sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
45d0477f4e36be623746c2a699333bf93451961490a0d69742ecd395d32fee51 | Text | 92 | 2 | # publ_graf_samiee_2024
Code related to Graf, Samiee, Flossmann, Holthoff and Kirmse (2024)
|
ffb25d9776c031a6eb41ad7461a91d154787319354acfc9c4c3fdc817730e2d1 | Text | 98 | 2 | # Southern_flounder_transcriptomics
Data for transcriptomic data processing for Southern Flounder
|
9d7372c2de08dbb60922c809019c4e6ea42effd11ea6b59c4ea00fef48989b55 | Text | 104 | 1 | Figure generation code for [Gillett & Brunel, 2023](https://elifesciences.org/reviewed-preprints/88805)
|
9787d169f0602402ce9948008f8eec2743002ca540a55fa304fa9b2328a1d44e | Text | 109 | 3 | # neuropower
Neuropower is a package used for power analysis and sample size calculations for neuroimaging.
|
864f66c8467d27c5b4e419e2763f8066a8a9afc49eff5fa91a1e68c153f39608 | Text | 116 | 2 | # McGrath2022_CP_analysis
Script used to analyze phalloidin labeling in the cuticular plates of auditory hair cells
|
209215668e8c1120efff5dcbdb2444055bd3034afab47151d824e09997cd72fc | Text | 118 | 3 | # bio_image_colorblindness
Evaluation of the use of colorblind-unfriendly images in biology-related journal articles
|
be3abc25cda3965dacb392e52f7b2371ad80f6187576eaba4aed16740e6baad2 | Text | 118 | 2 | # UR10-Detection
Detection dataset meant to train a YOLOv5-based object detector for the Universal Robots UR10 cobot.
|
431ca87b1922ecc4f20b92b4411f13944771f1bdcde2eb819e881886c8b6cb8d | Text | 121 | 3 | # Chandel_DeBeaubien_2023
Code used in Chandel and DeBeaubien et al. (2023)
An example can be found in the Demo folder.
|
36caf0eb77a2839c0e35dfe17bf02ae36af4b3132417d994fbc9250bbc872d47 | Text | 122 | 2 | # Patient-derived-Glioma-Cell-Lines
Multi-omics and Pharmacological Characterization of Patient-derived Glioma Cell Lines
|
ab59a4487e67e75efbe27cb36bc0e281269d650c9902f956db011270a7f0922f | Text | 122 | 2 | # aedes
AEDES is a graphic user interface (GUI) based tool for region of interest (ROI) analysis of (mainly) MRI images
|
ce16654a7355f32720d9375a0c6e87048ad005d94388fb017ac45fe5e1bdc1c4 | Text | 124 | 4 | ## About THUMS
The corresponding documentation is available at [THUMS official website](
https://www.toyota.co.jp/thums/).
|
85444d7780b609c582ab560b55eb14a86fa0a22d6625fe36ad942a7aa7ae29d5 | Text | 125 | 1 | # Code for the eLife paper - [https://elifesciences.org/reviewed-preprints/89911](https://elifesciences.org/articles/89911)
|
6defeea30d6503482a9f2304133c55e27b70088a2c00aa51cf36ca95488201e1 | Text | 127 | 1 | The Internet behavior datasets of "Anomaly prediction of Internet behavior based on Generative Adversarial Networks (APIBGAN)"
|
eee5f4c619ba060d63e6a9c5ac03a1f0d5079d1ae5fb8c9a0fdca283e980cd1a | Text | 127 | 2 | # EphysAnalysisCode-Helen
Analysis code for electrophysiology data. Pairs with EphysCode-Helen, which is used for acquisition.
|
ef8ad1f258d78967c5a8a2ba366f722b8f3d6256cfb340dc3f0281c2622fa23b | Text | 127 | 3 | # Computational-imaging-for-rapid-detection-of-grade-I-cerebral-small-vessel-disease-cSVD-
- Files will be added in few days.
|
8c980d9dff2cf177d80203842bd40290796d97c6dcc09260e45d4f07fe9641e7 | Text | 133 | 1 | The instructions to reproduce the paper's model simulations, data visualization and data analysis are found in the Jupyter notebook.
|
3a1390ab34936f5727450ba331302fd867aba135b139e13f3fce56a5722dc312 | Text | 134 | 7 | # mirna-disease-association-detection
## NER
Check folder src/nerex for code
## Relation extraction
Check folder src/relex for code
|
bcbf271429d7343b58676365d6cc0e31897f8c42bedca4387f0c2a1d2e86e34d | Text | 138 | 2 | # EgocentricVertexVectorCell
Codes and sample data of "Egocentric neural representation of geometric vertex in the retrosplenial cortex".
