sha256
stringlengths
64
64
language
stringclasses
28 values
size
int32
1
491k
lines
int32
1
23.2k
content
stringlengths
1
200k
3d341d568e3c87e2174b996af47735f15955457d564dcfd17e4b4d1775b72718
Text
6,209
126
# ESS: Learning Event-based Semantic Segmentation from Still Images <p align="center"> <a href="https://youtu.be/Tby5c9IDsDc"> <img src="resources/ESS.png" alt="Transfer" width="400"/> </a> </p> This is the code for the paper **ESS: Learning Event-based Semantic Segmentation from Still Images** ([PDF](https://rp...
9b87876f72f3efa46f700304ca5a6a0a5369873695ebce4809b9b75497b88905
Text
6,240
103
![](imgs/ciftify_banner.jpg) [![CircleCI](https://circleci.com/gh/edickie/ciftify.svg?style=shield)](https://circleci.com/gh/edickie/ciftify)[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/edickie/ciftify/master) [![DOI](https://zenodo.org/badge/67087965.svg)](https://zenodo.org/badge/latestdoi...
f16f3b6bc41290f5c032f3d99a48c5fd7a6bd15532aa7ba5d96220f3d843990b
Text
6,244
196
# Flight trajectory prediction enabled by time-frequency wavelet transform # Introduction This repository provides source codes of the proposed flight trajectory prediction framework, called WTFTP, and example samples for the paper <a href="https://www.nature.com/articles/s41467-023-40903-9">Flight trajectory predi...
b36839b3439836db7857b84b9e373a998d925f6e856a9efed788115d46e5914c
Text
6,249
164
# README ### **Github link**: [https://github.com/peterpark-git/neuroclear](https://github.com/peterpark-git/neuroclear) ### **Data repository: click [here](https://www.dropbox.com/sh/a83wfw31blf04x9/AACHBx16P9YPEHS7DDQUWBh6a?dl=0).** # Neuroclear Neuroclear is a deep-learning-based Python module to train a deep ne...
5da2fdc01ac7fa27253bc633617e8b121b56a865f488e12ab2917e962fd44a47
Text
6,272
168
# README ### This method is now published in *Nature Communications*: [Park et al., 2022](https://www.nature.com/articles/s41467-022-30949-6) # Neuroclear Neuroclear is a deep-learning-based Python module to train a deep neural network for the task of applying super-resolution to a degraded axial resolution in Fluor...
f5a62edeefa55e098d2b7435fb50e0bd4dcfffc0686f3340263e5fa472004b07
Text
6,344
95
## Deep detection (DD) model for climate change detection The deep detection (DD) model, which refers to the CNN model for detecting climate change signals embedded in daily precipitation anomalies, comprises an input layer, four convolution layers, two pooling layers, one fully connected layer, and an output layer. ...
f21a1175bd7090d49180f615ab7e9ab13af50797a44bd4d78ea67b8549bee65b
Text
6,422
106
# BraiNN Convolutional Neural Network for classifying sex from MRI Find the preprint of the related paper here: https://medrxiv.org/cgi/content/short/2022.04.27.22274355v1 ### Project Overview * `brainn.py` Use this script to train BraiNN on your data and to make predictions * `helper/createDataset.py` Helper module...
1d7af127f11f23cba63597fc17cc99a85801de15034ee0f743cbfc0ea9507b62
Text
6,570
152
pysteps - Python framework for short-term ensemble prediction systems ===================================================================== .. start-badges .. list-table:: :stub-columns: 1 :widths: 10 90 * - docs - |stable| |colab| |gallery| * - status - |test| |docs| |codecov| |codacy| |...
b1fa549c456ef49b1d7457a9edb79bb31f0d88d5509901db5ca4b8eb2e10072e
Text
6,606
96
## Deep detection (DD) model for climate change detection The deep detection (DD) model, which refers to the CNN model for detecting climate change signals embedded in daily precipitation anomalies, comprises an input layer, four convolution layers, two pooling layers, one fully connected layer, and an output layer. ...
5e40a5ba0d0a5885c7f0c5fc61d14be6a0510a3cb0992225ca4c8ea12072171a
Text
6,643
127
# 🔥Representation Bottleneck of Graph Neural Networks (IEEE TKDE) This is the official code for <span style="color:yellow">**Discovering the Representation Bottleneck of Graph Neural Networks from Multi-order Interactions**</span>. [[IEEE TKDE](https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=10640313)] [[arXi...
