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7e6cceb6d728f8954e9fd4437269494832f72e6e5953b079a28260878c176d62 | Text | 2,063 | 33 | # restingstate-reliability-spinalcord
This repository is associated with the following [manuscript](https://www.sciencedirect.com/science/article/pii/S1053811923003038?via%3Dihub#sec0036) and the corresponding [dataset](https://openneuro.org/datasets/ds004386).
This repository contains the preprocessing and analysis ... |
6e9cd20ed5c94953f7f4fdda59bd13f5bb2358f7129473e7c26ddc4d4f7e525a | Text | 2,115 | 45 | # BioImageOperation
Bio Image Operation or 'BIO', is a next generation Image processing tool focusing on biological applications, balancing ease of use with desired flexibility required for research.
This tool has been developed in collaboration with biologists, using extensive captured im... |
162bb9f9212255f512a1fb868d71cfac5fd14888e3919e3a03d50516f99a3dd5 | Text | 2,122 | 47 | # Celloscope
This directory contains the source code necessary to reproduce analyses presented in the manuscript:
> Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał, Igor Filipiuk, Alicja Rączkowska, Paulina Szymczak, Hosein Toosi, Leszek Kaczmarek, Łukasz Koperski, Jens Lagergren, Dominika Nowis and Ewa Szc... |
a79b7c07b17f2a966a7e790dea6347e30486fadfdfa25f7b393231019ee2ef50 | Text | 2,133 | 37 | # AD_biomarkers_clustering
<div id="top"></div>
## Description
This is the code repository for the paper entitled [A data-driven approach to complement the A/T/(N) classification system using CSF biomarkers](). The repository follows the methodology and results presented in the abovementioned work.
The Python scrip... |
d77ee2a61bebaa47a66ccd48f5d0959b4ff696196f4860217226f45970c924eb | Text | 2,139 | 76 | # Overview
This project is intended to use deep learning models for Crispr-Cas on-target efficiency prediction and off target specificity prediction.
Below is the layout of the whole model.
## AttnToMismatch_CNN
<p align="center">
<img src="pictures/New_attnToMismatch_CNN.png" width="900"/>
</p>
This model inclu... |
619a9a28b124dce591ad32112218a8a9e255274e456208f47cdf78a3c8e007ef | Text | 2,162 | 49 | # Celloscope
This directory contains the source code necessary to reproduce analyses presented in the manuscript:
> **Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data**
> Agnieszka Geras, Shadi Darvish Shafighi, Kacper Domżał, Igor Filipiuk, Łukasz ... |
aa7841a86a869385c73ffcc62c704751ad4119ab5c86eaf2d18d6358b086bdeb | Text | 2,166 | 40 | ## scRNA-seq data analysis: DOT1L activity affects cell lineage progression in the developing brain by controlling metabolic programs (Appiah et al)
Documentation of workflow used for analysing scRNA-seq data from labelled cells acquired following microinjection or electroporation in embryonic mouse brain (E14.5). Once... |
e2ae6aae953f11fc7025ec5b10a64d88d75f3c804846a29888d81ddcae230499 | Text | 2,172 | 82 | # Rice Yield CNN
Rice Yield CNN is a model to estimate the rice yield based on RGB image of rice canopy at harvest. The model is developed based on more than 22,000 images and yield database collected across 7 countries.
This project is the implementation of the paper "[Deep learning-based estimation of rice yield u... |
4781b1e508db8ca8262f0ce6a3d93db594003fa9f1ae21139fe4b3ace1920fe5 | Text | 2,180 | 44 | # ECG-AI_PD_Risk_Prediction
Externally Validated Deep Learning Model to Identify Prodromal Parkinson’s Disease from Electrocardiogram
# Requirements
* Python 3.7.7
* scikit-learn 0.22.1
* scipy ... |
5decc432a2ae9c8a7cf7c8d1d40221811adc13f4f19764217c4499ea262af51b | Text | 2,186 | 33 | # NCOM_Antonenko_2023
## Microstructural and functional plasticity following repeated brain stimulation during cognitive training in older adults
Author List:
Daria Antonenko, Anna Elisabeth Fromm, Friederike Thams, Ulrike Grittner, Marcus Meinzer, Agnes Flöel
### Data and Code Availability
The data of this study ar... |
f57c15882192468728edd4c3c3caed1591f8dda82a66f7690e0a2c19e7d95116 | Text | 2,220 | 36 | # Trustworthy AI
This repository is a collection of trustworthy AI related works from Huawei Noah's Ark Lab.
---
### gCastle
- A causal structure learning toolchain containing various functionalities related to causal learning and evaluation. A tech report describing the toolbox is available [here](https://arxiv.... |
437b6b4c92a81d3fbe64f0099d2be3c8cf7a30c95d3a7454cc53d00c2513e058 | Text | 2,233 | 53 | ## The Potential of Convolutional Neural Networks for Identifying Neural States based on Electrophysiological Signals: Code and Figures
This repository accompanies the manuscript
> *The potential of convolutional neural networks for identifying neural states based on electrophysiological signals: experiments on synt... |
c3e11de0633ffc7077ddc106ccbdd469a77a80bbccd7c5ed4d26bc32d3d50439 | Text | 2,234 | 45 | # Open-MAC
Design files for an open-source motorized all-in-one commutator (Open-MAC).
