osmnx
seurat
| osmnx | seurat | |
|---|---|---|
| 14 | 13 | |
| 4,671 | 2,125 | |
| - | 1.9% | |
| 9.5 | 9.6 | |
| 6 days ago | 26 days ago | |
| Python | R | |
| MIT License | GNU General Public License v3.0 or later |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
osmnx
- I played with a python module called OSMnx to create the roadmaps of some cities. These include major highways,motorways,roads and streets that carry most of the traffic.
- Planning a straight line across Norwich, the best route I could find just scraped a silver.
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Anyone here familiar with GeoPandas in Python? Can GeoPandas calculate driving distances and drive time?
You want osmnx
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[OC] Neighborhood walkability in Delhi
OSM road network data was analyzed using osmnx (https://github.com/gboeing/osmnx). Plotted using QGIS.
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Rate Limit Causing Pause
I think you’re hitting this issue right now: https://github.com/gboeing/osmnx/issues/832
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Video: Why Open Data Matters for Cycling: Visualizing a Cycling City
RDS-TMC transmits traffic data over FM radio. https://en.wikipedia.org/wiki/Traffic_message_channel Some is encrypted, some not.
It might be possible to model traffic with OSMnx to assign weights to roads by expected traffic levels https://github.com/gboeing/osmnx
Depending on where you live you might be able to get traffic data and maybe traffic models from public authorities using Freedom of Information requests.
- I just want things to work
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Number of Public Transport Stations & Doctors in each city in Germany
Osmnx might also be a way to download data for the whole country. It breaks the area up in smaller parts automatically and also downloads the parts from Overpass. https://github.com/gboeing/osmnx
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Tacoma!
You can make your own with a variety of tools, but I like the results from OSMnx offhand.
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Need to get a national (US) file of cycleways.
I have no idea if this works for such large regions, but https://geoffboeing.com/publications/osmnx-complex-street-networks/ is an awesome tool to visualize street (and maybe bike) networks.
seurat
- Help with spatial transcriptomic analysis
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Seurat installation issues on macbook (for RNA-seq analysis)
So there is an issue with the ModularityOptimizer? I looked it up and it comes from this script: https://github.com/satijalab/seurat/blob/master/src/RModularityOptimizer.cpp
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Does Seurat provide any advantage for UMAPs over other packages (e.g. uwot)?
With regards to using selected features for UMAP, my gut tells me it's possible, but it looks like the folks here were having some issues getting it work. Your mileage may vary.
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Weird Phishing attempt on GitHub
The strangest thing is that I'm not even a follower of this repo where the discussion was started, which by the way is a R toolkit for single cell genomics.
- I feel like nobody knows anything about what they're doing (including me) and it's making me think twice about working in bioinformatics. Is it a bioinformatics problem or is it a lab problem?
- Use of Seurat integrated assay
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Extract Log-Normalised Data From a Seurat Object
There is a good wiki of the Seurat data object and information about the slots and objects can be found here: https://github.com/satijalab/seurat/wiki
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Reference request: single cell RNA seq papers where cells originate from multiple individuals where the individual of origin was explicitly accounted for in the model?
Here is link number 1 - Previous text "1"
- Seurat
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Is there a way to obtain the raw source codes of Seurat functions?
Wow, it's not easy to find, indeed. They should do a better job commenting the code, and documenting the code organisation. But it's all in the Github repo, for example NormalizeData is defined here: https://github.com/satijalab/seurat/blob/4e868fcde49dc0a3df47f94f5fb54a421bfdf7bc/R/generics.R#L337
What are some alternatives?
BlenderGIS - Blender addons to make the bridge between Blender and geographic data
scvi-tools - Deep probabilistic analysis of single-cell and spatial omics data
pyosmium - Python bindings for libosmium
pagoda2 - R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
overpass-wizard - :dizzy: Human friendly way to generate Overpass API queries
frontends-team-compass - A repository for team interaction, syncing, and handling meeting notes across the JupyterLab ecosystem.
pytorch_geometric_temporal - PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models (CIKM 2021)
future - :rocket: R package: future: Unified Parallel and Distributed Processing in R for Everyone
atlas - OSM in memory
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
qgis-outdoor-map - QGIS project for an outdoor map based on OpenStreetMap data.
MAST - Tools and methods for analysis of single cell assay data in R