8313bae6ec45d83a250b959cec10d2b90175336d491fa9db70da540bda01b6c8
Text
6,684
70
# fMRI preprocessing pipeline for partially covered human brains This preprocessing pipeline was developed by Nan Xu and was used to preprocess EPI human brain data with partial coverage, which has been used in (Xu et al., 2022). EPI scans with >40% brain coverage can be sucessfully normalized to the MNI space and prep...
5c0c8416748f6e5135b881863be095d20eeff99d7c91b5ad6e3838437e5b3f11
Text
6,757
169
[![License MIT](https://img.shields.io/pypi/l/sc-3D.svg?color=green)](https://github.com/GuignardLab/sc3D/raw/main/LICENSE) [![PyPI](https://img.shields.io/pypi/v/sc-3D.svg?color=green)](https://pypi.org/project/sc-3D) [![Python Version](https://img.shields.io/pypi/pyversions/sc-3D.svg)](https://python.org) [![tests](...
12b4d1ec815e8c968dcd015cd1b3df0ad75fd1a401788b0d6e5c6f945ea4fafb
Text
6,964
82
# CMOT: Cross Modality Optimal Transport for multimodal inference [![DOI](https://zenodo.org/badge/551975347.svg)](https://zenodo.org/badge/latestdoi/551975347) ## Abstract <p align="justify"> Biological mechanisms are complex spanning multiple facets, each providing a unique view of the underlying mechanism. Recent ...
adcaa9f302a9fc41c1c2a2b62d29805952aa3825442f45963e4e2e75a78da7ab
Text
7,261
91
![GitHub-Mark-Light](https://github.com/mlcommons/GaNDLF/blob/master/docs/images/logo/full.png?raw=true#gh-light-mode-only) ![GitHub-Mark-Dark](https://github.com/mlcommons/GaNDLF/blob/master/docs/images/logo/full_black.png?raw=true#gh-dark-mode-only) <p align="center"> <a href="https://github.com/mlcommons/GaNDLF/...
7c9539bb2ed8e2efb123382169260bbb5ca7b2b3a5e52c4dfdd21c910c92f5f2
Text
7,267
116
# Data and code for reproducing our study on *Sex-related patterns in the electroencephalogram and their relevance in machine learning classifiers* and for implementing the Mini-SpaTeN neural network architecture This code, data, and repository was authored by Marc S. Seibel and Thomas Jochmann. *When using the code...
901a43d6d51dcec559faa7ba7637c5a1a20e1075113c25c67270dd17cf152202
Text
7,361
183
========= pyunicorn ========= .. image:: https://app.travis-ci.com/pik-copan/pyunicorn.svg?branch=main :target: https://app.travis-ci.com/github/pik-copan/pyunicorn .. image:: https://codecov.io/gh/pik-copan/pyunicorn/branch/main/graph/badge.svg :target: https://codecov.io/gh/pik-copan/pyunicorn .. image:: https...
9fb85efcb002012aa7561ae2a575e37483944f88dcc4857dc55bf26a1c3297dc
Text
7,924
128
<img src="logo.png" width:100px > ## SigmaCCS This is the code repo for the paper *Highly accurate and large-scale collision cross section prediction with graph neural network for compound identification*. We developed a method named Structure included graph merging with adduct method for CCS prediction ([SigmaC...
60e73cc3c727d3d0af1ea8dc0311add3f15f8846672d30658d0cb8333ff724da
Text
8,012
145
<h1> DRAGen - <ins>D</ins>iscrete <ins>R</ins>VE <ins>A</ins>utomation and <ins>Gen</ins>eration</h1> <!--**D**iscrete **R**VE **A**utomation and **Gen**eration--> <!--## Overview--> <!--![logo](docs/GUI.PNG)--> [**Installation**](#Installation) | [**Related Projects**](#Related-Projects) | [**Tutorial**](Tutorial) ...
fa2f0e18f10c0936439ed08a908480aeb823ba2a39bf64a824b4264570d8e4f9
Text
8,079
133
<img src="logo.png" width:100px > ## SigmaCCS This is the code repo for the paper *Highly accurate and large-scale collision cross section prediction with graph neural network for compound identification*. We developed a method named Structure included graph merging with adduct method for CCS prediction ([SigmaC...
