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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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difference between raw-data/10x_files/Lieber_Transfer and Lieber_Transfer_10x_Alignments
#85
JiawenChenn
opened
4 months ago
0
Use full gene set in Samui apps
#84
Nick-Eagles
opened
11 months ago
2
Update deconvolution plots
#83
lcolladotor
closed
11 months ago
0
Spot deconvolution using Mathys et al as the reference
#82
lcolladotor
closed
11 months ago
1
Twitter thread describing the pre-print
#81
lcolladotor
closed
1 year ago
1
Samui
#80
shkwon17
closed
1 year ago
4
Dropping data about (N&P)GFAP, (N&P)Lipofuscin, and (N&P)MAP2 from SpatialLIBD
#79
shkwon17
closed
1 year ago
0
Determining average DAPI+ nuclei per spot
#78
shkwon17
closed
1 year ago
1
Methods Writing with Sowmya
#77
shkwon17
closed
1 year ago
0
Methods Writing with Leo
#76
shkwon17
closed
1 year ago
1
Confirm with Sowmya
#75
shkwon17
closed
1 year ago
8
Confirm with Leo
#74
shkwon17
closed
1 year ago
1
GO-BP and KEGG analyses
#73
shkwon17
closed
1 year ago
2
Volcano plots to better visualize DGE results (Fig.2)
#72
shkwon17
closed
1 year ago
0
Morabito et al 2021
#71
lcolladotor
closed
1 year ago
0
Leung et al 2021
#70
lcolladotor
closed
1 year ago
0
Grubman et al 2019
#69
lcolladotor
closed
1 year ago
2
Mathys et al 2019
#68
lcolladotor
closed
1 year ago
1
Raj et al 2018
#67
lcolladotor
closed
1 year ago
0
Mostafavi et al 2018
#66
lcolladotor
closed
1 year ago
0
Update labels
#65
lcolladotor
closed
1 year ago
3
Check in more detail RPN2 in TGE
#64
lcolladotor
closed
1 year ago
1
Check FDR thresholds for the enrichment t-stats
#63
lcolladotor
closed
1 year ago
0
Are there publications with targeted sequencing panels?
#62
lcolladotor
closed
1 year ago
2
How many of the targeted genes pass filterByExpr()?
#61
lcolladotor
closed
1 year ago
0
Fix `low_expr` confusing names
#60
lcolladotor
closed
1 year ago
0
Percent of reads assigned to targeted genes vs others
#59
lcolladotor
closed
1 year ago
0
re-make pseudobulked objects
#58
abspangler13
closed
2 years ago
2
Update authors_biorxiv.tsv
#57
lcolladotor
closed
1 year ago
0
Create Zenodo DOI
#56
lcolladotor
closed
1 year ago
1
Document internal directories
#55
lcolladotor
closed
1 year ago
1
Create Globus endpoint
#54
lcolladotor
closed
1 year ago
0
Prepare to share files through spatialLIBD / ExperimentHub
#53
lcolladotor
closed
1 year ago
0
Create iSEE app for the pseudo-bulk data
#52
lcolladotor
closed
1 year ago
3
Create shiny app documentation files
#51
lcolladotor
closed
1 year ago
5
Compare pathology spots (7 categories) vs bayespace k = 28 in a heatmap
#50
lcolladotor
closed
1 year ago
1
Compare pathology t-stats between wholegenome and targeted
#49
lcolladotor
closed
1 year ago
1
Gene grid plot(s)
#48
lcolladotor
closed
1 year ago
2
Low number of reads + distance to edge QC supp figures
#47
lcolladotor
closed
1 year ago
4
Drop AF noise
#46
lcolladotor
closed
1 year ago
1
Locating WM using the controls
#45
lcolladotor
closed
1 year ago
1
Figure 2: add boxplots
#44
lcolladotor
closed
1 year ago
1
Update pre and post harmony UMAP plots
#43
lcolladotor
closed
1 year ago
2
Update alignment metrics plots comparing Visium IF vs Visium
#42
lcolladotor
closed
1 year ago
1
Improve thresholding plots
#41
lcolladotor
closed
1 year ago
0
Improve resolution of spotspotcheck screenshots
#40
lcolladotor
closed
1 year ago
0
Lipofuscin supp fig
#39
lcolladotor
closed
1 year ago
0
[GM only] MAGMA analysis
#38
lcolladotor
closed
1 year ago
3
[GM only] Update shiny app
#37
lcolladotor
closed
2 years ago
0
[GM only] Modeling results
#36
lcolladotor
closed
2 years ago
0
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