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b98555cdee693cf26d646d1999f1742cb02bef1181a0cbc3b3dcfe3266404d19 | Text | 26 | 1 | # DENSE_2DMotionCorrection |
2222a13598e0acc7086b1b34998cf0ebe92dacd648c1ec000fc578265859d471 | Text | 27 | 1 | # acidoCEST_MachineLearning |
4411b30b366cba2c1ff28eeac7b1030ce5c5920fb6849a87e68a36a1962af622 | Text | 36 | 1 | # 具体内容请查看各文件夹
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e85bc1d41e55c203bcd9b6ab3f77e169493a3bd76ede28d4c42de4744b73cf9c | Text | 45 | 3 | # BRCA
Bayesian Residual Component Analysis
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aed6bb4eb2a1745b078fb15f5786cd628e93bf6d292a76f18ff82167985ae7de | Text | 58 | 2 | # VRFishTracker
Fish tracker for ANR-VRFishschool project
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e7d9f60ba0b9722f96419ea22fd9d35808d3f2c8d144af2b33c9ffdf06982c38 | Text | 60 | 4 | pyXdPhys
========
python reader for the XdPhys data formats |
37905b08ec85084c87140fd25769ef3f0e0fbe528860cf1fc2d833576bb7f0fe | Text | 61 | 3 | # Raw_data
Raw data for PLOS One as requested after revision |
c5617b3f4ca2845a370bf1898c139cddbb52a96a3b5b9e9c36c0cd1d108174c4 | Text | 61 | 2 | # SEEG_dataAnalysis
Preprocessing and analysis of SEEG data.
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761a3378eea018f228b5197374c8eab954fa26e51093fa53418828eabf1cc417 | Text | 71 | 2 | # PrimateMicrobiomeandBrainGrowth
Code for analysis for Mallott et al.
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2e0d117344b797828d203d1e5e52e61798874dd61cea3b38fd66ab008c1835c4 | Text | 73 | 2 | # VRFishSimulator
Fish trajectory simulator for ANR-VRFishschool project
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f4f391f842c3892c3ae735e3817e6a8eabb91ef6717421ba882de03e4d499858 | Text | 79 | 2 | # Laminar-SANDI
Scripts for analysis in the laminar SANDI diffusion MRI study.
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59d71b3830b0d56abd1993bd24e86b9f79b125eaec985142fef483c128be2a81 | Text | 80 | 2 | # VRFishProjectorCalibration
Projector calibration for ANR-VRFishschool project
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0fc67b3e10a0c5d5aabb93ca1c327239f242a4713c0f329158e90e2f807398a0 | Text | 83 | 1 | Raw data files are available from K. Lee on reasonable request (klee@dgist.ac.kr).
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38f35f0b619a29932177dc69264b9f493400c88d04cb7554f21b18c5d606b720 | Text | 83 | 2 | # published
publicly available code for papers published in the Constantinople lab
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91818f299408b68df4a7e60b46d77032a0333d0489d8ccb1d33ebe5341bc2c34 | Text | 91 | 2 | # ligand-receptor-interactions-mouse-cortical-development
Repository for the Paper figures
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22ee5cd4384b0427cde80e29dac9e207cf9893a2cea872f30df9593484464fc7 | Text | 92 | 2 | # mwf_rpca
Implementation of the BSS-rPCA by Song et al (2020) for MWI using mGRE MRI data.
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dbc1bd78fbe968e78cec5727c44cde6630d62fb071cd4cdb07c3acebd7ffd1a2 | Text | 92 | 3 | # ClinicoGenomicInsights
This repository contains all materials used in IJERP publication.
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6d034a3397154fe79e6b75da8a9bade84c54a52371a9c0ff6b3421449db7f3af | Text | 94 | 2 | # Dendrite_communication
Code for Dendritic Nonlinearities Mitigate Communication Costs paper
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baa55a9c5daf918c182471790276b9584d6755e54412f374ef3670337d2c34c5 | Text | 100 | 7 | # Baydiff
## First steps
Checkout the WIKI here
https://bitbucket.org/reisert/baydiff/wiki/Home
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7db5cd8b375edc33a0367c3970cb34091107145e4635ac3c11a357a4d6434a3f | Text | 113 | 2 | # install
install from Github : pip install git+https://github.com/ttttmmttddiikk/Energy_Landscape_Analysis.git |
382c64124b43b5c58f928525132707cc2bbb781fbb08ba2c3d69468b8120ec1e | Text | 115 | 5 | # Segmentation of brain tissues from spectral CT images
Code base for the publication ...