568c2cfdedb8c8632e35a41a404c8f75946650d6374a6d64973e4ee1088a0008
Text
8,132
133
# When Geometric Deep Learning Meets Protein Language Models ☀️☀️☀️ This is the official implementation of paper ***When Geometric Deep Learning Meets Protein Language Models*** [[arxiv](https://arxiv.org/abs/2212.03447)]. Our work addresses the gap that has long been ignored by the geometric deep learning community fo...
9f12377b8831eccaf429ee22747798481a4766afdd2c682537c3353fb629ef7e
Text
8,163
152
## Announcement: The Protigy v2.0 App is now available [here](https://github.com/broadinstitute/protigy-v2)! Please note the original ProTIGY will no longer be updated. The current release v1.1.8 is the final version. For future updates, please use the new [protigy-v2](https://github.com/broadinstitute/protigy-v2) r...
1d4dedc7e55b286a90acd02c213eb5f966f68f06a7a290df905adc8a1f961a53
Text
8,483
193
# Exact calculation of the overlap volume and area of spheres and mesh elements [![Build Status](https://img.shields.io/github/actions/workflow/status/severinstrobl/overlap/ci.yaml?branch=main)](https://github.com/severinstrobl/overlap/actions/workflows/ci.yaml) [![Coverage](https://sonarcloud.io/api/project_badges/me...
73a551896c2abacd5134e3052ed4e8c0999781948bf92e9e6aa1e3ec421d4089
Text
8,673
172
# EPU-CNN [![GitHub stars](https://img.shields.io/github/stars/innoisys/EPU-CNN.svg?style=flat&label=Star)](https://github.com/innoisys/EPU-CNN/) [![Readme](https://img.shields.io/badge/README-green.svg)](README.md) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/M...
9d5ab97d3c12709af1133b4bf2e1bf73982d49797c4dcb19418349e97d710e10
Text
8,759
129
# scAI: a single cell Aggregation and Integration method for analyzing single cell multi-omics data - scAI is an unsupervised approach for integrative analysis of gene expression and chromatin accessibility or DNA methylation proflies measured in the same individual cells. - scAI infers a set of biologically relevant ...
1191a60f1c64410030d2907001ec7afd3bc031a0cf1bdec916500f9e258fda43
Text
8,820
115
[![AFIDs](https://github.com/afids/afids-validator/blob/master/afidsvalidator/static/lib/afidsvalidator-react/public/afids_banner.png?raw=true)](./static/lib/afidsvalidator-react/public/afids_banner.png) [![](https://img.shields.io/twitter/url?style=social&url=https%3A%2F%2Ftwitter.com%2Fafids_project)](https://twitte...
79fe4c45e60fbbe4447e360df4e253f88f9578d7979bce6455f9f4378d56037d
Text
9,360
278
PTSA ==== .. image:: https://github.com/pennmem/ptsa/actions/workflows/build.yml/badge.svg?branch=master :target: https://github.com/pennmem/ptsa/actions/workflows/build.yml :alt: build status .. image:: https://codecov.io/gh/pennmem/ptsa/branch/master/graph/badge.svg :target: https://codecov.io/gh/pennme...
2047858ccabe7308f51d250951a6c52a7027179d008ce7c2c51f6b5a0688f730
Text
9,599
183
## Nature Story Listening 3T fMRI Data ## Summary This dataset contains BOLD fMRI responses in human subjects listening to a set of natural autobiographic stories. The functional data were collected in eleven subjects, in two sessions over two separate days for each subject. Details of the experiment are described in...
064923df10d208cf7dd108775f645dba90724b9604edc0f3acc94d036c132487
Text
9,738
230
# IBM Analog Hardware Acceleration Kit ![PyPI](https://img.shields.io/pypi/v/aihwkit) [![Documentation Status](https://readthedocs.org/projects/aihwkit/badge/?version=latest)](https://aihwkit.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.com/IBM/aihwkit.svg?branch=master)](https://travis-c...
48da93c38f223285cbd2865d98f6d4e0c78ea6dc3c4f37a3fb57724ca4862f0d
Text
9,868
146
# Matrix of Orthogonalised Atomic Orbital Coefficients Representation for Radicals and Ions <p align="center"> <img src="https://github.com/hits-ccc/MAOC/blob/main/Images/git_0.png" width="500" height="300"> </p> This repository offers some insight into the code behind the Matrix of Orthogonalized Atomic Orbital Coeffi...