BOM is updated, and we kindly request the users to refer BOM from GitHub to build the new version of the commutator
#### For Opto-Ephys commutator please visit below link
https://github.com/KaetzelLab/Open-MAC-opto-ephys-commutato... |
7b5f3812b27e7465592992edc557c81289986a09c0a71dcc56071d732df732c5 | Text | 2,240 | 24 | # Anatomical template of the Healthy Adult Human Hands
# Files in this repository:
(1) Hand template (.nii file, zipped): Hand_template_image.zip
(2) 3-D printable version of the template (.stl file, zipped): 3D_model_of_hand_template.zip
(3) 3-D printable version of the bones in the template (.stl file, zipped): ... |
f5aa431fb5ee3ff79e67c4297f1cecebd0865acca0279c3fb8b4ec35341c4f49 | Text | 2,268 | 58 | [](https://pypi.org/project/pyxdf/)
[](https://anaconda.org/conda-forge/pyxdf)
 STAR Protocols.
Example data are available:
Dagher, Sarah; Ishiyama, Shimpei (2023), “Signal synchronization in systems neuroscience (example data)”, Mendeley Data, V... |
9fec92fd80ed0f9693acc99eea01cfe9fe93d922d0c9a958837bb3f2ce439e58 | Text | 2,295 | 27 | # Analyzing_TD-NIRS
- The contents are Data and MATLAB scripts used for Publication in 2023. Please see file "Content.png"
> A. Sudakou, H. Wabnitz, A. Liemert, M. Wolf, and A. Liebert. "Two-layered blood-lipid phantom and method to determine absorption and oxygenation employing changes in moments of DTOFs". DOI : ... |
f7bb2d39ef9ac61e0d322cd93036a3a1122a3e10afc58279590549fe72f9e3ce | Text | 2,297 | 42 | # MEMES
**MRI Estimation for MEG Sourcespace (MEMES)** is a set of tools for estimating an appropriate structural MRI for MEG source analysis in Fieldtrip and/or SPM.
These set of scripts are customised for data acquired from the [Macquarie/KIT MEG laboratory](https://www.mq.edu.au/research/research-centres-groups-and... |
ab1994388fbd99dbd5554752e11a5998f18597873eff404e1c318de3e68c5a7c | Text | 2,303 | 50 | # Proteomics Resilience to Alzheimer's Disease
## Read our paper:
<b>Proteomics of Alzheimer’s disease resilience identifies brain regional soluble Aβ, actin processes, and injury response</b>
Zhi Huang, Gennifer E. Merrihew, Eric B. Larson, Jea Park, Deanna Plubell, Edward J. Fox, Kathleen S. Montine, Caitlin S. La... |
a603d6f987525eecf829485a3b127a1917599b76e4a170f4477195f4e35c3eee | Text | 2,320 | 8 | # Multimodal single-cell analysis of non-random heteroplasmy distribution in human retinal mitochondrial disease
code associated with Mullin et al. 2023 (https://insight.jci.org/articles/view/165937)
<b>TITLE:</b></p>
Multimodal single-cell analysis of non-random heteroplasmy distribution in human retinal mitochondria... |
6137d8d65adca8f660fe8be06864145ff1efb3f3962f301bdd6539b3ceb86562 | Text | 2,321 | 60 | The more numerous the longer: how the integration between numerosity and time leads to a common neural response
Fortunato G., Togoli I., Bueti D.
DATASET
these repository contains the data and statistics reported in the main text and supplementary materials
Folder structure
- AspectRatioData
- CorrelationData
- Pref... |
ea60595abfb8aaee876cab3b218c084eb91a98a2910c7825808ac6da407f43ee | Text | 2,359 | 36 | # mitochondria-pipeline
### Purpose :
Workflow for SNP and INDEL variant calling on mitochondria.
### Requirements/expectations :
- BAM or CRAM file
- Median of the coverage over the autosome (if available, another central statistic would work too)
- Reference fasta (along with its index and dictionary) is only re... |
f0c036b5a87fb4d57caae168e75f0ee8f628c6c54eeb6eb4f4a9917f868ff7dd | Text | 2,408 | 41 | # Frontiers Open Code LMD
## Long-short term memory networks for modeling track geometry in laser metal deposition
## Description
This repository contains the code used to produce the results published in the paper "Long-short term memory networks for modeling track geometry in laser metal deposition" (Martina Perani... |
35213f0ebd0c7e0562e91954cd12ab086fddb72e10530156319eb1338c189438 | Text | 2,426 | 53 | ## VFVS - VirtualFlow for Virtual Screening
Welcome to the VirtualFlow project!
VirtualFlow ([Homepage](https://virtual-flow.org/)) is a versatile, parallel workflow platform for carrying out virtual screening related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (su... |
9c3ebc880b631e0e76318e6bed772248460d041ba41c3d111909db617ea546b5 | Text | 2,441 | 39 | # SlicerElastix
This extension makes available Elastix medical image registration toolkit (https://elastix.dev) available in Slicer.
## Installation
* Download and install latest stable release or a recent nightly release of 3D Slicer (https://download.slicer.org).