|
de4700bc6780c8fd86a8de71b4bd24db826b92313a07e0656c92dbd1a7a54531 | Text | 147 | 3 | # dynRet
Use run_prmodel.py to see how to build a photoreceptor-CNN model
Use run_acnn_model.py to see how to build and adaptive-convolution model
|
549b00be98d12bab6354206ab1cebe39f4c59ecde6c192728a1609e7f102707f | Text | 154 | 2 | # lmgs
MATLAB add-on to SPM software for fMRI detrending with "Linear Model of the Global Signal" (LMGS) method. This is described in a Neuroimage paper.
|
31af0c2388c61523d9fe2a47b84b167f096eeb334f31885e5393790fd0fdac1d | Text | 156 | 2 | # SpontaneousPain_Code
The code for paper "A distinct neuronal ensemble of prelimbic cortex mediates spontaneous pain in rats with peripheral inflammation"
|
152c98414f16a54c312792fdc4739311b0e78291ea603149e41e682dd03d3e94 | Text | 159 | 2 | # DevMLEV
The Project ID : jimaging-3158907 shown source code of Development of a machine learning model for the classification of Enterobius vermicularis egg
|
43179dffe1bd656dd1540d39d580bf97d9996226ec6898279b3e52815b420a14 | Text | 162 | 1 | Code accompanying https://osf.io/sjvnw/ and https://openneuro.org/datasets/ds004636 to create event files from raw behavioral outputs and to evaluate MRIQC IQMs.
|
0c381fd53fec3579beccdc195413faa262f0d756343f070752260bfff6bd2b18 | Text | 166 | 2 | # eeg-fmri-tle
Tools and connectome data for comparing EEG and fMRI connectivity in healthy controls and temporal lobe epilepsy patients [Wirsich et al. MedRxiv 2022] |
2bcd66057dd7a8754aee0e546466c94e557ff147e7e150eec0aa7be9685727e5 | Text | 166 | 4 | # B03
Respository for analysis and code in the context of the SFB1158 B03 project.
Here I publish code, that belongs to certain published or to be published papers.
|
c9e6dc4f097b469daaebc43c0cec590d6f11b95cadf885d34e83ade2bad5e740 | Text | 166 | 3 | # predictRBD
This folder contains the code for the paper:
"Machine Learning Predicts Phenoconversion from Polysomnography in Isolated REM Sleep Behavior Disorder".
|
e5b0e46b6fd23f114b062ad25a902fce7b971f3232fe3b79fa09a21be62ab3db | Text | 171 | 5 | # playfulsong
R Script and associated data used to run all analyses in the Playful Song Manuscript.
See inline documentation in `playfulsong_script.R` for more details.
|
ff146e72e619f970fa651dc7275baea40dbaddca4ccd2ac0a209e3ecf8ef14ee | Text | 172 | 1 | Accompanying repository to the publication "Evolution of phenotypic plasticity leads to tumor heterogeneity with implications for therapy" DOI: 10.1371/journal.pcbi.1012003 |
5d646c9539242ccc524945edcde768c32d714dde639d8fdfe400153eaaa2ca32 | Text | 173 | 3 | # Slow_Wave_Sleep
Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain |
609a17802279cfd4c06ef98bf5e8a6031d1dffe2048d7a21dcb143512cb399e2 | Text | 175 | 4 | # IDIF
Code for creating a image-derived input function.
Requires a label mask of the entire aorta and a dynamic PET series from which the input function should be extracted
|
7f4fffbfba4134885ccd326889f01576b755d5bae9918fde3f1f972172849c8f | Text | 178 | 7 | # CVAE_VAE
funtions.py describes data preprocessing steps
cvae_vae.py contains two models call CVAE and VAE
S2.py - S7.py, each .py file is descrbes different analysis steps.
|
701f1a2f1973d5fe49abf64c42c59884e18bed8e4f7e6d179e6f1c13e4f35db8 | Text | 179 | 3 | # two_context
Code used to generate select figures in "Distinct neural mechanisms for heading retrieval and context recognition in the hippocampus during spatial reorientation"
|
d50b7a83155874944c0ad4fa40763759c1fedddb33799478b4f8899274c6e29e | Text | 182 | 1 | Data for the sorted spikes is in sorted_spikes folder and used in the representative task-modulated data figures as well as for computing the average waveforms and ISI histograms.