More will be added ...
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00e65388acfe4359eff7c80494b78a36077f46cf4d8c3a26e0591889e633c2e1 | Text | 119 | 3 | # hchs_ace
Code files are numbered based on their sequence in the analysis.
File 03 is R code taken from a JASP file. |
b1f3f2ca87b00bac7e94cd333875d4518bfac4e01f8cd599a25abbebb5a7d5ba | Text | 122 | 2 | # SVD_proteomics
Sample R code from Nature Aging paper on CSF proteomics and cerebral small vessel disease manifestations
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c7fc1e42e94c3c057f21e11604f5554e50420ad2f587f5a9a494bfe77e85e51b | Text | 124 | 3 | # Chen2026
Data and analysis of Chen et al. <br>
Preprint here: https://www.biorxiv.org/content/10.1101/2025.08.21.671364v2
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0614c49acd3207600d7da6bc978e8a04006089317d7f3864f9a2e158a9737b1c | Text | 126 | 1 | The explainability of radiomic-based machine learning models for brain glioma grading on amide proton transfer-weighted images |
d365299d28e918e9cab35373abd49cae3c111d4eb3a9f03aeaaef3f6280b6d0d | Text | 127 | 1 | additional materials from Genetic diversity and regulatory features of human-specific NOTCH2NL duplications (Real et al. 2025)
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ef7671ec5ea8fb5359223e142a13be238d22fffd739b3c6e3bf958bcf2f8ecfb | Text | 129 | 2 | # VRFishController
Application to display VR fish on hemispheric surface with anamorphic perspective for ANR-VRFishchool project
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9f2b05077ce4cbb96e46e2660a191e1accd9f647bdfe16afdccf9950af9ca6c1 | Text | 131 | 2 | # Neural-Markov-Models
This repository contains code to reproduce the results found in paper "Discrete-time neural Markov models".
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a1feb984958d334ca2b14ba8c11756aca248e131e11bccca89191eb2e1534496 | Text | 131 | 2 | # X-Ovary
Analysis of effects of primary ovarian cells derived from cortex and medulla after irradiation at different time points.
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35ca4a4012566cebd700814bf141b3b9b58760bd0f96f05f6abb51be80050f5a | Text | 133 | 3 | # Brain network features predating early adolescent alcohol initiation
Code for running analyses corresponding to paper (in press).
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d31ecf6216b66426f6c3ef3b8f98f9f2994a193653a793ae1c609988ad183d07 | Text | 139 | 2 | # PCDoUCTwDL
This is the repository for storing supplementary codes for "Pancreatic Cancer Diagnosis on Unenhanced CT with Deep Learning."
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80798a7a437613ad24d8e65741834a79cfdb4dd3e95f37e70030d7349b6f3d51 | Text | 142 | 2 | Data from 9 rats, 3 per condition: Sham, PV-Activation and PV-Inhibition
Each subject's folder contains the time-course and the spike sorting |
288adf86d130d66972f64557bb5a2ca73d350db70aec1b0f7008362cd7c85b8a | Text | 144 | 3 | # Two Axes of White Matter Development
Reproducibility guide: [https://pennlinc.github.io/luo_wm_dev/](https://pennlinc.github.io/luo_wm_dev/)
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c902c0c6c69579de4d98424d77c0936bf85077c995aa069908a897fcf8a7bd85 | Text | 146 | 1 | Simulation codes shared in this repository are for investigating the dependence of T1 and T2 measurement reliability on experimental parameters.
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01721e047fbf8ce2f46a9ee18bb6ceaefbe5263b13e1eb8646d9f85910bafb92 | Text | 153 | 3 | # Beta-Shifts-Working-Memory
EEG and Behavioural Data from "Human Beta Oscillations Reflect Magnitude and Fidelity of Priority Shifts in Working Memory" |
4be2fb5b73b2aacb00a9ede532d6a775c3f1857c5354eab5b2bfb286e4dee491 | Text | 156 | 4 | # Alzheimers-olfactory-biopsy-analysis
Olfactory cleft biopsy analysis of Alzheimer's Disease pathobiology across disease stages
#GEO accession: GSE302937
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8f6985324ee4540646e426e3b3c7cf30c51208351b6a6f1337e1c46e8002f479 | Text | 157 | 2 | # PollenForecasting
Source code for the paper: Comparison of machine learning methods in forecasting and characterizing the birch and grasses pollen season.
