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kharchenkolab
/
numbat
Haplotype-aware CNV analysis from single-cell RNA-seq
https://kharchenkolab.github.io/numbat/
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Troubleshoot Error - missing files in output directory
#141
RaghadShu
closed
7 months ago
1
No SNPs left
#140
moOsmanMD
opened
8 months ago
1
Why is there so much LoH in the mouse data tutorial?
#139
thomasveith
closed
7 months ago
3
Error in run_numbat (dpoilog: all x must be integers)
#138
RaghadShu
opened
8 months ago
4
Error in hclust(dist_mat, method = "ward.D2") : size cannot be NA nor exceed 65536
#137
YiweiNiu
opened
8 months ago
0
Target and ref have too few matching SNPs [pileup_and_phase.R]
#136
Franzili
opened
9 months ago
2
Issue about Interpretation of Results of the section Tumor phylogeny
#135
sunshine1126
closed
9 months ago
2
No CNVs detected for tumor data
#134
SirKuikka
closed
9 months ago
4
how to specify the number of clones in the bulk_clones_final.png and look at the allele frequency profile based on the specified number of clones
#133
rosaranli
opened
10 months ago
8
memuse is not installed by default - breaking your script
#132
stela2502
opened
11 months ago
1
How to re-run from the breakpoint
#131
daisyyr
opened
11 months ago
3
Phylogeny on merged samples
#130
freddie090
opened
11 months ago
6
analyse multiple samples from the same individual together to increase power
#129
rosaranli
closed
11 months ago
7
run_numbat() gives error: running hclust...Error in vectbl_assign(x[[j]], i, recycled_value[[j]])
#128
kzb193
opened
1 year ago
2
Error with SNP contamination for some samples
#127
Sarah145
opened
1 year ago
2
copynumber::pcf execution
#126
wyt14
closed
1 year ago
1
Combining multiple runs of pileup_and_phase script
#125
ms3389
opened
1 year ago
4
Which CNV_state to use from the output?
#124
aelhossiny
closed
1 year ago
1
error when running numbat::preprocess_allele in pileup_and_phase.R
#123
rosaranli
closed
12 months ago
2
Error in `mutate()` while running numbat with snRNAseq data generated by Takara SMART-Seq Stranded Kit
#122
xiaoxinchen2022
closed
11 months ago
3
Error Running HMMs running Numbat
#121
lopezCascales
opened
1 year ago
1
Does Numbat filter cells out during giving posterior probabilities on single-cell level?
#120
aelhossiny
closed
1 year ago
1
Z States output
#119
aelhossiny
closed
1 year ago
1
Fail when running with target subset of regions
#118
kokonech
closed
1 year ago
1
Understanding Numbat results
#117
acalcino
closed
1 year ago
2
Issues visualizing CNV posterior in tSNE embedding using pagoda
#116
bobbyshih
closed
1 year ago
2
difference between subtrees and clones?
#115
aelhossiny
closed
1 year ago
2
error in unused argument when running pileup_and_phase.R
#114
MigleMi
opened
1 year ago
1
Using numbat on multiple 10x visium spatial samples
#113
spatialbiology1
closed
1 year ago
2
Error in mutate(., state = run_joint_hmm(pAD = pAD, DP = DP, p_s = p_s,
#112
pcream
closed
1 year ago
7
Running Numbat on cells coming from multiple samples
#111
aelhossiny
closed
1 year ago
1
Error in optim(fn = function(w) {: non-finite value supplied by optim
#110
ccruizm
closed
1 year ago
4
Where to find Eagle genetic_map_hg38_withX.txt.gz since the mirror is down?
#109
EspressoKris
closed
1 year ago
2
Run Numbat on selected chromosomes
#108
aranham
closed
1 year ago
3
docker tags
#107
johnyaku
closed
1 year ago
1
Co-genotype with bulk WGS and scRNA-seq
#106
DrFengchenzhao
closed
1 year ago
4
Settings for Cellsnp
#105
JikaiShao
closed
1 year ago
2
Settings for running on large number of cells
#104
aranham
opened
1 year ago
4
Re-define clustering or subtrees based on the computed phylogeny
#103
kokonech
closed
1 year ago
1
Settings adjustment for single gene amplification
#102
kokonech
closed
1 year ago
1
Server for 1000G reference panel data not available
#101
cmsauer
closed
1 year ago
3
integer copy number
#100
xindd
closed
1 year ago
2
Parameter finetuning for cell line
#99
aranham
opened
1 year ago
0
no CNVs after run_numbat() and large run time
#98
sbamopoulos
closed
1 year ago
3
Numbat error with custom reference
#97
cv55
closed
1 year ago
1
Mouse genetic background SNP
#96
zqzneptune
closed
1 year ago
3
Problem with pileup_and_phase.R on 10X Visium Spatial transcriptomics
#95
mjakobs
closed
1 year ago
4
p_cnv threshold for event calling
#94
laijen000
closed
1 year ago
1
Expecting loss but getting CNLoH
#93
tinakeshav
opened
1 year ago
6
Tibble columns issue
#92
cbwang3
closed
1 year ago
5
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