|
a63f5702b94f8763e45eefd45cc705695798ab10c6cda2a059189118db637aa9 | Text | 184 | 3 | # Human-RA-Gastruloid
This repository includes code for analyzing the time-course scRNA-seq of human gastruloids and human RA gastruloids and in silico staging of gastruloid samples.
|
6fa26bb9b664cf20be95bf6e8d13e2c7444f964eccdec453d4b27f647e8063c8 | Text | 190 | 4 | # publ_graf_samiee_2024
Code related to Graf, Samiee, Flossmann, Holthoff and Kirmse (2024)
[](https://zenodo.org/doi/10.5281/zenodo.13767662)
|
eb83c0423cf0c39b3c5ce922ae9a88a6e6cfb9b708eb63b4c4e7b2a17db771bc | Text | 190 | 3 | # WhiteMatterDisconnection_PLOS
# Author-generated code to accompany the publication "White matter disconnection impacts proprioception post-stroke", Chilvers et al, submitted to PLOS ONE.
|
89e3d4d45ae4373f655b6667f483fb4b3197a891a9432aa7b306c4775f2cb34e | Text | 194 | 1 | ## These are the custom scripts (in jupyternotebook) for the INSCRIBE data processing and analysis, including SAILOR and FLARE config parameters, motif distance analysis and figure generation.
|
a17d73347577b1253f7c5e8f405ea449d1d8732dc413b85cb21a3433e2cfd375 | Text | 195 | 3 | # auditory-masking-stimuli
This repository contains the auditory masking stimuli used in 'Auditory confounds can drive online effects of transcranial ultrasonic stimulation in humans' (eLife).
|
8771c84fbc0b5ebe11799bd1fa84a9419835890442a046bb2566a853087723f2 | Text | 201 | 5 | # Brain Imaging Connectivity Extraction Program Solution
BICEPS installation directions are given in [INSTALL](./INSTALL.md).
See [README.m](./README/README.m) for instructions on how to use BICEPS.
|
013a4ae9565be2fc187116ef88c6a0256d531904456a934a1cf9686b3c86785d | Text | 203 | 3 | # pharmacological-perturbations
PerturbationsProjections.ipynb contains all the code to generate the figures. The folders Results/ and receptors/ must be filled with data in 10.6084/m9.figshare.26728804 |
5671e5674caed2bf9cbf3d5a1ff9479dc981f92f6d16236db2e354f40a643a58 | Text | 209 | 5 | System requirements:
Software: python=3.7 and windows
Hardware: .hamamatsu&meadowlark SLM and FILR camera
All the code is listed in the order of the figures in the main text and supplementary information. |
56cfd71ed2c380df1ac064a5384d3e14c3c9073066910d56b8af70c562b4ce65 | Text | 212 | 4 | # IntDegSeg
A repository for the article Integrative, Segregative, and Degenerate Harmonics of the Structural Connectome
For main text results, run each of the scripts `FigX_` to reproduce all primary analyses.
|
ab07a98647c8c85f374c2dc91e1346176233c4f5f7185d36db7e0333393946f0 | Text | 213 | 3 | # BrainIronWES
The code used in the paper Gong et al. "Whole-Exome Sequencing Identifies Protein-Coding Variants Associated with Brain Iron in 30,620 Individuals" under revision in Nature Human Behaviour (2024).
|
e30e280949144513ba0efd40004658fc0fea806b08420aee1242657c6460626c | Text | 216 | 2 | # PropTweet
Propaganda Detection using various classifiers, In this repository various Machine Learning and State of Art techniques are used for identifying propaganda on social network, especially the Twitter Data.
|
4d4f9bef15c50199fa09c66925c310c26955db7762fafa131c54919a12ba8a93 | Text | 219 | 3 | # eeg-fmri-tle
Tools and connectome data for comparing EEG and fMRI connectivity in healthy controls and temporal lobe epilepsy patients [Wirsich et al. 2024, NetworkNeuorscience,
https://doi.org/10.1162/netn_a_00362]
|
3712fcbea18525a920b9506c8ae9d51b163adb5008c8db7478f3bb40aca77a64 | Text | 225 | 3 | The database contains recordings of bees and drones in wav format, without compression. The sampling frequency is 44.1kHz.
