lieberinstitute/visium_spg_ad issues and pull requests

#85 - difference between raw-data/10x_files/Lieber_Transfer and Lieber_Transfer_10x_Alignments

Issue - State: closed - Opened by JiawenChenn 11 months ago - 1 comment

#84 - Use full gene set in Samui apps

Issue - State: closed - Opened by Nick-Eagles over 1 year ago - 3 comments

#83 - Update deconvolution plots

Issue - State: closed - Opened by lcolladotor over 1 year ago

#82 - Spot deconvolution using Mathys et al as the reference

Issue - State: closed - Opened by lcolladotor over 1 year ago - 1 comment

#81 - Twitter thread describing the pre-print

Issue - State: closed - Opened by lcolladotor almost 2 years ago - 1 comment

#80 - Samui

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 4 comments
Labels: Manuscript

#79 - Dropping data about (N&P)GFAP, (N&P)Lipofuscin, and (N&P)MAP2 from SpatialLIBD

Issue - State: closed - Opened by shkwon17 almost 2 years ago
Labels: SpatialLIBD

#78 - Determining average DAPI+ nuclei per spot

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 1 comment
Labels: Manuscript

#77 - Methods Writing with Sowmya

Issue - State: closed - Opened by shkwon17 almost 2 years ago
Labels: Manuscript2

#76 - Methods Writing with Leo

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 1 comment
Labels: Manuscript2

#76 - Methods Writing with Leo

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 1 comment
Labels: Manuscript2

#75 - Confirm with Sowmya

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 8 comments
Labels: Manuscript

#74 - Confirm with Leo

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 1 comment
Labels: Manuscript

#73 - GO-BP and KEGG analyses

Issue - State: closed - Opened by shkwon17 almost 2 years ago - 2 comments
Labels: Manuscript

#72 - Volcano plots to better visualize DGE results (Fig.2)

Issue - State: closed - Opened by shkwon17 over 2 years ago
Labels: Manuscript

#71 - Morabito et al 2021

Issue - State: closed - Opened by lcolladotor over 2 years ago
Labels: External gene sets

#70 - Leung et al 2021

Issue - State: closed - Opened by lcolladotor over 2 years ago
Labels: External gene sets

#69 - Grubman et al 2019

Issue - State: closed - Opened by lcolladotor over 2 years ago - 2 comments
Labels: External gene sets

#68 - Mathys et al 2019

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment
Labels: External gene sets

#67 - Raj et al 2018

Issue - State: closed - Opened by lcolladotor over 2 years ago
Labels: External gene sets

#66 - Mostafavi et al 2018

Issue - State: closed - Opened by lcolladotor over 2 years ago
Labels: External gene sets

#65 - Update labels

Issue - State: closed - Opened by lcolladotor over 2 years ago - 3 comments

#64 - Check in more detail RPN2 in TGE

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#63 - Check FDR thresholds for the enrichment t-stats

Issue - State: closed - Opened by lcolladotor over 2 years ago

#62 - Are there publications with targeted sequencing panels?

Issue - State: closed - Opened by lcolladotor over 2 years ago - 2 comments

#61 - How many of the targeted genes pass filterByExpr()?

Issue - State: closed - Opened by lcolladotor over 2 years ago

#60 - Fix `low_expr` confusing names

Issue - State: closed - Opened by lcolladotor over 2 years ago

#59 - Percent of reads assigned to targeted genes vs others

Issue - State: closed - Opened by lcolladotor over 2 years ago

#58 - re-make pseudobulked objects

Issue - State: closed - Opened by abspangler13 over 2 years ago - 2 comments

#57 - Update authors_biorxiv.tsv

Issue - State: closed - Opened by lcolladotor over 2 years ago

#56 - Create Zenodo DOI

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#55 - Document internal directories

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#54 - Create Globus endpoint

Issue - State: closed - Opened by lcolladotor over 2 years ago

#53 - Prepare to share files through spatialLIBD / ExperimentHub

Issue - State: closed - Opened by lcolladotor over 2 years ago

#52 - Create iSEE app for the pseudo-bulk data

Issue - State: closed - Opened by lcolladotor over 2 years ago - 3 comments

#51 - Create shiny app documentation files

Issue - State: closed - Opened by lcolladotor over 2 years ago - 5 comments
Labels: SpatialLIBD

#50 - Compare pathology spots (7 categories) vs bayespace k = 28 in a heatmap

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#49 - Compare pathology t-stats between wholegenome and targeted

