navinlabcode copykat issues

navinlabcode / copykat

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issues

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A simple sanity check for invalid input values

#123 ErfanMowlaei opened 1 week ago
0
Inconsistencies in cell numbers

#122 yitengfei120011 opened 2 weeks ago
0
Option for users to set the seed

#121 sjspielman opened 1 month ago
0
Error in hclust(d, method = "ward.D2"): size cannot be NA nor exceed 65536

#120 ChenlingTangMDA opened 2 months ago
1
Include all genes in copykat_CNA_raw_results_gene_by_cell.txt.

#119 Prakrithi-P opened 3 months ago
0
New human reference T2T CHM13

#118 ywzhang071394 opened 3 months ago
0
How to change min.gene.per.cell

#117 Rayan21100 opened 4 months ago
1
Output files are written to working directory

#116 rVMLql58 opened 6 months ago
3
Does it make sense to run copykat on tumor samples containing very low number of normal epithelial cells?

#115 kaizen89 opened 7 months ago
1
Outputs Heatmap Copykat

#114 LeaLe88 opened 7 months ago
0
formatted all R files

#113 wise-bit closed 8 months ago
0
Error in step 2: arguments imply differing number of rows

#112 carbui opened 8 months ago
1
Diploid and aneuploid reversed

#111 LeaLe88 opened 8 months ago
0
Error in hclust(parallelDist::parDist(t(tumor.mat), threads = 4, method = "euclidean"), : must have n >= 2 objects to cluster

#110 LeaLe88 closed 8 months ago
1
Example breast tumours Error in Step 4 - heatmap

#109 LeaLe88 opened 8 months ago
0
Tumor subclone

#108 Mashuaiii opened 9 months ago
0
macrophages with CNV?

#107 sadiexiaoyu opened 1 year ago
1
how to translate the copykat results to inferCNV i6 HMM (the six-state CNV model)

#106 sadiexiaoyu opened 1 year ago
0
Could Copycat be used for zebrafish analysis?

#105 UEATTOOMUCH260 opened 1 year ago
1
running at lower resolution

#104 vravik opened 1 year ago
0
Error in .External2(C_X11, paste0("jpeg::", quality, ":", filename), g$width

#103 decodebiology opened 1 year ago
3
WARNING! NOT CONVERGENT! number of iterations= 500

#102 mbihie opened 1 year ago
1
Adding gene annotation to CNAmatrix + p and q information

#101 RaghadShu opened 1 year ago
1
Question regarding "GMM definition mode"

#100 sjspielman opened 1 year ago
0
The results of diploid and aneuploid are reversed in test_copykat_heatmap.jpeg, why?

#99 lj20220425 opened 1 year ago
5
WARNING! NOT CONVERGENT!

#98 stroke1989 opened 1 year ago
4
Error in step4

#97 13021969200 opened 1 year ago
0
Error in step 5 when trying copykat for Visium Spatial Transcriptomics data

#96 linhuawang opened 1 year ago
0
Heatmap cannot be plotted

#95 Yijia-Jiang opened 1 year ago
3
CNV filtering

#94 SirKuikka opened 1 year ago
0
Suggestions on running copykat for multiple samples without cell type annotation?

#93 Yijia-Jiang opened 1 year ago
0
The error 'mcfork(): Unable to fork: Cannot allocate memory' when I run copykat

#92 caodudu opened 1 year ago
1
"step 4: measuring baselines ...": Error in mixtools::normalmixEM(data.c, lambda = rep(1, 3)/3, mu = c(-0.2, : NA/NaN/Inf in foreign function call (arg 4)

#91 confiya opened 1 year ago
0
CNAmat does not contain gene symbol when using genome = "hg20"

#90 WT215 opened 1 year ago
1
Is there any way to make re-analysis easier when change the parameter KS.cut?

#89 yunbokai opened 1 year ago
0
Error in norm.mat.relat[which(DR2 >= UP.DR), ] : subscript out of bounds

#88 GQLL opened 1 year ago
1
what reason of copykat analysis one sample compare to different samples with different result

#87 zqmiao-mzq opened 1 year ago
0
Whole genome duplication

#86 Leticia314 opened 1 year ago
0
Question - usage for bulk RNAseq

#85 akaviaLab opened 1 year ago
0
copykat issue: error in step 4

#84 YubinXie opened 1 year ago
2
Error in cluster mode

#83 AClab-sgarcia opened 1 year ago
2
Question about define subpopulations of aneuploid tumor cells

#82 lwlive opened 1 year ago
0
step 4 error

#81 fpengstudy opened 1 year ago
1
Too many cells and the heatmap too big too open!

#80 liaoshengguang opened 1 year ago
1
Normal cells assigned as aneuploid

#79 AnnaAntonatouPap opened 1 year ago
0
Error in match.arg(type) : 'arg' must be of length 1

#78 Lukadon77 opened 1 year ago
1
Can CopyKAT be used to distinguish normal cells from tumor cells in hematological tumors？

#77 HengqiLiu opened 1 year ago
0
Runing multiple times using same data but generate different results

#76 MaHaoran627 opened 2 years ago
1
Installation failure

#75 SGIlabes opened 2 years ago
0
Error in hclust(d, method = "ward.D2") :

#74 qiangfan2022 opened 2 years ago
1