The database contains 10000 one-second recordings of bees and 1700 one-second recordings of drones. |
f8dcbdeb3e19fabf48e0632fa31b5f0792021039ea0f58d6731c4e9ad91bdefb | Text | 226 | 2 | # Patient-derived-Glioma-Cell-Lines
Wu, M., Wang, T., Ji, N. et al. Multi-omics and pharmacological characterization of patient-derived glioma cell lines. Nat Commun 15, 6740 (2024). https://doi.org/10.1038/s41467-024-51214-y
|
fc0ff664b80d2f60e5b29f557e38fec05dce7118f5910628fa70015f97b2b0b9 | Text | 234 | 4 | # procgcn
This is the code of ProcGCN: Detecting Malicious Processes in Memory Based on DGCNN.<br />
This work implemented with torch_geometric. The data.7z contains the serialized FCG dateset, which can be read with "pickle".<br />
|
d6e17cfae9c7358957d6b472c87b758c397f9b65210bcd25b068fa58f21aec15 | Text | 236 | 7 | # Spectrin-topological-transition
Run Full_simulation.m for the control case.
The code to generate each plot is provided.
This code corresponds to the preprint: https://www.biorxiv.org/content/10.1101/2023.01.02.522381v1.abstract
|
87ef744a0ec43cbc38748eec393dd0037dec55f9f932a9303e3edd33c46670f6 | Text | 238 | 3 | # Neural network analysis of pharyngeal sounds in brachycephalic dogs
Code and data to support the research article "Neural network analysis of pharyngeal sounds can detect obstructive upper respiratory disease in brachycephalic dogs".
|
bff65a0221a001e427a494bcc2e50198496536b8d83bdae71f7be691e74c2af2 | Text | 239 | 1 | Transcript features: It contains Excel files with information regarding the coding potential identification of each transcript used to annotate genes as protein-coding, genes of unknown coding potential (GUCP), and long non-coding RNAs.
|
dabe42b3acc9ab2ea286f29a24ec56aee386b07cd61dc92d1f2e95ca581f2f9b | Text | 239 | 3 | This repository accompanies Read et al "Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart".
For questions, please contact corresponding author Cole Trapnell at coletrap@uw.edu
|
12a6d04f4c5aa4e7880bc9f61bcf143cdc6a0ce5e3bebe25a2bde2586e58bebd | Text | 243 | 2 | The package are MATLAB scripts, please run MATLAB software first, then change the folder to the scripts on your computer.
Then run run.m file you can get the figure for analysis of deltaF/F for fluorescent signal acquired by fiber photometry. |
ead2c24687f3c917124ee0e195e2dbe0456f15689a1189433dbdbcc59fd5aa89 | Text | 250 | 3 | # AAV-library
This R-script collection enables identification of fragments and barcodes and allows for barcode quantification
It utilizes knowledge on the surrounding sequenceto extract the barcode ad requires bbmap, Starcode and Bowtie2 to function
|
dbb30fcc8e50cf52a810d34f5c486868209a89f7408b3f076a06c35744d6e6a5 | Text | 251 | 3 | # Neurovascular Coupling with VASO
In this repository, we are collecting resources for a project on neurovascular coupling using high resolution cerebral blood volume (CBV) and blood oxygen level dependent (BOLD) measurements acquired by SS SI VASO.
|
1cbd6a8fbd069e601658698b265fc35ff5389acd144858b794fdb364db7bfe4f | Text | 258 | 12 | ## plot_fig_subcortex
---
3D Visualization of the brain subcortical regions in `Matlab`.
Basic usage:
```matlab
plot_fig_subcortex(file_path, output_plot_path, colormap, min_scale, max_scale, structure_label);
```
This project has already been used in:
|
2c2edf4c65647ad1d42daa6a8edacaab3fa25846c57b20b327d3bd8376c22250 | Text | 267 | 8 | # MRI-Substructures
MRI analysis using FSL in MATLAB: relationship between substructures and alpha modulation
First segments substructures automatically from the structural T1 MRI.
Second calculates substructures' sizes.
Then compares the sizes in right and left.
|
4f50cde38b0e93e190ffec8ac421bca50a794403a11d7cecc4f3463570fc10e8 | Text | 269 | 22 | # Tasks
EEG tasks commonly used by the Child Development Lab
Below is a list of citations you can use when referencing these tasks in manuscripts and/or presentations
Baseline/Resting-state (RS):
Mismatched Negativity (MMN):
Zoo (GNG):
Arrow (Flanker):
|
81b40ff8b635bde8be0112c78b7b5da1cca06938dd774c212a77872785fa7662 | Text | 270 | 3 | # Analysis code for "Identifying images in the biology literature that are problematic for people with a color-vision deficiency"
[This paper](https://elifesciences.org/reviewed-preprints/95524) describes the research study associated with the code in this repository.
|
50c8817fef0187c773dc23f786dab0f459da999a530ea04cf13408f0e04683b3 | Text | 271 | 7 | # vanBeest_iScience2024
Code used for vanBeest et al., iScience2024
DOI: 10.1016/j.isci.2024.110753
Please note that each subfolder contains requirements.
