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Visium_SPG_AD
Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.
https://research.libd.org/Visium_SPG_AD
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[GM only] Explore gene expression variability
#35
lcolladotor
closed
2 years ago
0
[GM only] Create pseudo-bulked data
#34
lcolladotor
closed
2 years ago
0
Summarize pathology across cases/controls samples
#33
lcolladotor
closed
2 years ago
0
Perform spatial registration of BayesSpace clusters
#32
lcolladotor
closed
2 years ago
0
Make the pathology exploration easier to reproduce
#31
lcolladotor
closed
2 years ago
0
Re-generate some objects and plots with the updated segmentation data
#30
lcolladotor
closed
2 years ago
0
Use fasthplus to try to choose a k for BayesSpace
#29
lcolladotor
closed
1 year ago
2
Heatmaps of DLPFC layer marker genes across BayesSpace clusters
#28
lcolladotor
closed
2 years ago
3
Create stacked barplots for percentage of spots. vs. clusters for all clusters
#27
sparthib
closed
2 years ago
1
Choose dynamic thresholds for pathologies
#26
sparthib
closed
2 years ago
1
Determine levels of pathogenicity
#25
lcolladotor
closed
2 years ago
1
Determine best k for the BayesSpace results
#24
lcolladotor
closed
2 years ago
1
Explore BayesSpace k results: are they related to pathology?
#23
lcolladotor
closed
2 years ago
1
Drop low library size edge spots
#22
lcolladotor
closed
2 years ago
0
Manually label "glare" spots
#21
lcolladotor
closed
2 years ago
2
Check spaceranger input images
#20
lcolladotor
closed
3 years ago
4
Select colors and directions for segmented data plots
#19
lcolladotor
closed
3 years ago
4
Images for shiny app
#18
lcolladotor
closed
2 years ago
13
Run spaceranger with targeted sequencing data
#17
lcolladotor
closed
3 years ago
0
Create list of AD related genes
#16
lcolladotor
closed
2 years ago
2
Assess layer-specificity of the targeted sequencing gene list
#15
lcolladotor
closed
1 year ago
1
DLPFC data driven marker genes
#14
lcolladotor
closed
2 years ago
2
Perform Loupe alignments
#13
lcolladotor
closed
3 years ago
9
Perform DE analyses using pseudo-bulked data
#12
lcolladotor
closed
2 years ago
2
Pseudo-bulk and perform QC
#11
lcolladotor
closed
2 years ago
5
Fig 1 spot plots
#10
lcolladotor
closed
2 years ago
2
Find DLPFC layers
#9
lcolladotor
closed
2 years ago
5
Perform initial QC on the SPE object
#8
lcolladotor
closed
2 years ago
4
Create initial SpatialExperiment R object
#7
lcolladotor
closed
2 years ago
2
Update spotspotcheck to accept multichannel image and produce final table for all channels
#6
lcolladotor
closed
3 years ago
7
Segment cells, plaques and tangles with dotdotdot
#5
lcolladotor
closed
3 years ago
3
Run spaceranger with new images from Maddy et al
#4
lcolladotor
closed
3 years ago
8
Generate individual capture area images
#3
lcolladotor
closed
3 years ago
10
Run initial image processing
#2
lcolladotor
closed
3 years ago
7
Extract FASTQs
#1
lcolladotor
closed
3 years ago
1
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