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navinlabcode

2 indexed repositories · View on GitHub

CellTrek

R · 135 stars
tnbc-chemo
Ecotypes of Triple-Negative Breast Cancer in Response to Chemotherapy

R · 15 stars

Beginner friendly Everything

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请问copykat_mix.R中的addPCA / addUMAP / run_phenograph / run_leiden是什么？ Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

navinlabcode/tnbc-chemo#3 · Opened Sep 18, 2026
CellTrek on other spatial data, like cosmx SMI data or stereo-seq data. Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

navinlabcode/CellTrek#46 · Opened May 29, 2025
Single cell data and spatial data matching requirement Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

navinlabcode/CellTrek#44 · Opened Dec 3, 2024
Using Celltrek on non-matching data ST and SC data. Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#42 · Opened May 27, 2024
[Question] Is it possible to superimpose a network on spatial image? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

navinlabcode/CellTrek#41 · Opened May 16, 2024
Error: package or namespace load failed for ‘CellTrek’ Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

navinlabcode/CellTrek#40 · Opened Mar 26, 2024
Error in rownames(st_data[[st_assay]]@data) : no slot of name "data" for this object of class "Assay5", Possible Seurat v5.0 error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#39 · 8 comments · Opened Dec 28, 2023
ERROR Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#38 · 1 comment · Opened Dec 16, 2023
celltrek_vis Error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#37 · Opened Dec 13, 2023
Errors in CellTrek::traint on example data from README Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

navinlabcode/CellTrek#36 · 4 comments · Opened Nov 3, 2023
Customized Plot Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

navinlabcode/CellTrek#34 · Opened Sep 22, 2023
Normalization methods Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

navinlabcode/CellTrek#33 · 1 reaction · Opened Sep 21, 2023
Request for cell type annotation of mouse kidney and DCIS1 datasets Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

navinlabcode/CellTrek#32 · Opened Sep 21, 2023
Dealing with spatial data with merged samples Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

navinlabcode/CellTrek#31 · Opened Jul 26, 2023
Celltrek output to spot and cell mapping Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

navinlabcode/CellTrek#30 · Opened Jul 5, 2023
"Celltrek"_Simualtion dataset Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

navinlabcode/CellTrek#29 · Opened May 15, 2023
lack of single-cell transcriptome data from the same patient Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

navinlabcode/CellTrek#28 · 1 comment · Opened May 6, 2023
keep raw data in celltrek object Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

navinlabcode/CellTrek#25 · 1 comment · Opened Oct 13, 2022
celltrek_vis error Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

navinlabcode/CellTrek#24 · 1 comment · Opened Oct 12, 2022
Error while running CellTrek:celltrek function Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#23 · 1 comment · Opened Oct 4, 2022
Error: 'DT_boot_mst' is not an exported object from 'namespace:CellTrek' Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

navinlabcode/CellTrek#22 · Opened Sep 17, 2022
Assigning all single cells Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

navinlabcode/CellTrek#21 · 1 comment · Opened Aug 28, 2022
clarification on overall method Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

navinlabcode/CellTrek#20 · 2 comments · Opened Aug 12, 2022
Error: invalid character indexing Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#19 · 1 comment · Opened Aug 2, 2022
Question about Supplementary Figure 7e Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#16 · 1 comment · Opened Jul 5, 2022
How to keep all the metadata from the seurat traint object after running CellTrek::celltrek() Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

navinlabcode/CellTrek#15 · 1 comment · Opened Jul 1, 2022
Visualization and error in celltrek_vis Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#14 · 3 comments · Opened Jun 9, 2022
Some cells are missing from output Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

navinlabcode/CellTrek#13 · 4 comments · Opened May 24, 2022
Coembedding shows batch effect Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

navinlabcode/CellTrek#12 · 4 comments · Opened May 16, 2022

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