navinlabcode Open Source Projects

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

Heatmap output appears abnormal Open

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

navinlabcode/copykat#141 · 1 comment · Opened Jul 10, 2026

License discrepency Open

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

navinlabcode/copykat#140 · Opened May 12, 2026

Running copyKAT on large datasets Open

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

navinlabcode/copykat#138 · 3 comments · Opened Mar 12, 2026

Copykat for Single cell Flex Open

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

navinlabcode/copykat#137 · Opened Mar 10, 2026

InferCNA plot logic Open

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

navinlabcode/copykat#136 · Opened Jan 16, 2026

Error : object 'anno.mat' not found Open

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

navinlabcode/copykat#135 · 1 comment · Opened Dec 2, 2025

CNA prediction clashing with cell type annotation Open

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

navinlabcode/copykat#134 · Opened Nov 26, 2025

Tumor specific Sublonal Grouping Open

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

navinlabcode/copykat#133 · Opened Oct 28, 2025

Unupdated Code Open

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

navinlabcode/copykat#132 · Opened Oct 10, 2025

Not.defined classification in predictions but not in matrix Open

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

navinlabcode/copykat#131 · Opened Aug 27, 2025

Run Time Open

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

navinlabcode/copykat#130 · Opened Jun 10, 2025

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

Regarding copykat, it defines aneuploidy for the specified normal group Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

navinlabcode/copykat#129 · 1 comment · Opened May 23, 2025

The definition of "not.defined" in the copykat result Open

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

navinlabcode/copykat#128 · 2 comments · Opened May 9, 2025

Assigning discrete copy number states Open

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

navinlabcode/copykat#127 · Opened Mar 27, 2025

Would prediction result change if the data was splitted into multiple smaller sets? Open

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

navinlabcode/copykat#126 · Opened Mar 10, 2025

Help with identifying true CNVs from false Open

Difficulty 5/5 Over a week Newbie friendliness 10/100

navinlabcode/copykat#125 · Opened Mar 6, 2025

all cells are filtered Open

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

navinlabcode/copykat#124 · 2 comments · Opened Jan 5, 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

Inconsistencies in cell numbers Open

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

navinlabcode/copykat#122 · Opened Nov 5, 2024

Option for users to set the seed Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

navinlabcode/copykat#121 · Opened Oct 9, 2024

Error in hclust(d, method = "ward.D2"): size cannot be NA nor exceed 65536 Open

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

navinlabcode/copykat#120 · 2 comments · Opened Aug 28, 2024

Include all genes in copykat_CNA_raw_results_gene_by_cell.txt. Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

navinlabcode/copykat#119 · Opened Aug 14, 2024

New human reference T2T CHM13 Open

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

navinlabcode/copykat#118 · Opened Jul 31, 2024

How to change min.gene.per.cell Open

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

navinlabcode/copykat#117 · 1 comment · Opened Jul 22, 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

Output files are written to working directory Open

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

navinlabcode/copykat#116 · 3 comments · Opened May 2, 2024

Does it make sense to run copykat on tumor samples containing very low number of normal epithelial cells? Open

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

navinlabcode/copykat#115 · 1 comment · Opened Apr 26, 2024

Outputs Heatmap Copykat Open

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

navinlabcode/copykat#114 · Opened Apr 2, 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 step 2: arguments imply differing number of rows Open

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

navinlabcode/copykat#112 · 1 comment · Opened Mar 20, 2024

Diploid and aneuploid reversed Open

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

navinlabcode/copykat#111 · 2 comments · Opened Mar 8, 2024

Example breast tumours Error in Step 4 - heatmap Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

navinlabcode/copykat#109 · Opened Mar 6, 2024

Tumor subclone Open

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

navinlabcode/copykat#108 · Opened Feb 2, 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

macrophages with CNV? Open

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

navinlabcode/copykat#107 · 1 comment · Opened Nov 23, 2023

how to translate the copykat results to inferCNV i6 HMM (the six-state CNV model) Open

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

navinlabcode/copykat#106 · Opened Nov 21, 2023

Could Copycat be used for zebrafish analysis? Open

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

navinlabcode/copykat#105 · 1 comment · Opened Nov 17, 2023

running at lower resolution Open

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

navinlabcode/copykat#104 · Opened Nov 16, 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

Error in .External2(C_X11, paste0("jpeg::", quality, ":", filename), g$width Open

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

navinlabcode/copykat#103 · 3 comments · 1 reaction · Opened Oct 4, 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

WARNING! NOT CONVERGENT! number of iterations= 500 Open

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

navinlabcode/copykat#102 · 3 comments · Opened Sep 6, 2023

Adding gene annotation to CNAmatrix + p and q information Open

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

navinlabcode/copykat#101 · 1 comment · Opened Sep 4, 2023

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