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copykat
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Output files are written to working directory
#116
rVMLql58
opened
1 month ago
3
Does it make sense to run copykat on tumor samples containing very low number of normal epithelial cells?
#115
kaizen89
opened
2 months ago
1
Outputs Heatmap Copykat
#114
LeaLe88
opened
2 months ago
0
formatted all R files
#113
wise-bit
closed
3 months ago
0
Error in step 2: arguments imply differing number of rows
#112
carbui
opened
3 months ago
0
Diploid and aneuploid reversed
#111
LeaLe88
opened
3 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
3 months ago
1
Example breast tumours Error in Step 4 - heatmap
#109
LeaLe88
opened
3 months ago
0
Tumor subclone
#108
Moey-git
opened
4 months ago
0
macrophages with CNV?
#107
sadiexiaoyu
opened
7 months ago
1
how to translate the copykat results to inferCNV i6 HMM (the six-state CNV model)
#106
sadiexiaoyu
opened
7 months ago
0
Could Copycat be used for zebrafish analysis?
#105
UEATTOOMUCH260
opened
7 months ago
1
running at lower resolution
#104
vravik
opened
7 months ago
0
Error in .External2(C_X11, paste0("jpeg::", quality, ":", filename), g$width
#103
decodebiology
opened
8 months ago
3
WARNING! NOT CONVERGENT! number of iterations= 500
#102
mbihie
opened
9 months ago
1
Adding gene annotation to CNAmatrix + p and q information
#101
RaghadShu
opened
9 months ago
1
Question regarding "GMM definition mode"
#100
sjspielman
opened
10 months ago
0
The results of diploid and aneuploid are reversed in test_copykat_heatmap.jpeg, why?
#99
lj20220425
opened
10 months ago
5
WARNING! NOT CONVERGENT!
#98
stroke1989
opened
11 months ago
4
Error in step4
#97
13021969200
opened
11 months 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
1
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
0
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
1 year ago
1
Installation failure
#75
SGIlabes
opened
1 year ago
0
Error in hclust(d, method = "ward.D2") :
#74
qiangfan2022
opened
1 year ago
0
Issue about dlm
#73
Junedays
opened
1 year ago
2
Segmentation by chromosome arm size
#72
jgarces02
opened
1 year ago
0
no applicable method for 'dlmSmooth' applied to an object of class "c('double', 'numeric')"
#71
050114dragon
opened
1 year ago
6
MHC genes and cell cycle genes are not filtered out in mouse version
#70
sky1ove
opened
1 year ago
0
Error while producing results
#69
Laolga
opened
1 year ago
0
Can I use the results of copykat to build phylogenetic tree?
#68
hahia
opened
1 year ago
1
warnings
#67
zhouyao315
opened
1 year ago
0
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