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LieberInstitute
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spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
http://research.libd.org/spatialDLPFC/
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Spot deconvolution: cell2location option
#97
lcolladotor
closed
2 years ago
1
Spot deconvolution: Tangram option
#96
lcolladotor
closed
2 years ago
1
Visium cell counts: cellpose option
#95
lcolladotor
closed
2 years ago
2
Visium IF cell counts: HALO option
#94
lcolladotor
closed
2 years ago
1
Visium IF cell counts: cellpose option
#93
lcolladotor
closed
2 years ago
5
Explore if VistoSeg parameters reduce some high cell count numbers
#92
lcolladotor
closed
2 years ago
1
Explore VistoSeg cell counts
#91
lcolladotor
closed
2 years ago
0
Explore feasibility of using SingleR with the snRNA-seq data
#90
lcolladotor
closed
2 years ago
1
Spot deconvolution: SPOTlight option
#89
lcolladotor
closed
2 years ago
3
snRNA-seq issues
#88
lcolladotor
closed
2 years ago
3
Relocate spot-deconvolution files and code to this repo
#87
lcolladotor
closed
2 years ago
4
Relocate snRNA-seq files to this repo
#86
lcolladotor
closed
2 years ago
4
Create Zenodo DOI
#85
lcolladotor
closed
1 year ago
0
Document internal directories
#84
lcolladotor
closed
1 year ago
10
Create Globus endpoint
#83
lcolladotor
closed
2 years ago
3
Let's consider making a new ExperimentHub package for the snRNA-seq LIBD data
#82
lcolladotor
closed
1 year ago
3
Make an iSEE::iSEE() app for the snRNA-seq data
#81
lcolladotor
closed
1 year ago
8
Prepare and eventually deploy iSEE shiny apps
#80
lcolladotor
closed
2 years ago
6
Prepare external data to show for spatial registration and clinical enrichment
#79
lcolladotor
closed
1 year ago
1
Optimize files for the shiny app
#78
lcolladotor
closed
2 years ago
0
Add pseudo-bulked data to the shiny app
#77
lcolladotor
closed
2 years ago
0
Prepare to share files through spatialLIBD / ExperimentHub
#76
lcolladotor
closed
1 year ago
4
Create shiny app documentation files
#75
lcolladotor
closed
1 year ago
8
sfigur_BayesSpace_k28_vs_k9
#74
lcolladotor
closed
2 years ago
1
sfigur_BayesSpace_k9
#73
lcolladotor
closed
2 years ago
0
sfigur_fasthplus
#72
lcolladotor
closed
2 years ago
0
sfigur_ari_pilot
#71
lcolladotor
closed
2 years ago
0
sfigur_harmony
#70
lcolladotor
closed
2 years ago
0
sfigur_low_library_size
#69
lcolladotor
closed
2 years ago
0
sfigu_known_markers
#68
lcolladotor
closed
2 years ago
1
figur_clusters
#67
lcolladotor
closed
2 years ago
3
Drop _2 from sample_id
#66
lcolladotor
closed
2 years ago
0
figur_overview
#65
lcolladotor
closed
2 years ago
0
differential expression between layers
#64
abspangler13
closed
2 years ago
0
differential expression analysis between regions of dlpfc
#63
abspangler13
closed
2 years ago
0
Exploratory analysis using PCs
#62
abspangler13
closed
2 years ago
0
make pseudobulked objects for DE analysis
#61
abspangler13
closed
2 years ago
0
Used Segmented to find fasthplus plateau point
#60
abspangler13
closed
2 years ago
0
Plot enriched genes in different clusters
#59
abspangler13
closed
2 years ago
1
Investigate "bad" clusters of spots from spatial registration
#58
abspangler13
closed
2 years ago
0
Adapt code to perform spatial registration as array job for all values of k
#57
abspangler13
closed
2 years ago
0
Run spaceranger for the IF samples
#56
lcolladotor
closed
2 years ago
2
silhouette for evaluating bayesSpace cluster
#55
abspangler13
closed
2 years ago
0
perform spatial registration
#54
abspangler13
closed
2 years ago
0
Re-make ARI plot for spaGCN
#53
abspangler13
closed
2 years ago
1
semi-supervised across samples w/ batch correction
#52
abspangler13
closed
2 years ago
0
Add spot cell counts to spe
#51
abspangler13
closed
2 years ago
0
Version control VistoSeg code for this project
#50
lcolladotor
closed
2 years ago
0
Copy the cell counts for all samples except the 2 problematic ones
#49
lcolladotor
closed
2 years ago
0
Re-run VistoSeg on the 2 problematic samples
#48
lcolladotor
closed
2 years ago
3
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