Example data is available at 10.5281/zenodo.13235302. Please contact ennyvanbeest@gmail.com for more information
|
6aaaad3fb5d4a98bd86b34fbaabd7dcc1dd25fbcd2620f81b002be54dc1783ee | Text | 275 | 4 | # BCS
# Welcome to the BCS repository!
# Here you will find the datasets and the code used in the computation and validation of the BCS.
# Note that python v 3.8, umap.learn v 0.5.1, numba v 0.53.1, and pickle v 0.7.5 are needed to open the BCS and project your data in it.
|
8cd6c46e8e0b34d16f6d5218cdf74b4d22ea6d526b62d4eebc0634220559987b | Text | 277 | 4 | This is an old version of the BiasAway tool. The newest CLI version is
available on `bitbucket <https://bitbucket.org/CBGR/biasaway/>`_ and the
web-interface at http://biasaway.uio.no. Documentation can be found at
`readthedoncs <https://biasaway.readthedocs.io/en/latest/>`_.
|
18e848d88c8b15cd8715400a28847f189c50887a6835045db85f9915c03c9496 | Text | 279 | 4 | ============================================================================
MGL (Matlab GL): A suite of mex/m files for displaying psychophysics stimuli.
SEE http://justingardner.net/mgl for more info
============================================================================
|
7d84c2c6ae53075699e99ec81899daa8f533605ec4b9401034ba24a998b61fb5 | Text | 281 | 6 | Scripts for Interpolation after DREDge
by Richard Hardstone and William Munoz
Dependecies:
- DREDge code per Windolf & Varol: https://github.com/evarol/dredge
- Kilosort 2.5: https://github.com/MouseLand/Kilosort/releases/tag/v2.5 (Remember to compile for GPU: \CUDA\mexGPUall.m)
|
e1d095ac5ec4bfadd1a524ddc5b4cc57abd4957bfbcb44ba5cb7b922a37cb063 | Text | 292 | 6 | # auditory-masking-stimuli
This repository contains the auditory masking stimuli used in 'Auditory confounds can drive online effects of transcranial ultrasonic stimulation in humans' (eLife).
[](https://zenodo.org/badge/latestdoi/693736471)
|
be864f02efd30d07524ecf32be0924568e63f48e8f0f187a700d92e9e77a76c8 | Text | 295 | 8 | The Matlab bead normalization tool is no longer actively supported.
We recommend using https://github.com/ParkerICI/premessa instead.
-------------------
Bead-based normalization of mass cytometry data
For more information, see the [wiki](https://github.com/nolanlab/bead-normalization/wiki)
|
429d19930e9d923d525b139e779d2c198b4f6868303f46ef219814d25709f336 | Text | 320 | 12 | Requirements
numpy == 1.26.1
torch == 2.0.1
torch-geometric == 2.4.0
torch-scatter == 2.1.2
torch-sparse == 0.6.18
dgl == 1.1.2
networkx == 2.8.8
scikit-learn == 1.1.2
TO RUN:
execute train.py
|
e3b2c21c3984af3ed7315a4f2c96d340fd86ec13055fc78f2206eb3d96201c1c | Text | 320 | 7 | # Facet V4.0.3
Software for reconstructing maps of visual acuity from insect eyes
The binary is downloadable under 'Releases'.
This version runs under the latest versions of MacOS. Tested on MacOS Monterey (12.1), Catalina (10.15.7) and Big Sur (11.4) using a Macbook pro (Intel) with an 8 core i9 and 6 core i7 CPU.
|
dc72700c8ad5a471547735c95c12a9960ef6db0c27640587b9c8c754bd9e76d6 | Text | 324 | 6 | # long-rna-seq-pipeline
STAR based ENCODE Long RNA-Seq processing pipeline
This pipeline has been deprecated in favor of https://github.com/ENCODE-DCC/rna-seq-pipeline.
It does have code for running RAMPAGE/CAGE experiments at DNA Nexus using https://github.com/nboley/rampage_pipeline if that is what you are looking ... |
35726b69067519f7c63686e691419d199491aef12e4cb0a328e98e917a3f3d29 | Text | 325 | 6 | # CTC
Matlab code for paper on attention and CTC: scope and limitations.