* Start 3D Slicer application... |
49e1f3cf7e22d4ff191c5e649720b3e082b1006feca130dbfd5ed9d57e4ecaea | Text | 2,509 | 53 | # Neural relational inference to learn allosteric long-range interactions in proteins from molecular dynamics simulations
**Abstract:** Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid mutation at a distant site affects the ... |
6b91047e505e503e1ef61fd2420083dc39613117665c1d9aa70d4f57faf69ca4 | Text | 2,516 | 57 | # ARDENT
**A**ffine and **R**egularized **DE**formative **N**umeric **T**ransform (ARDENT) is a Python package for performing automated image registration using LDDMM.
ARDENT stands out for its ability to predict and correct for artifacts and image nonuniformity, perform registrations across image modalities, ease of ... |
51d1e5adf04ed5148f97c70358e1d80b6a3850244e78d44e14ff226b10cc5429 | Text | 2,521 | 58 | # Baysor
**Bay**esian **s**egmentation **o**f imaging-based spatial t**r**anscriptomics data.
Baysor finds cells from molecule positions and gene composition, with or
without a prior segmentation. This is the native C++ release **cpp-0.9.0**.
## Quick start
**Linux x86-64** — download the release binary and run on y... |
5d2b678a15410573388bbe25aa47d834ae17cda5ae21192b3fd889563e19aece | Text | 2,617 | 79 | iScience-2023
================
This is the repository for the article: *Probabilistic integration of
preceding responses explains response bias in perceputal decision
making* by Schlunegger & Mast (2023) in *iScience*.
## Abstract
Expectations of sensory information change not only how... |
1e6a06477dfe244787fcb058f4058488205b1ee82eb8e6537fee133f301aa780 | Text | 2,634 | 67 | # Mega-Meta-paper-simulations
A code repository for:
>Active learning-based Systematic reviewing using switching classification
>models: the case of the onset, maintenance, and relapse of depressive disorders
## Abstract
Systematic reviews and meta-analyses are top of the bill in research. However,
the screening ph... |
a75e3d063402eec1e0105968830ba963a03ed107176d412df9404373d9dbf016 | Text | 2,670 | 50 | ============================================================================
Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion
============================================================================
.. image:: https://travis-ci.org/konstantint/pyliftover.png?branch=master :target: htt... |
9d8149d51ec790af9fa3ae6ba533cedb7d236ab69a36eadd9c53e0e853ebab04 | Text | 2,685 | 35 | # leifer-Behavior-Triggered-Averaging-Tracker-new
This is a repo for high-throughput worm tracking in the Leifer lab. The -new repo is edited to track worm behavior in the odor flow chamber, characterizing chemotaxis behavior in a large arena.
The pipeline is used to process raw recordings of C. elegans navigation be... |
c2582bcf3232f09c0d7ed994b2af3d42cf15de1315206dcdd747f34f0a818db2 | Text | 2,686 | 60 | digitalConfocal
==============================
digital confocal microscopy
Project Organization
------------
├── LICENSE
├── README.md <- how to configure the repo
├── data
│ ├── external <- Data from third party sources.
│ ├── interim <- the data as the final input to m... |
317ee13c54f5d01442c015278073b70cb9d56a6cb20f7a5649389ae9566f25b3 | Text | 2,698 | 103 | SymmetricFormats.jl defines the `SymmetricPacked` type which
[concatenates](http://www.netlib.org/lapack/lug/node123.html) the columns
of either the upper or lower triangle into a vector thereby using only a
little more than half the memory.
Other formats to efficiently store symmetric matrices, which
are not (yet) im... |
2107898e99c0d83670f790bb32e2fa154ec46a39fd39f98356ac99d5ed0f7e61 | Text | 2,700 | 59 | # Spillover
This repository contains simulation files used in the publication Trpevski, et al. "Glutamate spillover provides robust all-or-none behavior of plateau potentials in multicompartment models of striatal projection neurons", Authorea. March 29, 2023. DOI: 10.22541/au.168012861.16093883/v1
The simulations ar... |
3b9c3d2f17de50fb4259cbaa18bdf3cb3346e046e19ca4b931b663b280e2328e | Text | 2,700 | 88 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
# MetNormalizer <img src="man/figures/logo.png" align="right" alt="" width="120" />
[](https://cran.r-project.org/package=MetNormalizer)
[](https://doi.org/10.5281/zenodo.6799806)
A code repository for:
>Active learning-based Systematic reviewing using switching classification
>models: the case of the onset, maintenance, and relapse of depressive disorders
... |
86d80e248d6abc094af96097fa250e9adba1a3070da344244c07514d1473be05 | Text | 2,746 | 55 | Notice
======
This repository is no longer maintained. Further development of SSAM will be continued in the https://github.com/pnucolab/ssam repository.
SSAM (Spot-based Spatial cell-type Analysis by Multidimensional mRNA density estimation)
============================================================================... |
ac1455e4fc5859107b649ae7513bbf2d12086402fab2f0020f320982197ed4c6 | Text | 2,842 | 39 | # BrainPipe: Registration and object detection pipelines for three-dimensional whole-brain analysis.