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14cd51930785ce4a013344a28c101127c0874345be07396418a1871b393ea501 | Text | 158 | 6 | # fit_psychometric
Tutorials and functions to fit psychometric functions
[Open on colab](https://colab.research.google.com/github/jcouto/fit_psychometric)
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e622d0e2f9a1cadda2d9c0c9001493bec6259d5552afe3e3a9eef22e175af057 | Text | 158 | 3 | # BDsnRNAseq
Scripts for Nishioka et al. "Disturbances of paraventricular thalamic nucleus neurons in bipolar disorder revealed by single-nucleus analysis".
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3400748df446efa3ccd029826d0c75a909bafab429a97c5b0b5dcb2498851536 | Text | 164 | 2 | # subspace_generalization_paper_code
This directory contain analysis code for "Flexible and abstract neural representations of abstract structural knowledge" paper
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9f88613ed15e87c28d12825080da96937517a68c53280f2452db31de72de2e28 | Text | 168 | 5 | # ninai/pipeline
Processing pipeline for scans and behavioral files.
# Docker container
* [ninai/pipeline](https://hub.docker.com/r/ninai/pipeline/) `ninai/pipeline`
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85296c0ec4116077ac6e210e4e49d720d261b992f92f57c4e061bdc31a526324 | Text | 174 | 7 | Type:
java Origin "source file".txt "output file".txt N1 N2
where:
N1 - size of the first step (with no averaging)
N2 - number of points to average in the next step
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a033ef7342b4bc76676342d496ff1450a2f9530b7b35ca398e386dcbb948498d | Text | 178 | 2 | # Columbia-TMC-DLFPC_Senescence
Code repository for Sloan, Mares, Daly et al. paper, Uncovering the Signatures of Cellular Senescence in the Human Dorsolateral Prefrontal Cortex
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476d7607acbc1558a60734dec1186244866e7e0d3752e6d22af15db31be496f0 | Text | 179 | 2 | # psychomotor_timedelay
This repo contains the codes and necessary data for replicating the main findings in our article about the time delay changes among psychomotor subgroups
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664dd703c0323f36b61e2133435eb29c7cce375d74c34e52da4507edb11745df | Text | 180 | 4 | # Human Neocortical Glutamatergic Neurons Revealed Through Multimodal Profiling
## Resources
- Multichannel Igor Electrophysiology Suite - https://github.com/alleninstitute/mies
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7fcb2391e4b4ed3b889b9d426cd83ba89c67f7d2fc293257ba559d3cca604343 | Text | 184 | 3 | # ZF_ARTR_thermo
32 light-sheet microscopy recordings of spontaneous activity of the zebrafish ARTR brain region. The recordings are done for 13 fish at 5 different water temperature. |
380c1ce97c390620aab73c2f4f05df60a984defbd0b01a18ed396d5c001f48ee | Text | 185 | 3 | # Wang2026NatureCommunications
Simulation code for Wang et al. Neuronal feedback loop of the suprachiasmatic nucleus generates robust circadian rhythms. Nature Communications. DOI: XX
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4527b8336e82ddccb46e4581ce6e8a4413d2c3fdad55105b9c69d8be98bf9f20 | Text | 185 | 2 | # DECAM
This repository provides relevant code and data for our article titled "Diffusion-MRI-based Estimation of Cortical Architecture via Machine Learning (DECAM) in Primate Brains."
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452c166ec7b16578d8f2c953fd76423b8c1cf315e6fd924e107f40a4e45bada3 | Text | 189 | 2 | # MPOA_Phf6_Esr1
This repository contains all codes used to analyse the data reported in "Regulation of physical activity and energy expenditure through Phf6 in the medial preoptic area".
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e5b9b004528f482faa834bd5512d489eacfe77d90ef79fe85f1408a5614f6ed9 | Text | 191 | 3 | # BM-Pathology-Dataset
This repository contains the code accompanying the submission "Matched MRI, Segmentations, and Histopathologic Images of Brain Metastases from Primary Lung Cancer."