Please see the referring paper for details about how this code was
used for simulations of a mechanism to increase phase coherence in
the gamma range in simulated cortical areas by adding phase-matched
alpha oscillations from simulated pulvinar ar... |
90b88b43337e75cc51c281d040cdf51e8a9bd91cbf32c5d11111a51eaadf9c86 | Text | 329 | 6 | # The-mechanics-of-correlated-variability-in-segregated-cortical-excitatory-subnetworks
The respository provides Jupyter notebooks that reproduce the main figures in:
A Negron, MP Getz, G Handy, B Doiron, The mechanics of correlated variability in
segregated cortical excitatory subnetworks. Proc. Natl. Acad. Sci. (i... |
ca8e9bc67dbe860c0f8c492f3bedb527debd62b3979a4af439d66aaec09638cb | Text | 330 | 11 | Welcome to vtkplotlib!
====================================
Our homepage and quickstart page is hosted on [readthedocs](https://vtkplotlib.readthedocs.io/en/latest/index.html).
Our github page can be found [here](https://github.com/bwoodsend/vtkplotlib).
Releases are hosted on [PyPi](https://pypi.org/project/vtkpl... |
f31dfc350d3cc56d7fd3820574d8d0219284aa2e43f28c1ea2665fa4ee4838ea | Text | 330 | 5 | # RobotSDF
This is the code for the paper: RobotSDF: Implicit Morphology Modeling for the Robotic Arm
##
By setting the config parameter in reconstruct.py and running the reconstruct.py script, you can reconstruct the robotic arm model for any configuration. The reconstructed models are saved in the reconstruct_mesh d... |
470a93e67c18f54a2513c56aa607fde249ab6113091cef68529b338aff3f482c | Text | 331 | 2 | # Utashiro et al. Nat. Commun, 2024
This repository includes Python scripts and notebooks used to analyze data and generate figures for the manuscript from Utashiro, N. and colleagues, titled 'Long-range inhibition from prelimbic to cingulate areas of the medial prefrontal cortex enhances network activity and response ... |
d7f2d114e3e9d4b00a9cf125e267a8602ba1a922f9bacf872b65008ece0f7fb7 | Text | 334 | 3 | This is a classifier generated with the Janelia Automatic Animal Behavior Annotator (JAABA) to classify rolling as a drosophila larval behavior pattern (Kabra et al., 2013; Ohyama et al., 2015).
Combining this classifier with the scripts mentioned in cited articles, each time frame per larva will be classified as rol... |
73028d5b5c9f373589ffd1b776fc2d4b41ec5f16ff09c33c0b013263f56da9f9 | Text | 335 | 6 | # NatureNeuro_2024_proteomics
Sample R code from Nature Neuroscience paper on CSF proteomics and Alzheimer's disease pathology.
Reference: Pichet Binette et al. Proteomic changes in Alzheimer disease associated with progressive Aβ plaque and tau tangle pathologies. Nat Neurosci (2024). https://doi.org/10.1038/s41593... |
c369e62ddbf3fbd9d455884540a6a2e3867b58b15ad418a05209f2883271e1b4 | Text | 335 | 7 | ### AD multi-region analysis code
Code repository for single-cell atlas of Alzheimer's disease progression across brain regions
*Portal* for browsing data and processed data: https://compbio.mit.edu/ad_multiregion/
*Raw data* on Synapse: https://www.synapse.org/#!Synapse:syn52293442
*Contact:* cboix at mit-edu, mathy... |
2b6806b9b2124b41702157813d44b350c304ff0ac927db51dba505296b3a8c2b | Text | 340 | 4 | # cp2k-apt-extension
Electric field simulations with NNP and APT (atomic polar tensor) extension.
Uploaded is the src code for cp2k and a directory called APT_python_extension containing the python, input and run scripts necessary to use the APT extension. You will need the APT repo too (https://github.com/pschienbein... |
5fa664610633565448274359593cf7f110492a55085c912bf7df306c6f2103ac | Text | 343 | 4 | packages: seurat v4, ArchR 1.0.0, dplyr 1.1.4, tidyr 1.3.1, stringr 1.5.1
install in R < 1 hr wall time
sample bams are avaialable in gene expression omnibus
run commands in clusters_shendure_proj_geneintegration.R for expected output of RNA integrations, peak-to-gene links, and plotBrowserTrack() plots from ArchR pack... |
6c551f32fd5f9090093e5d1cb15d0e2aa71cfc09420728c226a27b0ce715ac7b | Text | 345 | 8 | # RunDisc
This is a hardware + software solution for the encoding and decoding of disc / wheel rotation
See wiki page for build and operation details (https://github.com/LurLab-UCI/RunDisc/wiki).