BrainPipe ([Pisano et al. 2021](https://www.sciencedirect.com/science/article/pii/S2211124721011700)) is an automated transsynaptic tracing pipeline that combines anatomical as... |
3d8543ee9d58de49e4f31ba7e4492cedb2f2ea87b7ce5163aef824b2605350b1 | Text | 2,853 | 79 | # ffian: Fluid Flow In Astrocyte Networks
ffian is an implementation of the KNP continuity equations for a
one-dimensional system containing two compartments:
one representing an astrocyte network (ICS) and one representing the
extracellular space (ECS). `ffian.flow_model` takes transmembrane- and
compartmental flui... |
813f71272ee47abe1bbb35486fe76530a0468fa5df44e8d1d050301d3ef36ce6 | Text | 2,853 | 47 | # Pyramidal neuron model for studying ***SCN2A*** mutations
[](https://www.anaconda.com/distribution/)
[](https://www.neuron.yale.edu/neuron/)
[**
```bibtex
@article{gala2021consistent,
title={Consistent cross-modal identification of cortical neurons with coupled autoencoders},
author={Gala, Rohan and Budzillo, Agata ... |
21e9fd2b96e05bab1dcbf304df518b17dec6b0ec2524ee0657ce00f26fa7b76d | Text | 2,968 | 58 | # IsoPrism
IsoPrism predicts **within-gene isoform proportions** for individual cells or spots from short-read gene-expression matrices. It combines short-read local context, program attention and terminal-aware isoform queries with iterative within-gene allocation. Paired long-read counts supervise training; predicti... |
ef0f0182b306664eb10cf543b02b30b6f3fac3449f556ade016300b639d3a0e2 | Text | 3,005 | 84 | gumpy
=====
``gumpy`` is a Python 3 toolbox to develop Brain-Computer Interfaces (BCI).
``gumpy`` contains implementations of several functions that are commonly used
during EEG and EMG decoding. For this purpose it heavily relies on other
numerical and scientific libraries, for instance ``numpy``, ``scipy``, or
``sc... |
91eeb130042ee048c2b058309b22c05dc7d974600678571411607f883efe2abc | Text | 3,012 | 81 | # AlphaFold-disorder
#### Disorder and binding region detection from AlphaFold predicted structures
The script parses and processes PDB files generated by AlphaFold. It expects the pLDDT score in the B-factor column. As intermediate (mandatory) step it calculates the Relative Solvent Accessibility (RSA) as provided by... |
aaee795effef77afc77b97a0087014d8b48f2d9e97b89b2a25dcd8a6a372aa52 | Text | 3,012 | 66 | abcd_paper
==============================
Goal: Explore predictability of various psychiatric diagnoses based on neuroimaging features in subjects from the ABCD study.
Getting started
===============
1. Copy the following files into ``data/raw/``:
From the baseline release of the ABCD study:
```
abcd_ksad0... |
e7b90daae2e575f20c19453f7a5df8fd8c0278271e91f40ae9db2ed98a9c59b4 | Text | 3,026 | 76 | <!-- TABLE OF CONTENTS -->
<details>
<summary>Table of Contents</summary>
<ol>
<li> <a href="#about-the-project">Project Description</a></li>
<li><a href="#getting-started">Dependencies</a></li>
<li><a href="#usage">Usage</a></li>
<li><a href="#contact">Contact</a></li>
<li><a href="#acknowledgm... |
fcacae75de67e03f93567ab30f58139e0883c8fc0f6fc4f63ac30f7d920243f5 | Text | 3,043 | 95 | Curveball
Pipeline for quantitative analysis of cortical surface meshes from Freesurfer ({h}.pial / {h}.white).
Computes:
- Cortical thickness
- Sulcal depth (standard + shrunken alpha surface)
- Mean & Gaussian curvature
- Principal curvatures (k1, k2), shape index (SI), **curvedness (CVD)
- Intrinsic curvature ind... |
5b4a52cdd8d901d08a1be72ecee5f062a7e98d4c3a436f63dd7a46a6c34e2947 | Text | 3,044 | 52 | # GCN_SHS_NET
Suguru Honda, Koichiro Yano, Eiichi Tanaka, Katsunori Ikari, Masayoshi Harigai
The objective of this project is to validate whether graph neural networks and random forests can accurately predict the progression of joint destruction. The Sharp/van der Heijde score (SHS) using in this study is based on AI... |
6e404699412cb687bd737c4423c568f6ece1bad9f62a13e15ac1785062ccccd1 | Text | 3,071 | 90 | # ATOM3D: Tasks On Molecules in 3 Dimensions
[](http://atom3d.readthedocs.io/?badge=latest)
[![codecov](https://codecov.io/gh/drorlab/atom3d/branch/master/grap... |
bd845c7075b2af4c1e5b9c1455433a431ab59aa977c43dce8e88b313ae2d5042 | Text | 3,097 | 79 | # Integrated Algorithm Combining Plasma Biomarkers and Cognitive Assessments Accurately Predicts Brain β-Amyloid Pathology
This repository contains the source code for the research paper "Integrated algorithm combining plasma biomarkers and cognitive assessments accurately predicts brain β-amyloid pathology" published ... |
acd13c4cfafec26e1a6ae2258a5f62bf0d97f07696270b043c6cef734374d10a | Text | 3,099 | 57 | ParaDime: A Framework for Parametric Dimensionality Reduction
=============================================================
|ReadTheDocs Badge| |License Badge| |PyPi Badge| |Black Badge|
ParaDime is a modular framework for specifying and training parametric dimensionality reduction (DR) models. These models allow ... |
bed0deef146e2fb2bb40c420466589a20b1ca4cddeea89b495fedcc1385e7089 | Text | 3,146 | 51 | ConvertTDMS
============
Repo of submissions to MATLAB File Exchange (http://www.mathworks.com/matlabcentral/fileexchange/44206-converttdms--v10-)
Import or convert a LabView TDMS file (version 1.0 through 2.0). Interleaved and Non-Interleaved tdms files are supported.