790d73c3392e40d3b9c7a36a356a08041dade4d96c883a0d13a6efcc6dfebb3d
Text
10,314
141
# scTIGER (Single-cell Temporal Inference of Gene Regulatory Networks) The **S**ingle-**c**ell **T**emporal **I**nference of **Ge**ne **R**egulatory (scTIGER) Networks method is a computational method designed to predict gene regulatory networks (GRNs) using paired datasets of case versus control experiments. After con...
4e745d28b544c8662d0490832e6359e32bb5394a604aa2df1e23977bde45139c
Text
10,377
178
[![PyPI Version](https://img.shields.io/pypi/v/pyGenomeTracks.svg?style=plastic)](https://pypi.org/project/pyGenomeTracks/) [![bioconda-badge](https://img.shields.io/conda/vn/bioconda/pyGenomeTracks.svg?style=plastic)](https://anaconda.org/bioconda/pygenometracks) [![bioconda-badge](https://img.shields.io/badge/install...
178e284c10bd1314cc9f6a1d8e400b964991bf96e1345b24543e5ec76d7c9af6
Text
10,545
155
# Synthetic whole-slide imaging tile generation with gene expression profiles infused deep generative models **Francisco Carrillo-Perez<sup>1,2</sup>, Marija Pizurica<sup>1,3</sup>, Michael G. Ozawa<sup>4</sup>, Hannes Vogel<sup>4</sup>, Robert B. West<sup>4</sup>, Christina S. Kong<sup>4</sup>, Luis Javier Herrera<su...
ea29f07ac4d85d4d8d8065cb167816fffdb7b289a208cbf8b8b78663b6db4a28
Text
10,575
259
# :warning: Archiving Note This repository is no longer being maintained and has been archived for historical purposes. We have now developed [DeepRank2](https://github.com/DeepRank/deeprank2), an improved and unified version of DeepRank-Mut, [DeepRank](https://github.com/DeepRank/deeprank), and [DeepRank-GNN](https...
3297239986cb22fbebe5fe6f8b6d072b1f33f45e7d14ff7cfc9771ecb2df6b92
Text
10,648
202
![PentaMind Logo](https://github.com/stasaki/PentaMind/raw/main/pentamind-logo.png) -------------------------------------------------------------------------------- PentaMind is a deep learning model that predicts **global cognition** from a scanned drawing of **intersecting pentagons** (the pentagon copying item of ...
061c175e53e95e4415b9b5600e5573b080dbb5f565e12a9b898d74bccaf2ecc7
Text
10,755
253
# napari-sc3D-viewer [![License](https://img.shields.io/pypi/l/napari-sc3D-viewer.svg?color=green)](https://raw.githubusercontent.com/GuignardLab/napari-sc3D-viewer/main/LICENSE) [![Python Version](https://img.shields.io/pypi/pyversions/napari-sc3D-viewer.svg?color=green)](https://python.org) [![PyPI](https://img.shie...
b9e715268385f9a8c3d75ea545f2f0d281d7ebe2bb7d4cc23dd1560662a55fc4
Text
10,756
192
# Acute-stroke_Detection_Segmentation (ADS) ## Introduction We provide a tool for detection and segmentation of ischemic acute and sub-acute strokes in brain diffusion weighted MRIs (DWIs). The deep learning networks were trained and tested on a large dataset of 2,348 clinical images, and further tested on 280 images...
a9935eb0ec5d306dcb27e1c89ca4146e65d838944819ae84fa354b5e35bd1b3c
Text
10,807
192
# DCiPatho - [DCiPatho](#dcipatho) - [Introduction](#introduction) - [Features](#features) - [DCiPatho Configuration](#dcipatho-configuration) - [Train and Evaluation Settings](#train-and-evaluation-settings) - [Prediction Settings](#prediction-settings) - [Requirements](#requirements) - [Inst...