Created by Mikko Oijala and Gyorgy Lur, PhD; Neuronal Signal Integration laboratory, UC Irvine;
This work was supported b... |
aab5565793ae32db1d51baba69800eb6ca2385e0f0743ddfec1bc412400de21c | Text | 352 | 5 | # Ube3a RNA-seq
This repository has all of the analysis code to accompany the RNA-seq analyses that go along with **Montani et al., Sex-biasing influence of autism-associated Ube3a over-expression at connectomics, behavioral and transcriptomic levels.**
Analysis code is contained in `analysis_final.Rmd`, `utils_final... |
15bbac26438b74949a2eaddc953a0eea3866f2d8da24dfdf374d9375f01a3de3 | Text | 368 | 5 | # Daniel-GranadosF-et.-al.-2024
Raw data and analysis scripts used for Daniel-Granados etal 2024
Python scripts folder contains:
- PixAR2.0 main, script used for circadian pixel analysis of movies, it calculates period, phase, amplitude, with corresponding maps as well as sync index, etc.
- Neuron tracker, similar sc... |
0805bc7dbee573c61d1b3846cb13aa692ccb52cd57fe9f70956584e94eb5bd68 | Text | 370 | 8 | # Why prepare?
This repository contains code to run simulations and analyses corresponding to the paper "When and why does motor preparation arise in recurrent neural network models of motor control?" (Schimel et al., 2023, eLife).
# Dependencies
- Owl/Owl-ode/Owl-opt
- Cmadargs : https://github.com/hennequin-lab/cm... |
9eaf9b0d616dca4ec6d72048b6e4b8fec87d505d2c93d49806b4982fad4233d1 | Text | 383 | 8 | # BANDA Resources
This repository contains:
1. ScanningProtocols: Details of BANDA scanning protocols and when they changed
2. NDAsubmission: Scripts used to convert Redcap to NDA data dictionaries and to calculate composite scores
3. Documents: The latest (BANDAv1.1) data release documentation
4. Citations: referenc... |
cdbc61b91993b67930abc2a0533e9456feb1d6bd4b546a199612479e7a942416 | Text | 392 | 7 | # SeqPHASE
https://eeg-ebe.github.io/SeqPHASE/
Code of the haxe re-implementation of the SeqPHASE program. For more information, see the corresponding paper
Flot (2010) SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments Molecular Ecology Ressources 10 (1): 162-166 [[here]... |
a65ff4f603b213413dd97d9c3c24a6abd6f39aded0ac83ee5e91e5ed6c27df79 | Text | 395 | 6 | # Datasets and Model Predictions for "Scalable Spatiotemporal Prediction with Bayesian Neural Fields".
This repository contains the evaluation datasets (datasets.zip) and model
predictions (results.zip) that appear in the research article Scalable
Spatiotemporal Prediction with Bayesian Neural Fields (Saad et al., 202... |
8f9a3f82ca8b4fe50b6f2f77f266392608ff69bb384dcef928a017c80dbe6fa5 | Text | 396 | 7 | # pharmacological-perturbations
PerturbationsProjections.ipynb contains all the code to generate the figures. The folders Results/ and receptors/ must be filled with data in 10.6084/m9.figshare.26728804
To run the codes create conda environment for Keras and Neuromaps separetly.
conda create --name <env> --file requ... |
e2e14dd7d512258eaf05666333e6a68e8f13ba5c1f80ca58b80832b54e409c94 | Text | 409 | 11 | # Data and Code for "The Adjoint Is All You Need: Characterizing Barren Plateaus in Quantum Ansätze"
## Setup
Note that we tested our code using Python 3.9. Although other Python versions may also work, it is not guaranteed to be so.