These functions also work with tdms files that... |
4f3f20f06efb6d5b25608c576d8a5ddc3ae0e2b6dca381ce793f07a938b08b0a | Text | 3,166 | 21 | # sleeping_pigeon_fMRI
Guide for preprocessing rsfMRI data and quality check.
All scripts are written in jupyter-notebook.
To run the codes, you need to install FSL, AFNI, and ANTs.
These codes will apply following preprocessing steps:
1) converting dcm 2 nifti format (dcm2nii function) and upscale voxel size by factor... |
6f81d3b20fc7e3e0480084b3b9b13aad5eb8dab820ed09ff29f126ad3ee165f3 | Text | 3,170 | 80 | # chART
This is a collection of functions for making nice scientific plots. I make it for myself, so its not exhaustive, and its always a work in progress.
## The plots
### average line plot
`chART.plot.average_rows()`
Averages rows of data into a classic line plot with error bars.
<img src="docs/average_rows.PNG" ... |
2a87bbcf2072c6f91ca1ce38b6a14de9daa21cdd6ddee974e20b511e4d411b7b | Text | 3,194 | 81 | # Integrated Algorithm Combining Plasma Biomarkers and Cognitive Assessments Accurately Predicts Brain β-Amyloid Pathology
This repository contains the source code for the research paper "Integrated algorithm combining plasma biomarkers and cognitive assessments accurately predicts brain β-amyloid pathology" published ... |
379183609dfd014e153d493a6fbd8db7e3b9ec25b5cd88e79a8a6ce7ec4405a5 | Text | 3,199 | 54 | [](https://zenodo.org/badge/latestdoi/630230253)
# Predicting preterm births from electrohysterogram recordings via deep learning
This is the code developed for our paper "[Predicting preterm births from electrohysterogram recordings via deep learning](https://journals.pl... |
cd52449d1cc7da93c2ef3d1735efd17ab5f9fe4331efd06666848a98fd4d9cc8 | Text | 3,211 | 136 | Read and write ImageJ ROI format
================================
Roifile is a Python library to read, write, create, and plot `ImageJ`_ ROIs,
an undocumented and ImageJ application specific format to store regions of
interest, geometric shapes, paths, text, and whatnot for image overlays.
.. _ImageJ: https://imagej.... |
8cd69fb716093ca99a3c080c7d3a7faa57944cf7cce6d04735c3ca9a7648500d | Text | 3,214 | 84 | seaborn: statistical data visualization
=======================================
<div class="row">
<a href=https://seaborn.pydata.org/examples/anscombes_quartet.html>
<img src="https://seaborn.pydata.org/_static/anscombes_quartet_thumb.png" height="135" width="135">
</a>
<a href=https://seaborn.pydata.org/examples/mul... |
306629e15b8ccc2f64868c493da94ee47fbe57f309757627dd0724d8331edf36 | Text | 3,236 | 64 | # Can We Diagnose Mental Disorders in Children? – A Large-Scale Assessment of Machine Learning on Structural Neuroimaging of 6916 Children in the ABCD Study
[](https:... |
a7ffe078ec885eaaf5aa73aa475593973e1b8d1c2ce4c9abad6cc633a2b93376 | Text | 3,285 | 54 | # Guide to code and data
This repository contains analysis code and data to reproduce key results in [Wang et al. (2023) Temporal stability of intracranial EEG abnormality maps for localizing epileptogenic tissue, *Epilepsia*](https://doi.org/10.1111/epi.17663).
## Requirements
All code was developed in Python ver... |
9b7522463a93bb82f6446e50dac8be1c9fc25bf970f32c133f98731a26114703 | Text | 3,324 | 120 | Nvidia only provides batched versions of the BLAS `gemv`, `gemm`, and `trsm`
functions. Further, they only support floating point, and alpha and beta
can only be scalars. BatchedBLAS.jl extends support for batched arrays by
(currently) providing batched versions of `dot`, `gemv`, `symv`, `spmv`,
`ger`, `syr`, and `sp... |
2e01bda9d20a97c65e37415b99b01d9491861871b9c848ab92c7d239dfed06d4 | Text | 3,355 | 70 | # BIO-R-BERT
## Model
<p float="left" align="center">
<img width="600" src="https://user-images.githubusercontent.com/28896432/68673458-1b090d00-0597-11ea-96b1-7c1453e6edbb.png" />
</p>
## Dataset
- DDI (Drug-Drug Interaction) 2013 dataset ([link](http://labda.inf.uc3m.es/ddicorpus))
- Relation Extraction ... |
a7a35e626f89129e0f40245b7155465c89e1e14b30dc66949ab3a7c951919f14 | Text | 3,402 | 90 | <img align="right" src="https://raw.githubusercontent.com/FZJ-INM1-BDA/siibra-explorer/master/docs/images/siibra-explorer-square.jpeg" width="200">
[](https://siibra-explorer.readthedocs.io/)
[
The supporting materials of cuprate superconducting materials above liquid nitrogen temperature from machine learning
- ① This software is written as a simple and practical program, which does not need other supporting environment, but can be used directly on the Windows system.
