LieberInstitute/spatialDLPFC

Issues

• Where can I get the full size H&E images?

  #146 opened 4 months ago by amssljc
  5

• Spot deconvolution

  #147 opened 2 months ago by tkcaccia
  2

• Download of Histology Image of Visium(n=30) data

  #145 opened 3 months ago by Weiqin-Zhao
  2

• manual annotation

  #143 opened 7 months ago by JiawenChenn
  2

• Update Samui Browser & VistoSeg citations

  #144 opened 7 months ago by lcolladotor
  0

• Region white-matter enrichment trends

  #125 opened 2 years ago by lcolladotor
  7

• Provide anndata files out of the box

  #142 opened 2 years ago by chaichontat
  1

• Supplementary Table Export

  #141 opened 2 years ago by lahuuki
  10

• Add tissue imperfections to R object + spatialLIBD app

  #137 opened 2 years ago by lcolladotor
  9

• Add Melissa' & Prashanthi's code to this repo

  #139 opened 2 years ago by lcolladotor
  8

• Extract new clinical gene sets from the literature

  #113 opened 2 years ago by kmaynard12
  6

• Supp fig: spatial location of manually annotated tissue imperfections

  #138 opened 2 years ago by lcolladotor
  2

• Explore _position_ enrichment results

  #140 opened 2 years ago by lcolladotor
  6

• Update Visium and Visium IF shiny apps with deconvolution results

  #98 opened 2 years ago by lcolladotor
  8

• Density and/or proportion changes for each cell type across region

  #126 opened 2 years ago by lcolladotor
  2

• Make SPOTlight results reproducible + use all input snRNA-seq data

  #136 opened 2 years ago by lcolladotor
  1

• Region differential expression without white matter

  #124 opened 2 years ago by abspangler13
  0

• Cell-cell communication of Visium data

  #130 opened 2 years ago by boyiguo1
  3

• Test cell type composition acrosss anterior, mid, posterior

  #131 opened 2 years ago by boyiguo1
  4

• MAGMA clinical enrichment analysis

  #101 opened 2 years ago by lcolladotor
  3

• Fix Spatial Plot Dimensions

  #135 opened 2 years ago by lahuuki
  1

• Compare spot-deconvolution vs IF cell counts

  #99 opened 2 years ago by lcolladotor
  6

• spatial registration of snRNAseq data

  #117 opened 2 years ago by abspangler13
  2

• New Figure 3

  #123 opened 2 years ago by abspangler13
  8

• Deconvolution: Visium data

  #129 opened 2 years ago by lcolladotor
  1

• Figure 3 enrichment heatmap

  #115 opened 2 years ago by abspangler13
  2

• Gene ontology

  #118 opened 2 years ago by abspangler13
  5

• snRNA Cell-cell Communication Results

  #132 opened 2 years ago by boyiguo1
  3

• Inconsistent naming convention for Brain positions in the raw cluster results

  #133 opened 2 years ago by boyiguo1
  4

• spatially variable genes (svgs)

  #119 opened 2 years ago by abspangler13
  5

• spatial registration of psychENCODE Data

  #122 opened 2 years ago by abspangler13
  3

• Deconvolution: Visium IF data

  #128 opened 2 years ago by lcolladotor
  1

• Spot deconvolution: cell2location option

  #97 opened 2 years ago by lcolladotor
  1

• Explore deconvolution marker genes (mean ratio)

  #127 opened 2 years ago by lcolladotor
  0

• Update PCA plots for the region analysis

  #120 opened 2 years ago by lcolladotor
  1

• Updates and fixes to k = 9 and k = 16 shiny apps

  #114 opened 2 years ago by abspangler13
  0

• Figure 3 other summary plots

  #116 opened 2 years ago by abspangler13
  0

• sfigu_harmony

  #107 opened 2 years ago by kmaynard12
  0

• sfigu_k=2_hist

  #108 opened 2 years ago by kmaynard12
  0

• sfigu_Bayespace

  #109 opened 2 years ago by kmaynard12
  0

• Replicate clinical enrichment results

  #111 opened 2 years ago by lcolladotor
  2

• make k = 16 shiny app for Kristen

  #110 opened 2 years ago by abspangler13
  1

• Process psychENCODE datasets

  #100 opened 2 years ago by lcolladotor
  10

• Figure_2 Polish

  #103 opened 2 years ago by kmaynard12
  2

• Fig 2 Cluster registration schematic

  #104 opened 2 years ago by kmaynard12
  0

• sfigu_marker_genes

  #106 opened 2 years ago by kmaynard12
  0

• Demographic Table

  #105 opened 2 years ago by kmaynard12
  2

• spatial registration of psychE

  #121 opened 2 years ago by abspangler13
  0

• Merge github history from snRNA-seq processing into this repo

  #112 opened 2 years ago by lcolladotor
  2

• re-make pseudobulked objects

  #102 opened 3 years ago by abspangler13
  0