### Directory for Output
A directory named `figures` must be created before execut... |
5daf4e85ca8acf8bb704fe13daa8655b757ce102ec920211237b249fdc638916 | Text | 412 | 3 | # Code for "Assessing Time Series Correlation Significance: A Parametric Approach with Application to Physiological Signals"
This code is used to produce the experiments in [Medrano, Johan et al. “Assessing Time Series Correlation Significance: A Parametric Approach with Application to Physiological Signals.” (2024)... |
3930dd2d5b5b0f9def335f6a4e415d8e43987983cb6d966c654abefd50ef1d94 | Text | 425 | 6 | # Graceffo_et_al_2024_IJMS
This repository contains the R code used to run the analyses and generate plots of both bulk and single-cell RNA-seq datasets of the publication "RNA-sequencing reveals predominance of THRA splicing isoform 2 in developing and adult human brain".\
\
The files have been named according to the ... |
99540587b096a5fc5944e956c21fe7d4bf7098de7e9acd6504f7405f36de1514 | Text | 428 | 5 | # "Sex-dependent, lateralized engagement of anterior insular cortex inputs to the dorsolateral striatum in binge alcohol drinking"
## Haggerty & Atwood, 2024
Data and Code for the generation of the Figures in "Sex-dependent, lateralized engagement of anterior insular cortex inputs to the dorsolateral striatum in bing... |
eee972ce6f314a669525bb7bcb0bbe29037c2d876ed5a1423917279ac500688f | Text | 429 | 7 | # Neocortical-Size-and-Microcephaly
This is the link related to Transcriptional Control of Neocortical Size and Microcephaly submission.
All the processed DATA is uploaded on: [OneDrive Link](https://livejohnshopkins-my.sharepoint.com/:f:/g/personal/yxu95_jh_edu/EvB_CIgYmyJAmfuYPgJ6sFUBq6BU0olGjGhArqof712wdA).
The m... |
6c4370cb95f35135c3639d7e9afdeb14da2403dc2831223c6db81a228d4d161e | Text | 432 | 18 | # Code for "Whole nervous system expression of glutamate receptors reveals distinct receptor roles in sensorimotor circuits"
This repository hosts the codes for the paper *Whole nervous system expression
of glutamate receptors reveals distinct receptor roles in sensorimotor
circuits*.
## Software
Unity 2021.3.40f1
... |
4c600415425daec390a1018614bf84a53290b5e47e2bf24a6823d0d320b819fc | Text | 456 | 4 | # ZIV
* This repository contains code for the paper: Estimating the Total Variance Explained by Whole-Brain Imaging for Zero-inflated
* To start please install conda and create the environment using the following code: conda env create -f environment.yml. This evironment is setup for M1 or M2 Mac OS. For other OS, plea... |
1bbfdedd21bf63e74acfa37948ede53a784b1b1237d9716f418eff3cfd355a62 | Text | 457 | 5 | Welcome to the GDYlabcode wiki!
In this space, we are sharing code developed and used by our lab with the goal of making our discoveries publicly available. Please cite our relevant papers if you use this code for your work. This space is under development. Please feel free to reach out to us or open an issue if you h... |
ddbbb36c11aabe629c7281b84309e838d280c8a30849f76dc148f496ae2136e4 | Text | 458 | 10 | # Wearable Data Embedding
An unsupervised learning framework for embedding multi-channel timeseries data.
The approach is demonstrated in main.py through comments and modular imports.
The primary contribution is the data scrambling technique that is used to fabricate labels for unsupervised CNN training.
Demonstrati... |
2be6e3b5b34d9a0c1a9207f9aaf2a0fa45f72295d3caf63c6ae5e04ef7ed0eb9 | Text | 460 | 11 | # Multi Scale 1D ResNet
This is a variation of our [CSI-Net](https://github.com/geekfeiw/CSI-Net), but it is a super light-weighted classification network for time serial data with 1D convolutional operation, where 1D kernels sweep along with the *time* axis. The multi scale setting is in... |
24bb04d01ee0571e6e4912db5444be503311896cf527be06f954b5ce10f24ce7 | Text | 474 | 9 | # In situ genome sequencing processing
Processing and feature extraction pipeline for In situ genome sequencing resolves DNA sequence and structure in intact biological samples (Payne, Chiang, Reginato et al.).
- Python scripts are implemented in Python 3.7.
- MATLAB scripts require >=2019b
- Contributors: A. Payne, ... |
8a83950fc788a56f9b587ec4d674952a59cbe52d3f632803ee1138d485c5696f | Text | 484 | 4 | # Lindsey-Issa-Factorization
<a href="https://github.com/hchau630/nn-analysis"> Link to analysis code</a> for computing factorization/invariance/dimensionality of image representations in a population feature space accompanying this publication:
<p align="center"><b><a href="https://elifesciences.org/reviewed-preprint... |
81ec9911091e642f998e05d688e674c1c1fc9604b32175b9253c033d2ebb226e | Text | 488 | 6 | # fof-visually-guided
A repository for code associated with our behaviour and recordings in the visually-guided orienting task.
Li, L., Flesch, T., Ma, C., Li, J., Chen, Y., Chen, H.-T., & Erlich, J. C. (2024). Encoding of 2D self-centered plans and world-centered positions in the rat frontal orienting field. The Jour... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.