- ② The... |
9de79bf9eb8e6e11414e0b8096a95ff02ecdce70ffda48289276db0afc7018ff | Text | 3,454 | 32 | :warning: **_NOTE:_** AlphaZe** is now part of the official [CrazyAra framework](https://github.com/QueensGambit/CrazyAra). :warning:
# AlphaZe**
AlphaZe** is an adaptation of [AlphaZero](https://arxiv.org/abs/1712.01815) and combines is with our own version of the so-called [Perfect Information Monte-Carlo](https:/... |
6b3e4307de5c33dca7df16a6e04c4df501eaf9036dd9e85e7abcf8f915d6469a | Text | 3,464 | 69 |
<img src="docs/Epiphany_prediction.png" width="1000">
# Epiphany
### **Epiphany: predicting Hi-C contact maps from 1D epigenomic signals**
Epiphany, a neural network to predict cell-type-specific Hi-C contact maps from widely available epigenomic tracks. Epiphany uses bidirectional long short-term memory layers to... |
b18811cc92bc20e92de238583b88de46318a991129b90d8e26f621e020819258 | Text | 3,493 | 65 | # deep-sleep-pytorch
<!-- Dasdf;lkj -->
<!-- ========== -->
## Requirements
Principal requirements are Python 3.7.3, PyTorch 1.1.0, CUDA 10 and cuDNN 7.5.1.
An environment YAML has been provided with other packages required for this repository, which can be installed by running `conda env create -f env.yaml`.
## Prel... |
fd0cb370a7d851a56995954604dc5cb386b90e119872a4e8067a9f2d58afefd6 | Text | 3,531 | 70 | <img src="https://raw.githubusercontent.com/mwaskom/seaborn/master/doc/_static/logo-wide-lightbg.svg"><br>
--------------------------------------
seaborn: statistical data visualization
=======================================
[](https://pypi.org/project/seabo... |
3a9304ee360443616aa74d5a275c5a4fdaafde3692565b3522bd9b50ab49ea32 | Text | 3,562 | 64 | # Original algorithm developed by: Dr. Piroon Jenjaroenpun (2011-2012)
# Updated and modified for publication by Csaba Papp (2020-2023)
Project data for the pG4-BS manuscript (2022/2023)
This is a documentation of the steps we took in our analysis of potential bulged G4 forming sequences (pG4-BS) and potential canonic... |
f7ac0bde7387c723723db8ec0453d22c2080d931adbf5689a01b0245ba45d770 | Text | 3,578 | 67 | # computer_model_for_epilepsy
This repository contains a MATLAB library to simulate seizure propagation as a SI spreading process and fit the model to a spreading pattern. The main script is
spreading_master.m
The script allows for two types of SI dynamics and optimization:
1.- Slow Limit (SL):
A slow propogation... |
b15a453ce10ed8b7626bbfa9677395230ccb99e98144c9e2ea792f17c040ccba | Text | 3,581 | 65 | # EmbryoNet
## Introduction
This repository provides supplementary implementation materials to our paper "EmbryoNet: Using deep learning to link embryonic phenotypes to signaling pathways".
During zebrafish development, seven major signaling pathways orchestrate the formation of the body plan: BMP, RA, Wnt, FGF and... |
041e0ad5ec6dd3b5f9e160eb8241d57a55c6d49d0093d6ad6385bd562970fb84 | Text | 3,659 | 40 | # CAJAL <a href='https://github.com/CamaraLab/CAJAL'><img src="docs/images/logo.png" align="right" width="24%"/></a>
[](https://github.com/CamaraLab/CAJAL/actions/workflows/python-package.yml)
[
AAmpD is an R package developed to identify focal amplification detection from cluster aggregate of single cell/nuclei ATAC-seq data. Pipeline was developed based on analysis of single nuclei ATAC-seq (snATAC-seq, sci-method) data from glioblastoma multiforme (GBMS) tumors. Manuscipt in prepa... |
1bdca677a5923660322254cfae76976f0845991ee628cb3e5c35b20e00869758 | Text | 3,794 | 49 | # BrainMesh
**A MATLAB graphical user interface (GUI) for rendering 3D mouse brain structures**
## Getting Started
Run ```BrainMesh.m``` in MATLAB (developed in R2019)
## Highlighted Features
* Select Allen brain structures direc... |
4078f15cea29c17875982e90d4b2c2e0deedbbfbc65358aee2e93855af200654 | Text | 3,821 | 69 | # Elfn1 reconstruction
Computationally reconstruct the ELFN1 protein from the last amniote ancestor. See the preprint for context:
[Cortical interneurons: fit for function and fit to function?](https://doi.org/10.1101/2023.02.23.529671). See the [interneuron_evolution repo](https://github.com/JoramKeijser/interneuron_e... |
59e947c8b185569ef5a2c26c04931c3892cfbc0f4c6f73604bba10a4709c88f5 | Text | 3,843 | 87 | # scCODA - Single-cell differential composition analysis
> **Note**
> This implementation is no longer maintained. A new version in Jax is available in [pertpy](https://pertpy.readthedocs.io/en/latest).