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#48 - Gene grid plot(s)

Issue - State: closed - Opened by lcolladotor over 2 years ago - 2 comments

#47 - Low number of reads + distance to edge QC supp figures

Issue - State: closed - Opened by lcolladotor over 2 years ago - 4 comments

#46 - Drop AF noise

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#45 - Locating WM using the controls

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#44 - Figure 2: add boxplots

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#43 - Update pre and post harmony UMAP plots

Issue - State: closed - Opened by lcolladotor over 2 years ago - 2 comments

#42 - Update alignment metrics plots comparing Visium IF vs Visium

Issue - State: closed - Opened by lcolladotor over 2 years ago - 1 comment

#41 - Improve thresholding plots

Issue - State: closed - Opened by lcolladotor over 2 years ago

#40 - Improve resolution of spotspotcheck screenshots

Issue - State: closed - Opened by lcolladotor over 2 years ago

#39 - Lipofuscin supp fig

Issue - State: closed - Opened by lcolladotor over 2 years ago

#38 - [GM only] MAGMA analysis

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 3 comments

#37 - [GM only] Update shiny app

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#36 - [GM only] Modeling results

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#35 - [GM only] Explore gene expression variability

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#34 - [GM only] Create pseudo-bulked data

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#33 - Summarize pathology across cases/controls samples

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#32 - Perform spatial registration of BayesSpace clusters

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#31 - Make the pathology exploration easier to reproduce

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#30 - Re-generate some objects and plots with the updated segmentation data

Issue - State: closed - Opened by lcolladotor almost 3 years ago

#29 - Use fasthplus to try to choose a k for BayesSpace

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 2 comments

#28 - Heatmaps of DLPFC layer marker genes across BayesSpace clusters

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 3 comments

#27 - Create stacked barplots for percentage of spots. vs. clusters for all clusters

Issue - State: closed - Opened by sparthib almost 3 years ago - 1 comment

#26 - Choose dynamic thresholds for pathologies

Issue - State: closed - Opened by sparthib almost 3 years ago - 1 comment

#25 - Determine levels of pathogenicity

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 1 comment

#24 - Determine best k for the BayesSpace results

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 1 comment

#23 - Explore BayesSpace k results: are they related to pathology?

Issue - State: closed - Opened by lcolladotor almost 3 years ago - 1 comment

#22 - Drop low library size edge spots

Issue - State: closed - Opened by lcolladotor about 3 years ago

#21 - Manually label "glare" spots

Issue - State: closed - Opened by lcolladotor about 3 years ago - 2 comments

#20 - Check spaceranger input images

Issue - State: closed - Opened by lcolladotor about 3 years ago - 4 comments

#19 - Select colors and directions for segmented data plots

Issue - State: closed - Opened by lcolladotor about 3 years ago - 4 comments

#18 - Images for shiny app

Issue - State: closed - Opened by lcolladotor over 3 years ago - 13 comments

#17 - Run spaceranger with targeted sequencing data

Issue - State: closed - Opened by lcolladotor over 3 years ago

#16 - Create list of AD related genes

Issue - State: closed - Opened by lcolladotor over 3 years ago - 2 comments
Labels: External gene sets

#15 - Assess layer-specificity of the targeted sequencing gene list

Issue - State: closed - Opened by lcolladotor over 3 years ago - 1 comment

#14 - DLPFC data driven marker genes

Issue - State: closed - Opened by lcolladotor over 3 years ago - 2 comments

#13 - Perform Loupe alignments

Issue - State: closed - Opened by lcolladotor over 3 years ago - 9 comments

#12 - Perform DE analyses using pseudo-bulked data

Issue - State: closed - Opened by lcolladotor over 3 years ago - 2 comments

#11 - Pseudo-bulk and perform QC

Issue - State: closed - Opened by lcolladotor over 3 years ago - 5 comments

#10 - Fig 1 spot plots

Issue - State: closed - Opened by lcolladotor over 3 years ago - 2 comments

#9 - Find DLPFC layers

Issue - State: closed - Opened by lcolladotor over 3 years ago - 5 comments

#8 - Perform initial QC on the SPE object

Issue - State: closed - Opened by lcolladotor over 3 years ago - 4 comments

#7 - Create initial SpatialExperiment R object

Issue - State: closed - Opened by lcolladotor over 3 years ago - 2 comments

GitHub / lieberinstitute/visium_spg_ad issues and pull requests