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084bb6b56023704ceecf799d31cabcc356fa915b6f2383d43d7df9a665795390 | Text | 198 | 2 | # Predicting-acute-pancreatitis-severity-with-multi-machine-learning-models
Predicting the acute pancreatitis severity with multi-machine learning models: constructing an online prediction platform
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3cebc04c7b949890db16447a4c84a31fca32a691c70dea165f488d5c1fccddc5 | Text | 202 | 2 | # Breast-Cancer-Component-Segmentation
High-frequency ultrasound-based mapping of intratumoral heterogeneity for predicting tumor components in breast cancer: Correlation with histopathologic findings.
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062598fd74930720a6e484be36b3da07fb938420a6e6d1e77f1bf5628a83285c | Text | 204 | 5 | # Tau-PET-Graphical-Model
Graphical Modeling of Cortical Tau Pathology Topography for its Subtyping in Alzheimer's Disease
## Getting started
See the tutorial graphical_model_tutorial.m for more details
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5fcf5a3a785f0d29e4ad37ed01dfec56ed742fe7be7f2e0000efa948ef2e3b5b | Text | 205 | 5 | Usage subject to Apache License, Version 2.0 see LICENSE file
Please use a web browser to look at doc/index.html for a guide on how to setup and run HOLE.
For help please see http://www.holeprogram.org/
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79d91a0b4c1ec244b63fd0f8b3d98b541be033b1f86e6e482764c7de4d780ddd | Text | 209 | 3 | # FovealFeedback
Includes the code to preprocess and analyse the fMRI data from the study "Feedback of peripheral saccade targets to early foveal cortex" (https://elifesciences.org/reviewed-preprints/107053)
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149f08f81d398f6d4f992f1c682a2b07717087e48b0ffbd92a6d104c1b93718d | Text | 211 | 3 | # OCTA-Volumetrics-MS-code-2025-10-BrainComms
R code used for analysis of this project: OCTA reveals insights into complementary vascular & neurodegenerative mechanisms in MS
Code uploaded is in .qmd format
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f44ad8dfdbe789ab9e7c27fe2d8f801236277b51d0b9be380b5046fa999cc5d1 | Text | 216 | 2 | # Setbp1_Alternative_Splicing_Shiny_App
Shiny App for our 2025 manuscript, Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1 S858R Schinzel-Giedion Syndrome patient variant mouse.
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b5451677506e57bf5cf917d1b2d8ca66eac4e7992e6036af5879ad165af61af2 | Text | 229 | 5 | # AD–PD Overlap Study
This repository contains the code used to process and analyze the data presented in the paper
*"Cell type transcriptomics reveal shared genetic mechanisms in Alzheimer’s and Parkinson’s disease"*.
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5df037e21cdace54392b902484917de06a2093d1176373a157fdd60f0870463b | Text | 232 | 2 | Beijing's images are collected by YiZou, one of our co-author. The images are copyrighted, and Yi Zou is the copyright holder.
The readers who are interested in Beijing's photos can contact with him.(email: zouyi3149@hotmail.com)
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a40b77e94cf644c56c7086e063144ce758cc67a62597e5388835f3112efd1a73 | Text | 239 | 7 | ## 🤖 About
> [!CAUTION]
> **This is not the official repository and it is not guaranteed to be maintained**.
> **If you want to star, please star the official one**.
>
> For the official 👉 https://github.com/adosar/retnext.
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3d5fb6a55c603097200f3be103ee43f7e3258ec02c8c083fcfbf722ddfe5faa2 | Text | 244 | 2 | The codes are provided for the manuscript "Longitudinal metabolome profiling from pregnancy through childhood and risk of neurodevelopmental disorders at age 10"
(https://github.com/user-attachments/assets/a6856c47-0a1f-4e0a-b846-c33ab4aec5ff)
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978464ce51cbbf973b4fe4a4f25338a303df1a6a7555fc0114a38c1044089dec | Text | 245 | 3 | # Accelerating CEST MRI Through Complementary Undersampling and Multi-offset Transformer Reconstruction
Rodent brain CEST images are accessible via this [link](https://drive.google.com/file/d/1zvfu4y5HKrQMx3JiUVQ9bKZe6eFZ5mA5/view?usp=sharing)
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7848f3e244fd747255d9792e96e268339c8f30f350d66981970b380e9b94fcb6 | Text | 248 | 3 | This is a git repo of my EEGlab plugin for doing Carbon-Wire regression.
