Published May 8, 2024
| Version v1
Software
Open
Supplementary data and code for Gupta and Heinrichs et al. 2024
Creators
- 1. University of California Los Angeles David Geffen School of Medicine
- 2. UCLA Geffen School of Medicine
Description
Code and R data files for publication: "Investigating the basis of lineage decisions and developmental trajectories in the dorsal spinal cord through pseudotime analyses" Development, 2024.
RDS are processed data files
- subRA.rds is just RA protocol
- generated in object creation - individual datasets.R
- subBMP.rds is just BMP protocol
- generated in object creation - individual datasets.R
- with pseudotime updated.rds is RA and BMP combined with pseudotime analysis added
- generated in Data loading and integration.R and then monocle.R and then analyzed mainly in object analysis.R but also in other files
- briscoe.sub.intergrated is dataset from delile et al
- generated in briscoe analysis.R
- integration with our dataset.R is briscoe dataset and our two datasets combined with further analysis in knn UMAP analysis.R
- each shiny data rds file goes with its respective app.R file
- these rds files have more genes than could be uploaded to the online shiny app
Relevant citations for code available in linked publication
Files
Files
(4.1 GB)
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md5:5dbee8717bad41991cd01126c4c9c8a1
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md5:b174d09912719f163331d94fabfe86c9
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md5:1aec43a5d48c60399a850f9827f44e8a
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md5:cb7cbe0037848e7d3d43a25acfc684d8
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md5:d784422fcd215f453552bc00802d5bba
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md5:844c6116b90f2f837be599aefe514190
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md5:a55e0c206374572c07d96ec232bfeaa7
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md5:5b8275aacb46a504ba18ac1fce5ca14f
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744 Bytes | Download |
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md5:4a5179533ec549a1959d15425b01bfc6
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md5:1a003b0a9497160836dcfa95d8cbfef7
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md5:aa4f357b0a8471ad5a4afaf1d77702a3
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md5:99ba903686a2029801334e9fbe840b8e
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md5:acab6c10d7cc5e472e584748f8198b00
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2.5 kB | Download |
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md5:fce08eceddd5070c4deea87e3cb1caa8
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52.4 MB | Download |
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md5:88ab346b0db8d3bf9e16415d62a24507
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5.0 kB | Download |
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md5:e677a256ee2496fd7ad7fc74bcdcbb3b
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371.4 MB | Download |
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md5:e9c1a9d32403ba984e31583203306b28
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311.2 MB | Download |
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md5:36b555f1b6b5d3a85c73c8edb6c5235d
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6.1 kB | Download |
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md5:db3b3d7968e519a7c52a9eca415c89b4
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1.2 GB | Download |
Additional details
Related works
- Is supplement to
- Publication: 10.1242/dev.202209 (DOI)