>
> For more information and contribution guidelines please visit the associated Github repository: https://github.c... |
b94a19fd28b32b8a74f3546bb8197075e430d7f59bdddb68e5a3d60735185167 | Text | 3,863 | 101 |
## h-BiP
h-BiP is a python package that predicts the human Binding Potential from the S protein sequences of alpha and beta coronaviruses as described in the following paper:
*Gonzalez-Isunza, G., Jawaid, M.Z., Liu, P., Cox, D.L., Vazquez, M. and Arsuaga, J., 2023. Using machine learning to detect coronaviruses pot... |
632fd17927f8496aafd6efb5273cae46e39d5ca0b541d044943ebb956482f56a | Text | 3,938 | 69 | # vgp-assembly
VGP repository for the genome assembly working group
## Contents
* Galaxy Workflow
* DNAnexus Workflow
* Docker images with WDL Workflow
* Pipeline for local run
* MitoVGP pipeline
* Instructions for AWS s3 genomeark
* Meta data
* Citation
## Galaxy Workflow
Starting the VGP v2.0 pipeline, the product... |
fbda973440c7747588f1b282543a491ebc64760aa4f2b17b38bb1792a57e766c | Text | 3,944 | 105 | # DeepBindGCN
## Background
The core of large-scale drug virtual screening is to accurately and efficiently select the binders with high affinity from large libraries of small molecules in which non-binders are usually dominant. The protein pocket, ligand spatial information, and residue types/atom types play a pivotal... |
a5b630caec1f23c59bc90620288062ddefdc2a636b8a84edab83a5b6162effbb | Text | 3,949 | 84 | # SpineTool
> ⚠️ **Important notice**
> The actively maintained and up-to-date version of SpineTool is available in the laboratory repository:
> https://github.com/Biomed-imaging-lab/SpineTool
>
> The new version includes multiple fixes related to:
> - handling of original input datasets,
> - TIFF file reading,... |
85742de3ee3f142da50bac364518a986d18f6134d1325846bde66306acc41fa7 | Text | 3,985 | 73 | VCNModel
========
VCNModel is a set of Python routines in a repository for running simulations of fully reconstructed neurons from the mouse cochlear nucleus.
Neurons, including their dendrites and the portion of the axon that remained withing the volume, afferent fibers,
and afferent terminals were reconstructed fro... |
d86778f0590c1ff3f8c9a934364124dc419270119eb66fcb317628b60be6a31c | Text | 3,989 | 70 | # Tutorial to accompany Fink et al. (2023)
This repository contains code and toy data associated with the paper:
Fink, L., Simola, J., Tavano, A., Lange, E. B., Wallot, S., & Laeng, B. (2023). From pre-processing to advanced dynamic modeling of pupil data. *Behavior Research Methods*. [https://doi.org/10.3758/s13428-0... |
eebad605b49332a31fef6f870fc3ba0a83f7b8d4dc6af3d5de2c4ffbb533ba8a | Text | 4,016 | 82 |
# OpenSpiel: A Framework for Reinforcement Learning in Games
[](https://openspiel.readthedocs.io/en/latest/?badge=latest)
OpenSpiel is ... |
8c6b59c9466179669b54320ed295b207418e73ce71e8bdbedf9819c427cce6ca | Text | 4,036 | 142 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
<br>
<div style="text-align:left">
<span><a href="https://nightingalehealth.github.io/ggforestplot/index.html">
<img src="man/figures/logo.png" width=110 alt="Logo"/> </a>
<h2>
<strong>ggforestplot</strong>
</h2>
<h4>
Visualizing Measures o... |
8c585cb660b5f013661c81b8207712116ae721e4c6defa25e6a3b9b81a1c3327 | Text | 4,037 | 96 | <p align="center">
<img width="600" src="https://raw.githubusercontent.com/jvendrow/fnnls/master/fnnls_logo.png?raw=true" alt="logo">
</p>
# fnnls
[](https://pypi.org/project/fnnls/)
[... |
c01ceb7b6c29bc207b245d1c05c36c789605efbe1bae3225904708e576f28632 | Text | 4,039 | 67 | # netplotbrain: visualizing networks in 3D on a brain
[](https://app.circleci.com/pipelines/github/wiheto/netplotbrain)
[](https://www.codacy.com/gh/wihet... |
d25aa8b0832ca9eaff1989f9eaa380cea5ff54b0929f1fd0cf35bd635783c79e | Text | 4,052 | 64 | # Subject Specific IHTT Estimation
Estimation of Interhemispheric Transfer Time (IHTT) from EEG data for each subject individually.