0b690eef8094957b0f8cea6b2e9d067800a26042c00423c791d8fd4aa2fd888e
Text
11,016
186
# Source code for EquiDock: Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking (ICLR 2022) ![EquiDock banner and concept](https://github.com/octavian-ganea/equidock_public/blob/main/equidock.png) Please cite ```angular2html @article{ganea2021independent, title={Independent SE (3)-Equivariant...
e44486b2d0846e04f7ae28229201115b32328caa60a25cc13c94e073d0e3a42c
Text
11,412
137
# Twins This module contains an efficient data laoder and training structure for Hi-C data. The aim is to learn patterns from observations made along the diagonal of the Hi-C maps. This data is made up of reads which have typically been aligned, processed and normalised using either the HiCPro or the distiller pipeline...
346dcf1c46a54582bf574d56f8cef12fca151c44f3a32505036c8e752792d93c
Text
11,976
167
<p align="center"> <img src="docs/assets/celery_logo.svg" alt="CeLEry" width="180"> </p> <!-- badges: start --> <p align="center"> <a href="https://github.com/QihuangZhang/CeLEry/actions/workflows/tests.yml"><img src="https://github.com/QihuangZhang/CeLEry/actions/workflows/tests.yml/badge.svg?branch=main" alt="te...
07fd2563d0853aac0be58e6589631d0b2745d291d57d846776ec7b35da51fb6d
Text
13,311
357
# Brain Persistent Homology Using persistent homology and multidimensional scaling on Wasserstein distance matrix ## Data pre-processing ### Input matrix - S x C x N x N, where S = #subjects, C = #cohorts, N = #ROIs - Mat file - Size: 316 x 3 x 114 x 114 - Three cohorts: mx645, mx1400, std2500 ### Data normalizati...
e8287fdbada680acea5a8ec6b0c9169f0f8c3cda560bcac4c6376a36e0ee7588
Text
13,438
84
# Ordinal, full-context prognosis-based trajectories of traumatic brain injury patients in European ICUs Contribution of clinical course to outcome after traumatic brain injury: mining patient trajectories from European intensive care unit data ## Contents - [Overview](#overview) - [Abstract](#abstract) - [Code](#cod...
7d1666a7d6570dca48ae3981c3cf9bf0b7921ffb61ecb8438285b566a068bf33
Text
13,931
91
# Deprecated This repository is no longer actively maintained. For updated MIBI preprocessing, please see our [toffy](https://github.com/angelolab/toffy) repository # MIBI_GUI ## Overview * Introduction * Background removal * Denoising * Aggregate removal ## Introduction MIBI_GUI is a set of three graphical user ...
e65cfc1a62be50f98d6e1688453b57b78f51b6712b7fbcae99e8ac676f7d7fe3
Text
14,927
254
## Schott et al., 2023 Code to generate analyses and figures in *Schott et al., 2023* *** ### Overview * System Requirements and Installation Information * Data Organization * ```data``` * Data Analysis Modules * ```pwaves.py```, ```AS.py```, ```sleepy.py```, and ```pyphi.py``` * Live Data Annotation *...
74f766c82c79033abc0e893d6e1c385595d87f64479735730954b95841e382f6
Text
15,249
91
[![DOI](https://zenodo.org/badge/453184440.svg)](https://zenodo.org/badge/latestdoi/453184440) # Ordinal, full-context prognosis-based trajectories of traumatic brain injury patients in European ICUs [Mining the contribution of intensive care clinical course to outcome after traumatic brain injury](https://doi.org/10.1...
24df3d61ccdeab93da100d693f8612a68aeb08bf91b3c0923d7ef274d0faf199
Text
15,551
174
# Spiking Semantic SLAM with Spatial Semantic Pointers <img src="https://github.com/nsdumont/Semantic-Spiking-Neural-SLAM-2023/blob/main/slam.png?raw=true" alt="SLAM diagram" width="500px"> To navigate in new environments, an animal or robot must be able to keep track of it’s own position while simultaneously creating...
6398f9033adc60c8e364ee4f88080b1a4609401ad71fa69c310897b6002d9423
Text
18,169
387
# ![nf-core/circrnasponging](docs/images/circRNAsponging_logo.png) **Analysis of circRNA and miRNA sponging**. <!--[![GitHub Actions CI Status](https://github.com/nf-core/circrnasponging/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/circrnasponging/actions) [![GitHub Actions Linting Status](https://gi...
