, hspace="10px">
<img src="images/dendrometer.webp" width=auto, height=300px>
</p>
## A Toolbox designed around neural networks for time series analysis
<!--Let people know what your project can do specifically. Provide context and ad... |
cffe32599d2af740d8685c6d5d3bc3bc781dea110b5af02e4f848f37cff20a4e | Text | 12,244 | 130 | #  
[](https://github.com/nf-core/rnaseq/actions?query=workflow%3A%2... |
00ba4b95cb14c14350e09be65007ecb13c7f4636dba96c5f18ef24934c99ee06 | Text | 12,400 | 259 | # Introduction
UNIFAN (**Un**supervised S**i**ngle-cell **F**unctional **An**notation) simultaneously clusters and annotates cells with known biological processes (including pathways). For each single cell, UNIFAN first infers gene set activity scores (denoted by r in the figure below) associated with this cell using t... |
af82bde094292800ddb6a5334c6765d9983e135fe8799f2e2ffe81a4a3d0b7d7 | Text | 12,692 | 334 | [](https://zenodo.org/badge/latestdoi/120343858)
# ReproIn
This project is a part of the [ReproNim Center](http://ReproNim.org)
suite of tools and frameworks. Its goal is to provide a
turnkey flexible setup for automatic generation of shareable,
version-controlled BIDS d... |
4f4cf7117740a756822af2503ada31eb7c3748bde445219878229302566b61fd | Text | 12,788 | 249 | # PARC
PARC, “phenotyping by accelerated refined community-partitioning” - is a fast, automated, combinatorial graph-based clustering approach that integrates hierarchical graph construction (HNSW) and data-driven graph-pruning with the new Leiden community-detection algorithm. [PARC:ultrafast and accurate clustering ... |
08dbdb1ee83491e6d83f156e3d8c5c9734c083c84b9a22e5a3a6ad932b2feead | Text | 12,974 | 242 | # SphericalLabeling: Cortical Surface Labeling using Spherical Data Augmentation and Context-aware Training
## Description
We adapt [spherical convolutional neural networks](https://github.com/maxjiang93/ugscnn) designed for generic semantic segmentation tasks. Yet, direct use of the generic networks for our sulcal la... |
6bea469d43a0d694a29a5a1de3bc5dc22b92e926c2ef3b5b9c3e54449154c672 | Text | 13,082 | 206 | <p align="center"><img width="25%" src="https://raw.githubusercontent.com/BindsNET/bindsnet/master/docs/logo.png"/></p>
A Python package used for simulating spiking neural networks (SNNs) on CPUs or GPUs using [PyTorch](https://pytorch.org/) `Tensor` functionality.
BindsNET is a spiking neural network simulation libr... |
b0d7048fcd442d4fad6af352f790fb2449b3c260b8829b644edfddf5c93cc9fd | Text | 14,036 | 208 | [](https://travis-ci.com/bids-standard/bids-matlab)
[](https://mybinder.org/v2/gh/bids-standard/bids-matlab/master?filepath=examples/tutorial.ipynb)
[  
**openSEApy** i... |
8c23a325ab7ab59f46688c309b70cbe206d1658a0b8a145ff126ee7de0c03563 | Text | 14,449 | 203 | [](https://github.com/openmm/openmmforcefields/actions/workflows/ci.yaml)
[](https://anaconda.org/conda-forge/openmmforcefields)
[ and reconstruction of super-resolution images. The python scripts in this toolbox were used in our paper, **Semi-automated single-molecule microscopy screening of fast-dissociating specific antibodies directly from hybridoma cultures**, [p... |
d38ea0ea519ed967845dc61c2b77e7fcdc7d5a7063cab2a58ffacae34b27b4e7 | Text | 16,355 | 255 | # Molecular Property Prediction
This repository contains message passing neural networks for molecular property prediction as described in the paper [Analyzing Learned Molecular Representations for Property Prediction](https://pubs.acs.org/doi/abs/10.1021/acs.jcim.9b00237).
## Table of Contents
- [Requirements](#requ... |
ad77cfd3c0c0873ef9cb345eb28db9df62cd4d7cd1d69ea76361526811f97609 | Text | 16,417 | 140 | 
# Folk music style modelling using LSTMs
See the following websites:
3. [Let's Have Another Gan Ainm](https://soundcloud.com/oconaillfamilyandfriends) (music album)
1. [folkrnn.org](https://folkrnn.org/)
2. [The Machine Folk Session]... |
3f7af2b22e255ad710366fa314974af1723b8d6a3e2c12d642802f4458a16ef3 | Text | 16,984 | 214 |      ](https://github.com/joaopauloschuler/k-neural-api/releases)[](https://zenodo.org/badge/latestdoi/221215803)
<img align="right" src="docs/cai.png" height="192">
K-CAI NEURA... |
5560650b1f8c6861c756840182db62467682e770f5b8a365850fa4c00fe63b39 | Text | 19,577 | 116 | [](https://travis-ci.org/datalad-handbook/book) [](http://handbook.datalad.org/en/latest/?badge=latest)
[ alignment pipeline for the analysis of DNA methylation
CpG_Me is an optimized and comprehensive WGBS alignment pipeline for a SLURM job scheduler on a high-performance computing cluster. CpG_Me takes you from raw fastq files to CpG methylation count matrices (Bi... |
51eaafba3d61502787c0620b6c2108a94c5e89e9b42f31930d6d6045098d39cb | Text | 23,567 | 233 | **Note:** This project is not currently being updated. Also, it is distinct from [Google's COVID-19 Open-Data](https://github.com/GoogleCloudPlatform/covid-19-open-data) project, which has similar goals, and is being actively developed and maintained by a team spanning Google Health, Google Research, Google Cloud, Goog... |
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