## Introduction:
This repository is related to the scientific article:
Single-subject EEG measurement of interhemispheric transfer time for the in-vivo estimation of axonal morphology ... |
4b96f2f32e9c11107c07059a8a9e673af6f81777e73e6b2361ffcb2ce23dcb3d | Text | 4,070 | 68 | # ILP
This repository is the place where you can find the data and ML codes for the published manuscript with title of "Machine learning-guided discovery of ionic polymer electrolytes for lithium metal batteries"
1. Document Introduction
1. data_manuscript_figures folder: all the raw data to generate figures in... |
fecc78c530d6954550a3679c6a5dcadc31ecce4c90e1fcc5b6d3ebe2178aa9cb | Text | 4,078 | 68 | # ILP
This repository is the place where you can find the data and ML codes for the published manuscript with title of "Machine learning-guided discovery of ionic polymer electrolytes for lithium metal batteries"
1. Document Introduction
1. Raw_data_for_figure2-6_manuscript.xlsx: all the raw data to generate fi... |
f64c65a8b042c48b3d84bbb137e8fa89b32137e36c18b62708d9ea363b2f7aa8 | Text | 4,080 | 41 | # autolfads-tf2
A TensorFlow 2.0 implementation of LFADS and AutoLFADS.
# Installation
Clone the `autolfads-tf2` repo and create and activate a `conda` environment with Python 3.7. Use `conda` to install `cudatoolkit` and `cudnn` and `pip install` the `lfads_tf2` and `tune_tf2` packages with the `-e` (editable) flag. ... |
1a78385ddaee824b184b8c50024c0ee0462b25d57245b609e486ce0146af328a | Text | 4,145 | 135 | # EvoAug
EvoAug is a PyTorch package to pretrain sequence-based deep learning models for regulatory genomics data with evolution-inspired data augmentations followed by a finetuning on the original, unperturbed sequence data. This work uses PyTorch Lightning -- LightningModule -- to define a model wrapper that is used... |
2beda92ac1dfbf915e860989af4cce2ffd9e15bf5cb64ab2a4eb3c0cd49663bd | Text | 4,191 | 76 | # BRNet
This repository contains the code for performing model training along with various models trained on the ICSD dataset using Elemental Fraction (EF) as the model input.
## Installation Requirements
The basic requirement for using the files is a Python 3.6.3 environment with the packages listed in requirements... |
cfceea1b0aa26c715543fa6af8f65d50ffa93d5126a3e129d7971b244d81ca8a | Text | 4,202 | 85 | # Partitioning
## License
Metab-Partitioning is licensed under the 2-Clause BSD License - see the [LICENSE](LICENSE) file for details.
----------------------
General Information
----------------------
Deposit Title: PCB partitioning in multiwell setup experiments
Contributor information:
Andres Martinez, PhD
Univ... |
82b28fe50080c2b6f4589012ad598931adb3668823725c855819a78fbcf0cbbb | Text | 4,237 | 105 |
# DeepCRISTL
A tool to predict CRISPR/Cas9 gRNA on-target efficiency for specific cellular contexts utilizing transfer-learning. The repository for the paper [DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency](https://academic.oup.com/bioinformatics/artic... |
4af70ac2275c36bbcf9636fe8b4842cea51dae6e4826757d7122b06a7476d058 | Text | 4,260 | 42 | If you use our tool or dataset, please cite [Kataras, T.J., Jang, T.J., Koury, J. et al. *ACCT is a fast and accessible automatic cell counting tool using machine learning for 2D image segmentation*. Sci Rep 13, 8213 (2023).](https://doi.org/10.1038/s41598-023-34943-w).
# Iba-1-Data
The Iba-1 staining data used in the... |
3b6988781de27af783161e73c8e1d74deb43fdb268e384eb333976f81ecf535a | Text | 4,278 | 68 | # Optical Flow estimation from Event Cameras and Spiking Neural Networks
This work has been published in _Frontiers in Neuroscience_ (section _Neuromorphic Engineering)_. Our manuscript can be found on https://doi.org/10.3389/fnins.2023.1160034
## Introduction
We present here the code we have used to develop our Spi... |
e0f02d312584c2fd68f02b7289c9e04493adabfec35c15d08d68811ca079634c | Text | 4,298 | 46 | # Sampling strategies and integrated reconstruction for reducing distortion and boundary slice aliasing in high-resolution 3D diffusion MRI
MATLAB implementation of distortion-free parallel imaging reconstruction for 3D multi-slab diffusion MRI
## 1. Framework
**Figure 1. Propos... |
b8eb184fc2c3e2bf86414ea0d9a2f84f999d254e911ad150f7ec0fc2da3ce943 | Text | 4,318 | 92 | # Introduction
Supporting code and analyses for [Explaining compound activity predictions with a substructure-aware loss for graph neural networks](https://chemrxiv.org/engage/chemrxiv/article-details/63cfabd3ae221a94e93b4b2d)
# Getting Started
## Installation process
We recommend the [conda](https://docs.c... |
f2ffcc3508049ab52edc8c3340e074fae6d7207166d39cf39515b031c347ec4d | Text | 4,347 | 78 | # fast_tvb
Fast and parallel C implementation of TVB
## Pull and run fast_tvb as a Docker container here
## https://hub.docker.com/r/thevirtualbrain/fast_tvb
The code implements a brain network model composed of connected ReducedWongWang neural mass models (Wong & Wang, 2006) with feedback inhibition control (FIC). ... |
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