It's a way to remove movement artifacts out of the EEG while doing EEG-fMRI. You measure the movements with carbon-wires and use basic regression much like in fMRI analyses.
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c2926af3eb878f61dc5c1f28780c07bd50a9b48eadc7aae15d425e4f9dd1c597 | Text | 259 | 4 | Microscopy image files.
The STED and confocal microscopy image files available through this Zenodo deposit are raw (unmodified) TIFF images. It is recommended to open them in Fiji/ImageJ as meta data related to pixel, voxel and image size are embedded.
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e534c9fe0d9ce7576e20725292e25c013350fa155ddf3eb8f51e84191a4cb7f7 | Text | 261 | 2 | This repository includes the scripts for processing, data analysis and figure generation of the single-cell data from this preprint:
"An in vivo and in vitro spatiotemporal profile of human midbrain development", Budinger D., Puigdevall P., Hall G. et al. 2025
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df2492edaa6018d367f86ef2c87d5ba88d6ff84b8e8fec247b21c4365d3eb4c1 | Text | 266 | 2 | # Connectivity-and-function-across-domains
Here is the code used for data analysis and plotting for the following manuscript: Hiersche, K. J., Saygin, Z. M., & Osher, D. E. (2025). Connectivity and function are coupled across cognitive domains throughout the brain.
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94b6c8fa39106e1ff967ef3a0e3f38e967d2ec1bf0232d35ee3d2a503f4486f5 | Text | 278 | 7 | # TransDecoder
Visit the project [wiki](https://github.com/TransDecoder/TransDecoder/wiki) for all TransDecoder documentation.
Primary entrypoint: `./TransDecoder`
Phase-specific utilities are available under `./util/TransDecoder.LongOrfs` and `./util/TransDecoder.Predict`.
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eec499592737c6779c1208e1e90503ab4751ee5834cb52dd2a071588e96052a0 | Text | 286 | 5 | I am forever indebted to Salem from cboard.cprogramming.com for his tireless
efforts and patience while helping a complete stranger debug their code. You can find the
relevant thread here: https://cboard.cprogramming.com/c-programming/172520-debugging-multi-threaded-code-openmp.html
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f248de7969e28a1a7e3dde09890097b7e1831e235ece53985cb9be0f709bd562 | Text | 295 | 9 | # CoLiM: Core–Ligand Matching for Coinage-Metal Nanoclusters
This repository will host the code and data for the paper:
> "Deep Learning Framework for Atomic-Level Design and Pre-Synthesis
Prediction of Coinage-Metal Nanoclusters" by J. Wang et al.
The code is currently being cleaned up.
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131b36c0c6864362b617341e559edfe740a9dc1a16a41536a79750625ec06e19 | Text | 297 | 9 | ### Stereoscopic depth discrimination task
#### Code for [Mitigating age-related stereo decline with perceptual training]
###### Needs: MATLAB + Psychtoolbox
###### Tasks: Signal-in-noise + fine discrimination
###### Run: Open Depth.m
###### How to cite this material: 10.5281/zenodo.18414906
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253be94046b14922656142cbac51159b2fed028e2f2dba9a581c6d46d252fc41 | Text | 301 | 5 | This repository contains the Jupyter Notebooks needed to reproduce all analyses presented in [ICLR publication](https://openreview.net/forum?id=Tqdsruwyac) and [manuscript](https://arxiv.org/abs/2409.05804).
Also refer to the method repository for [Celcomen](https://github.com/Teichlab/celcomen).
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46c87e7f4a7063045acc2224f27a4272e0639c165550517dfb62f9417f0a3843 | Text | 315 | 4 | # Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's Disease
This repository contains scripts used for data processing, analysis and visualization in this manuscript.
It is written by Matas Vitkauskas with inputs from members of Jinyue Liu's lab.