14b544d13fc900052aa29e0aa580230c433e2bf1005f81a480b7730e33acc199
Text
18,231
163
## [Low-Light Image and Video Enhancement Using Deep Learning: A Survey](https://arxiv.org/pdf/2104.10729.pdf) ![teaser](/teaser.jpg) This repository provides: **1)** a unified online platform, **LLIE-Platform http://mc.nankai.edu.cn/ll/**, that covers many popular deep learning-based LLIE methods, of which the resu...
a6c3bd9f628f76ee67c4623025ab0f5966175a1fc85a7668bd0a24b6406f73cf
Text
20,689
202
# CellWalker Morphological analysis tool for segmented 3D microscopy images of biological cells ### Installation This program does not require specific installation procedure. The script is tested on Python 3.6 on Ubuntu 18.04. ## User guide<br> **Versions** The latest version is 'cellwalker_v0.9-beta.py' and can...
ad87e3c1c14d3608e5ab6d6c40d4776cc73eaec71d3138ed5eef16296a4f2c9b
Text
21,344
459
# DeepReac+: An universal framework for quantitative modeling of chemical reaction based on deep active learning ## introduction DeepReac+ is an efficient and universal computational framework for the prediction of chemical reaction outcomes and selection of optimized reaction conditions. To accelerate the automation ...
51ad71bb25657bf40320b227daf5eb266e36264eb3ca7ef16b697af3eea9be20
Text
23,690
441
[![Version][version-shield]][version-url] [![Python versions][python-shield]][python-url] [![Platforms][platform-shield]][python-url] # guideseq: The GUIDE-Seq Analysis Package **Note that an updated version of this package, including Python 3 support, is maintained by the Tsai Lab: https://github.com/tsailabSJ/guid...
461c63de6596aec6c09813d18e6090ea9c13d1ace69d93045b528d9c581dfdc5
Text
25,913
422
<p align="center"><picture><source srcset="misc/filtlong_logo-dark.png" media="(prefers-color-scheme: dark)"><img src="misc/filtlong_logo.png" alt="Filtlong" width="450"></picture></p> Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses ...
57d30b049b6c75ff54627aac2184b4dc5658d77e45fc788f96b55cde9d735f45
Text
27,742
432
<img src="./.img/logo_bollito.png" width="500"> ## bollito: single-cell RNA-seq pipeline. [Pipeline status](https://gitlab.com/bu_cnio/bollito/commits/master) ## Introduction **bollito** is a **[Snakemake](https://snakemake.readthedocs.io/en/stable/) pipeline** that performs a comprehensive single-cell RNA-seq analy...
e87f01ba8c31b53f7850856d079c9ea43c62ce843883984aa72ce630b9d5cc0b
Text
27,895
660
<p align="center"><img src="figs/logo_deeppurpose_horizontal.png" alt="logo" width="400px" /></p> <h3 align="center"> <p> A Deep Learning Library for Compound and Protein Modeling <br>DTI, Drug Property, PPI, DDI, Protein Function Prediction<br></h3> <h4 align="center"> <p> Applications in Drug Repurposing, Virtual S...
47ad10e225aaaed5d9ed3d587dac920e9276154902054607e11b6573ca007332
Text
30,806
540
# [Chinese-LLaMA-Alpaca-2 v1.0版本](https://github.com/ymcui/Chinese-LLaMA-Alpaca-2)已正式发布! [**中文说明**](https://github.com/ymcui/Chinese-BERT-wwm/) | [**English**](https://github.com/ymcui/Chinese-BERT-wwm/blob/master/README_EN.md) <p align="center"> <br> <img src="./pics/banner.png" width="500"/> <br> </p> <...
1a4db23324b012914bbb2baaa96d2abe653ca54c6c2443483d4a0f2b9876684d
Text
31,955
707
# Small Immuno Age (SImAge) [![pytorch](https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white)](https://pytorch.org/get-started/locally/) [![lightning](https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlightning&logoColor=white)](https://pytorchlightning.ai/) [![hydra](https://img.shields...
a4a8c5fec66041197c7cb95c3142b0124adb43795b0626e14768e1251562755c
Text
34,457
650
This pipeline has been deprecated as of June 2018. Please update your pipelines to the WDL-based pipeline at [https://github.com/ENCODE-DCC/atac-seq-pipeline](https://github.com/ENCODE-DCC/atac-seq-pipeline) =================================================== ATAC-Seq / DNase-Seq Pipeline =============================...
