LieberInstitute/Visium_SPG_AD

Issues

• difference between raw-data/10x_files/Lieber_Transfer and Lieber_Transfer_10x_Alignments

  #85 opened 8 months ago by JiawenChenn
  0

• Use full gene set in Samui apps

  #84 opened a year ago by Nick-Eagles
  2

• Update deconvolution plots

  #83 opened a year ago by lcolladotor
  0

• Spot deconvolution using Mathys et al as the reference

  #82 opened a year ago by lcolladotor
  1

• Samui

  #80 opened 2 years ago by shkwon17
  4

• Twitter thread describing the pre-print

  #81 opened 2 years ago by lcolladotor
  1

• Document internal directories

  #55 opened 2 years ago by lcolladotor
  1

• Methods Writing with Sowmya

  #77 opened 2 years ago by shkwon17
  0

• Methods Writing with Leo

  #76 opened 2 years ago by shkwon17
  1

• Create shiny app documentation files

  #51 opened 2 years ago by lcolladotor
  5

• GO-BP and KEGG analyses

  #73 opened 2 years ago by shkwon17
  2

• Confirm with Leo

  #74 opened 2 years ago by shkwon17
  1

• Confirm with Sowmya

  #75 opened 2 years ago by shkwon17
  8

• Dropping data about (N&P)GFAP, (N&P)Lipofuscin, and (N&P)MAP2 from SpatialLIBD

  #79 opened 2 years ago by shkwon17
  0

• Grubman et al 2019

  #69 opened 2 years ago by lcolladotor
  2

• Create Zenodo DOI

  #56 opened 2 years ago by lcolladotor
  1

• Create Globus endpoint

  #54 opened 2 years ago by lcolladotor
  0

• Prepare to share files through spatialLIBD / ExperimentHub

  #53 opened 2 years ago by lcolladotor
  0

• Low number of reads + distance to edge QC supp figures

  #47 opened 2 years ago by lcolladotor
  4

• Check FDR thresholds for the enrichment t-stats

  #63 opened 2 years ago by lcolladotor
  0

• Compare pathology spots (7 categories) vs bayespace k = 28 in a heatmap

  #50 opened 2 years ago by lcolladotor
  1

• Update authors_biorxiv.tsv

  #57 opened 2 years ago by lcolladotor
  0

• Update pre and post harmony UMAP plots

  #43 opened 2 years ago by lcolladotor
  2

• Figure 2: add boxplots

  #44 opened 2 years ago by lcolladotor
  1

• Gene grid plot(s)

  #48 opened 2 years ago by lcolladotor
  2

• Locating WM using the controls

  #45 opened 2 years ago by lcolladotor
  1

• Compare pathology t-stats between wholegenome and targeted

  #49 opened 2 years ago by lcolladotor
  1

• Update alignment metrics plots comparing Visium IF vs Visium

  #42 opened 2 years ago by lcolladotor
  1

• Drop AF noise

  #46 opened 2 years ago by lcolladotor
  1

• Are there publications with targeted sequencing panels?

  #62 opened 2 years ago by lcolladotor
  2

• Check in more detail RPN2 in TGE

  #64 opened 2 years ago by lcolladotor
  1

• Morabito et al 2021

  #71 opened 2 years ago by lcolladotor
  0

• Mathys et al 2019

  #68 opened 2 years ago by lcolladotor
  1

• Leung et al 2021

  #70 opened 2 years ago by lcolladotor
  0

• Determining average DAPI+ nuclei per spot

  #78 opened 2 years ago by shkwon17
  1

• Volcano plots to better visualize DGE results (Fig.2)

  #72 opened 2 years ago by shkwon17
  0

• [GM only] MAGMA analysis

  #38 opened 2 years ago by lcolladotor
  3

• Raj et al 2018

  #67 opened 2 years ago by lcolladotor
  0

• Mostafavi et al 2018

  #66 opened 2 years ago by lcolladotor
  0

• Improve resolution of spotspotcheck screenshots

  #40 opened 2 years ago by lcolladotor
  0

• Lipofuscin supp fig

  #39 opened 2 years ago by lcolladotor
  0

• Create iSEE app for the pseudo-bulk data

  #52 opened 2 years ago by lcolladotor
  3

• Fix `low_expr` confusing names

  #60 opened 2 years ago by lcolladotor
  0

• How many of the targeted genes pass filterByExpr()?

  #61 opened 2 years ago by lcolladotor
  0

• Update labels

  #65 opened 2 years ago by lcolladotor
  3

• Improve thresholding plots

  #41 opened 2 years ago by lcolladotor
  0

• Percent of reads assigned to targeted genes vs others

  #59 opened 2 years ago by lcolladotor
  0

• re-make pseudobulked objects

  #58 opened 3 years ago by abspangler13
  2

• [GM only] Update shiny app

  #37 opened 3 years ago by lcolladotor
  0

• [GM only] Modeling results

  #36 opened 3 years ago by lcolladotor
  0