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62a9bdf42c9407066379c3dbd3db7f4201a784020d41d46ab2b22a7d70720041 | Text | 316 | 6 | Requirements:
- MATLAB 2020a (or later)
- ScanImageTiffReader https://www.mathworks.com/matlabcentral/fileexchange/69279-scanimagetiffreader
- add to "support" as folder with name "+ScanImageTiffReader"
- Wavesurfer https://wavesurfer.janelia.org/
- add to "support" as folder with name "Wavesurfer-master" |
117b4cf86df9e5b128817480a04d567c5218d67ad83dc04634d5907cba03bca9 | Text | 340 | 9 | ### scripts used for data analysis in KIF1A ASO pilot study
Procedure to estimate the number of SNPs required for covering the haplotypes of most of individuals:
1. download data from 1000 Genomes project
2. extract KIF1A region `get_SNP_data.sh`
3. run a ruby script implementing a greedy algorithm to estimate number... |
1fcf687d51cf638608a51a47e608b117e21ff2d210d3dc5089af23cb328d319f | Text | 341 | 8 | ## miyawaki2022_NatCommun
scripts for the following paper
**De novo inter-regional coactivations of preconfigured local ensembles support memory.**
Miyawaki, H., Mizuseki, K.
*Nature Communications 13*, 1272 (2022). doi: 10.1038/s41467-022-28929-x
Full text of the paper is available at https://www.nature.com/article... |
ed4716b38c2d4a006dd4e2fed5a24865b2c2ffc3fc5e1fbd63cfc677e3445e33 | Text | 346 | 5 | # Network propagation for primary ciliopathies
This repository contains the code to perform the analysis as described in doi:
In the gene_prioritization folder, a simple code file with the necessary data files can be found to run your own gene prioritization using our approach. In the code folder all the scripts for... |
5293db982f5117e430dbc65bdc7f8ee8c80fb90ad9579f9fd57d1c75e55a4db1 | Text | 347 | 7 | # Neurodegenerative_Autoantibodyome
Codes used in the original research paper "Integrative Analysis Reveals The Autoantibodyome Neuroimmune Signature of Neurodegeneration", by Usuda et al..
Preprint available at: https://papers.ssrn.com/abstract=5561403 (https://doi.org/10.2139/ssrn.5561403)
Licensed under the GNU G... |
2a9f6ce9eb09cdbfb4988135fddd39ddfa2517da83f025ba21f7f9749ff317cf | Text | 358 | 1 | The "Neural Barcode.mlappinstall" file is a MATLAB installer file for the MATLAB GUI application of the "Markovian Neural Barcode" technique for mesoscale cortical imaging analysis. There is an in-app tab that has access to the application "READ ME" file that contains all the application specific information. This appl... |
840a9245e881b1dd694f90ed9e6b3c90f2571dbf2ac9d8af9de373fca4f8a525 | Text | 362 | 7 | # MP2RAGE scripts
- T1 maps estimation using the MP2RAGE sequence
- T1 map correction using an additional B1 map
- Background noise removal by using a "robust"/regularized version of the combination of the two inversion time images
These functions can be called with BIDS-wrappers (the functions named `bids_*`) to aut... |
80cded3cfc1ef81ddf566755dfced75d69cbf88d795876ca1c0af916a6be350d | Text | 364 | 2 | # Object-Change-Detection-VR
VR Change Detection task build for "Beyond Flatland: Naturalistic Three-Dimensional Stimuli and Visual Working Memory Processing". A stereoscopic VR change detection task adaptation of the classic change detection task to investigate how stimulus dimensionality (2D vs. 3D) affects visual wo... |
14f949777659ab12ffa1659f099c8b62296b7e96ea3a222e9936f712497fcd4c | Text | 392 | 4 | ## Contribution
**Tape Analyzer** (v1.0) was developed by Yixiao Yan in the Changyang Linghu lab (University of Michigan, Ann Arbor) for signal extraction and analysis of intracellular protein tape recorders.
Citation: Zheng, L., Shi, D., Yan, Y. et al. Scalable and multiplexed recorders of gene regulation dynamics ac... |
141b4d1486d36e576cff81a7f9ce202e49f33887949269cddd117728b06e8fc6 | Text | 399 | 3 | The "Neural Barcode.mlappinstall" file is a MATLAB installer file for the MATLAB GUI application of the "Markovian Neural Barcode" technique for mesoscale cortical imaging analysis. There is an in-app tab that has access to the application "READ ME" file that contains all the application specific information. This appl... |
7babe48230cd8aa2dc47e28da0d5dab1a9cb9d22da9cff84eac5da98bfe36730 | Text | 401 | 3 | Simulations of the **Deep-STMIA** model, an E2E learning-based model for multi-user MISO BC systems with imperfect CSIT proposed in the following paper are provided in `Deep-STMIA.ipynb` and `Baselines.ipynb`.