2bec4defa116dc900f5071ef519fbcc9c57b2d0fbe33e27c2fbb23c034226d0a
Text
34,604
623
# somata Github: https://github.com/mh105/somata **State-space Oscillator Modeling And Time-series Analysis (SOMATA)** is a Python library for state-space neural signal processing algorithms developed in the [Purdon Lab](https://purdonlab.stanford.edu). Basic state-space models are introduced as class objects for fle...
dcc7f3a0323ef76bcceee82cdf1674c68e37368c87feaac719a489710d19d880
Text
37,013
283
# BrainCog BrainCog is an open source spiking neural network based brain-inspired cognitive intelligence engine for Brain-inspired Artificial Intelligence and brain simulation. More information on BrainCog can be found on its homepage http://www.brain-cog.network/ The current version of BrainCog contains at least 18 ...
10f0efe4f3b1a47e8b5d23ffe2db670beb7877809d8826f93271fd9aae36d6e1
Text
40,746
554
# PyTorch Image Models - [What's New](#whats-new) - [Introduction](#introduction) - [Models](#models) - [Features](#features) - [Results](#results) - [Getting Started (Documentation)](#getting-started-documentation) - [Train, Validation, Inference Scripts](#train-validation-inference-scripts) - [Awesome PyTorch Resourc...
84b0d1bec9776c5f997b6a0af0b971e66b74dfe12ad521400a200c629a1a527d
Text
49,694
987
Controlling RGB LED display with Raspberry Pi GPIO ================================================== A library to control commonly available 128x64, 64x64, 32x32 or 16x32 RGB LED panels with the Raspberry Pi. Can support PWM up to 11Bit per channel, providing true 24bpp color with CIE1931 profile. Supports 3 chains ...
9869104b61b1efbbfe08c71095e1b84c603705e86d24526527ee65fa2df40c71
Text
55,775
1,244
.. image:: Logo.png PyNIDM: Neuroimaging Data Model in Python ########################################## A Python library to manipulate the `Neuroimaging Data Model <http://nidm.nidash.org>`_. |PyNIDM Testing| |Docs| .. |PyNIDM Testing| image:: https://github.com/incf-nidash/PyNIDM/actions/workflows/pythontest.yml/...
8c727b16e53d066c8c59b86386017768f4ef5f3a2e0fd940bf9b982a87bd6538
Text
55,958
889
![](mocha_logo.png) A BCFtools extension to call mosaic chromosomal alterations starting from phased VCF files with either B Allele Frequency (BAF) and Log R Ratio (LRR) or allelic depth (AD). If you use this tool in your publication, please cite the following papers from [2018](http://doi.org/10.1038/s41586-018-0321-...
22a9250750283d8c963a539d1ad56b9aa2102ed1ece27185f3f1dafa63363da9
Text
56,669
1,270
<img src="/images/TGen_Color_LOGO_medium.png" width="208.3" height="78" title="TGen Logo"> <br/> # Phoenix Workflow - A JetStream Workflow This workflow supports the analysis of human sequencing samples against the GRCh38 reference genome using ensembl version 98 gene models. The workflow is designed to support proje...
6554b933b6f2d74bb1412b2a2f923c2906c691823019bd23f94935240e575568
TypeScript
229
10
import renderFooter from './components/footer'; import renderNavbar from './components/navbar'; globalThis.renderNavbar = renderNavbar; globalThis.renderFooter = renderFooter; export default { renderNavbar, renderFooter };
a1f7a1f8e12433402216a97b20aa500fac43939e4673bca4bddf7188089b1b52
TypeScript
1,175
23
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
a837967ff49f8880c236381725e2ff12c4932a307516c839252dafa3e6be01ed
TypeScript
1,181
23
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
e5d2b2416bfc5b3b2da24451ba9a3a46af5d0ddaa48d51a5c2ce275705924ed1
TypeScript
1,199
24
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
32a6662061ab2e78a813fee74519fd3ab860146edbf1a1024a217ba4c0df5537
TypeScript
1,200
24
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
0d5f2abef5f96d076558c9147293776656bcdc7a6726acbc2c0a1ed60ddbbb0b
TypeScript
1,201
24
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
221d0f033752bae83107cd63313ae003f0788c8241eb326ab4142c873acfd95d
TypeScript
1,221
25
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
55aedb2ef045d0a7252100a358ddca2b72d9d4b200d614a60b1d94d23b131d24
TypeScript
1,221
25
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
034ce30026733324c81773cdeedfce140e16134641a347ba4932484db93f0414
TypeScript
1,223
25
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
e1fa314ac66fcfd01cd854e3391dd30a0e11adfa418b600c17056e10f46e0937
TypeScript
1,230
27
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
7ea4f8f5f89dc588e101f9c8da192e96ccdcf2c4d3408b4de2cdf246487bc564
TypeScript
1,248
26
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
1bdb7ad9f838f76d7799aaeb96ce95e38eeb4bc0616b36e4ea0e3a8a44e922fe
TypeScript
1,250
26
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
8cc28c17f17ffcffe1b2d78e515e59d1a20ce823cf1833e39429fb1693344d56
TypeScript
1,257
26
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
956374c0ea1474be58bdd94bbdbdd7db16290bca4852b2ac952d803857fa2b2d
TypeScript
1,272
27
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
17e771eeba20ba83d67d2e96215035fced2a40d4e0a6cc250551d1237ae9fea8
TypeScript
1,285
27
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
c9aeca0249d5036362332e1c5531485299bffb4730618d30551c316e92889b3b
TypeScript
1,286
27
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
335baf80d0ffd40866b9668a6d2d9afc94613c1c50edb3350c83dff58e1adfb8
TypeScript
1,306
28
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
fbf13eb44f4ccb0e2d0781b963df4dd6753444753dea7b7b6ef2e39ee13cff30
TypeScript
1,363
30
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
344fdb230eedf13228fdc3d8d9e92be431f63457a6dd415e2e3aa506bb535fcd
TypeScript
1,370
31
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
af2396708b3edb72568d51dcf9afeed573261764476ed897388fa6afe4fb0e53
TypeScript
1,491
33
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
c04df66c2fc85b133f0088cd338cadad89abb23d62861b0e86e0391c60dd6fc6
TypeScript
1,504
33
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
4a9ebfdd86747339f318aeba72c38b8b70b9c75bdf0b34ac851e842f97315427
TypeScript
1,560
39
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
09d37cdb820bb32aaf27c25100768b4ba216c2a3bb27fddcf8028301db35c239
TypeScript
1,669
44
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
389c947f9bbbb485efbc8308cb0089289e328eea455787d9d4bfe7a349d7bd3a
TypeScript
1,732
48
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
c9982dd1a856c6c30f2f77013a8d31abc90bf235ab012dadf9f08bbbfc3fff60
TypeScript
1,732
48
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
e0837f4b3e165b38a5215b6c8b42197075125d5363722bbd2bcaab37d86f99f1
TypeScript
1,742
48
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
13fc6a576c920275c9c05b104115462964ede68c60e9213495624d72e83b2527
TypeScript
1,775
48
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
1b27482ff579fa93efcc2b141c5a287d47edd32116c6c99687c4e764fd1442bd
TypeScript
1,798
46
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
33f9e003b35dfb15217d301e3726def10dbc13f1b27ebd154e26d598d3eeb4c9
TypeScript
1,928
49
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
99a33b99d04dac920e086104b5489520894f5b173c4c5a033119912ca6f3825c
TypeScript
1,970
56
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
b482659c6e66738d472168f91b11700e643569b203e3babf76cb2a63caf5cf0a
TypeScript
1,975
57
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
81494ccb8f05fe640c6d2bcd5f1fff13c650b872faa7b85c680ab1c47d940e7c
TypeScript
1,996
63
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
8cb0dd2b7e93b3d4d33d27c81b2ff61c55a59de05da4904b7cd6bec677e8033b
TypeScript
1,996
63
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
61e5a670f9ae91839dd30b3042d71b672f6aaf70cd7dfdb67702f9be019916c6
TypeScript
2,098
55
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
ad353bdcbf993f32486e7883d7e467bdcd05b89cf8defc77f653b7bd7ab082b6
TypeScript
2,135
73
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...
af30ab11909b57e04289f470cdbea9525a769404cab9f94f81b50f5d66aa5c4c
TypeScript
2,162
59
/* * Copyright (c) 2016-2020 Martin Donath <martin.donath@squidfunk.com> * * Permission is hereby granted, free of charge, to any person obtaining a copy * of this software and associated documentation files (the "Software"), to * deal in the Software without restriction, including without limitation the * rights...