[1] Sadeghabadi E, Blostein S. **"Unified Space-Time-Message Interference Alignment: An End-to-End Learning A... |
7bcf9c9ba22b3945fad05bef4d884e141825a8d76f5a7546a12b00a50793ef77 | Text | 405 | 7 | Code to reproduce analysis in `An in vivo and in vitro spatiotemporal atlas of human midbrain development`.
A compiled version of the Rmarkdown notebook can be viewed [here](mlo_analysis_code.md).
Run with `rmarkdown::render("mlo_analysis_code.Rmd")`.
The contents of this repository are copyright (c) 2025- Universit... |
cc8024e61c8a173761c4c43e7af59b42ffbaac6d53b3ed49373e7bc5d82b87d6 | Text | 407 | 7 | # issue_opto_npx
This Matlab code produces the analysis and figures for the manuscript:
Overcoming off-target optical stimulation-evoked cortical activity in the mouse brain in vivo
Simon Weiler, Mateo Vélez-Fort, Troy W. Margrie
https://www.biorxiv.org/content/10.1101/2024.08.14.607152v2
This Matlab code NEEDS the s... |
df55bf226912277214a4e7b1050fddcd867f5ba3ae4f5e23dec398b7e56f44fb | Text | 416 | 7 | # DestVI-reproducibility
This repository contains the code to reproduce the analyses performed in the DestVI manuscript.
The code here requires the versions of the packages specified in the requirements.txt file. We may update the API of the scvi-tools package so not all code is guaranteed to work with the latest vers... |
9bc2c5bc525ee6a8d2f595b73b686b2ce5ae42c41b7ab026fbac05c8ef3c9704 | Text | 425 | 6 | This is the repository containing data and analysis scripts for RNAseq analysis in the following publicaiton:
Malin Schmidt, Anne Hoffrichter, Mahnaz Davoudi, Sandra Horschitz, Thorsten Lau, Marcus W Meinhardt, Rainer Spanagel, Julia Ladewig, Georg Köhr, Philipp Koch (2026) Psilocin fosters neuroplasticity in iPSC-de... |
aaf0a8b85a865ba474b3184e289f6d5933a92e8be06b1a9a805ffefcaf908340 | Text | 426 | 8 | Dataset:
Full dataset (1R, 2R, 4R, 9R, 19R) of atrophy over all timesteps for one brain (OAS1_0002_MR2_atrophy_fine.zip)
Full dataset (1R, 2R, 4R, 9R, 19R) of atrophy over last timestep for 6 brains, OAS1_0002_MR1_atrophy, OAS1_0004_MR1_atrophy, OAS1_0005_MR1_atrophy, OAS1_0006_MR1_atrophy, OAS1_0007_MR1_atrophy, and... |
125c207addd2c6b60060694f78a1ce274e476f62bbf2dec8ed1d9ca5e450888a | Text | 430 | 8 | # sgce_interneuron
scRNAseq analysis of SGCE mutation positive MGE-derived interneurons published by
Li, Z., Abram, L., Cruz-Santos, M., Petter, O., & Peall, K. J. (2026).
Transcriptomic disruption and hypoactivity in DYT-SGCE medial ganglionic eminence-patterned inhibitory neurons.
Brain, 149(1), 209-225.
Av... |
a762690689fcc7ac573133880b6ab4e4a3426b483924f53c08a65adb6f43f0e8 | Text | 431 | 3 | Protein tyrosine phosphatase receptor type D - A convergent risk gene for MDD, BPD, and ADHD and regulator of dopaminergic neuroplasticity in reward associated circuits; A multivariate GWAS, brain tissue and cell type enrichment, and gene fine-mapping
This repository contains all of the core scripts used in the paper.... |
a4985af5cce0c8cc589d8bfe09b6fbaae35e9b614ca5522fafea0df552ee3624 | Text | 444 | 21 | # TurboReg_macro
macro code for advanced usage of TurboReg (ImageJ plugin)
<img src="doc/demo.gif" width="800" align="below">
## Dependencies
Fiji (https://imagej.net/Fiji)
TurboReg (http://bigwww.epfl.ch/thevenaz/turboreg/)
## Author
Takehiro Ajioka
E-mail:1790651m@stu.kobe-u.ac.jp
## Affiliation
Division of ... |
e3ed21f177701a57dc9b08fd05099bff1de5fb5037059b2236cf5899a7edcbdb | Text | 447 | 5 | Contact info: michael.heneka@uni.lu or pablo.botellalucena@uni.lu
Please cite: Inflammasome adaptor ASC promotes sustained neuroinflammation and mild cognitive impairment in a closed-head injury model (2026) - The Journal of Clinical Investigation (https://www.jci.org/articles/view/199818)
The scripts require a r... |
c7c13a3b3af7c6a8c6b610c7c770a6f37c751adced83d3c16783c7b8e5d3e9a7 | Text | 449 | 7 | ## Mouse sensorimotor cortex reflects complex kinematic details during reaching and grasping
This repository contains code to recreate the figures associated with the manuscript by Grier, Salimian and Kaufman published at eLife: https://elifesciences.org/articles/106270.
For orientation to the repository, see docs/SU... |
ac6ce2ea4d3bb84c9b3eb4ff605e332330b3ded683c10511ee9a2f8096d7e359 | Text | 451 | 7 | # Identification of Chlamydia pneumoniae and NLRP3 Inflammasome Activation in Alzheimer’s Disease Retina Linked to Disease Status
This repository contains the code used for:
1) predicting pathological measures in the brain of subjects with varying levels of Alzheimer's Disease (AD) severity using data from the retina,... |
f9ce20a132943dfc6bfe7f99b0de8c3cbafcc1ca77aa0305c9b2ff6b2a6a2df2 | Text | 458 | 3 | 2020_02_28_MasterDF_WellNumbers.csv has the samples with the sequencing run (MiSeqOSVXXX), Plate Number, Row Letter, and Column Number.
The compressed folders contain the .fastq files for each sequencing run. There are a forward and reverse file for each Plate/Row/Column combination.
The BioinformaticsProtocol contai... |
b29722fe12777bfd945591885d8868de9b6b95c17e326816ccf25c02ea067ce0 | Text | 459 | 6 | # aav_immuno_gene_therapy_for_HGG
This repository contains scripts to generate the sequencing-based analyses included in the "AAV immuno‑gene therapy platform delivering vectorized cytokines defines a new modality for high-grade glioma treatment" manuscript in Molecular Therapy Oncology. These are organized by experime... |
94cc17c1f4efec4533b4cd6ffba195a35ac403f085d41abeed29d5615637eb6f | Text | 464 | 20 | 
# SKOOTS
<img src="resources/overview.png" align="center" width="150px"/>
SKeletOn ObjecT Segmentation - 2D/3D instance segmentation of arbitrary biomedical images.
## <img src="resources/installation.png" align="center" width="150px"/>
<!-- start installation -->
To inst... |
b346c98fda03d98e1ec06704297c6283ee5c26daac91fee240521f4f0d383b32 | Text | 465 | 6 | # bilingualism_semantics
This repo contains analysis code for Chen et al., 2026 "Bilingual Language Processing Relies on Shared Semantic Representations that are Modulated by Each Language"
The data used by these scripts, and reproduced analysis are available on our [CodeOcean Code Capsule](https://codeocean.com/capsu... |
b3e471793abd24686345a1bb4d6f74a87f466acd6b8cf311e63c382ea01456b2 | Text | 468 | 11 | # ac4CRIP-seq-analysis
This repository contains the code used to perform the data analysis in the following publication:
## Reference
Zhou HQ, Zhu Z, Zhang JW, Lin WP, Jin HJY, Ding YY, Liu S, Yin DM (2026). Dynamic regulation of mRNA acetylation at synapses by spatial memory in mouse hippocampus. *eLife* 14:RP10899... |
dbac310d53f034975425e50843b27dd9fe655982b5f35c7473f892eabdfa2e3a | Text | 469 | 8 | # QoLPredictionWithML
[Predicting health-related quality of life two years post-diagnosis across seven cancer types: using machine learning to identify vulnerable patients](https://doi.org/10.1007/s11136-026-04165-4)
The following scripts are included:
* create_figures_for_manuscript.R: code to create the figures for... |
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