kharchenkolab numbat issues

kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

https://kharchenkolab.github.io/numbat/

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issues

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Error because of dplyr version

#189 KatharinaSchmid opened 3 days ago
0
segfault, caught bus error, non-existent physical address

#188 ahwanpandey opened 5 days ago
5
Input only the gene expression matrix

#187 Moey-git closed 3 weeks ago
2
Fail during numbat : object 'seg' not found

#186 sxf-ux opened 3 weeks ago
0
saving numbat object after changing n_cut=k kvalue

#185 whitneyt1 opened 1 month ago
0
Duplicated segments in segs_consensus for NCI-N87

#184 teng-gao opened 1 month ago
0
Excluding segs_loh causes multiple CNV states for the same segment

#183 teng-gao closed 2 weeks ago
2
bulk_clones plot "CNV state" legend colors

#182 igordot opened 1 month ago
2
```run_numbat()``` error unclear

#181 cathalgking opened 1 month ago
4
No SNPs left

#180 xiaoshanpai opened 2 months ago
1
Better error handling when one of the pileup fails

#179 teng-gao closed 1 month ago
0
n_states is 0 for CNV region with multiallelic CNVs are not called

#178 teng-gao opened 2 months ago
0
Error in mutate(., state = run_allele_hmm ... Not a matrix

#177 whitneyt1 closed 1 month ago
2
Running numbat in multiple samples from same patient

#176 ccruizm closed 1 month ago
1
Chromosome Arms Summaries File Lacking

#175 DarioS opened 2 months ago
0
How to use numbat in other species with a phased genome?

#174 xinghua1001 opened 2 months ago
3
High Similarity of Clones' Profiles

#173 DarioS opened 2 months ago
0
why genotype1 have tumor cells?

#172 BioAmelie opened 2 months ago
1
memory usage error during run_numbat

#171 sxf-ux opened 2 months ago
0
plot_phylo_heatmap

#170 Moey-git opened 2 months ago
1
gexp_roll_wide

#169 Moey-git opened 2 months ago
1
How to generate the plotEmbedding in a numbat object?

#168 christophechu closed 2 weeks ago
1
Error in `mutate()`: ℹ In argument: `snp_index = 1:n()`. Caused by error: ! `snp_index` must be size 0 or 1, not 2.

#167 cathalgking closed 1 month ago
8
Numbat fails with 10X Visium Sample Data - Normal Human Prostate

#166 corecontingency opened 3 months ago
1
error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': 'seqnames' cannot contain NAs

#165 yulijia opened 3 months ago
4
Unclear Equivalence Between Different Patients

#164 DarioS opened 3 months ago
2
Error in find_common_diploid(bulks, gamma = gamma, alpha = alpha, ncores = ncores) : Error in smooth_segs(., min_genes = min_genes) :

#163 whitneyt1 closed 1 month ago
6
run_numbat error

#162 sneupane04 opened 3 months ago
2
singularity - Error in value

#161 cathalgking opened 3 months ago
4
Error: scheduled core X did not deliver a result

#160 ArthurDondi opened 3 months ago
3
how to remove cnv like noise

#159 hanjun98 opened 3 months ago
2
comprehension for 'Using prephased SNP profiles'

#158 hanjun98 opened 3 months ago
0
Mouse data. "subscript out of bounds" error.

#157 zackb9 opened 4 months ago
1
Overwrite identifiers

#156 SollyBunny closed 4 months ago
1
Cell Ranger Count Default Intronic Counting Impact

#155 DarioS closed 3 months ago
1
Experimental Data Expectation is Unclear

#154 DarioS opened 4 months ago
1
how to prepare "segs_consensus_fix" if I have WES data of multiple samples from the same patient

#153 daisyyr opened 4 months ago
1
cnv_state Column Description is Vague

#152 DarioS closed 3 months ago
4
clone_opt starts from 2 (ie, clone 1 is missing)

#151 ChelseaCHENX opened 4 months ago
1
Subtrees disappear

#150 acalcino opened 5 months ago
7
WASHU MM study Bioproject data not available

#149 juniajvs closed 6 months ago
1
Error in h(simpleError(msg, call)) : error in evaluating the argument 'query' in selecting a method for function 'findOverlaps': 'start' and 'end' must be numeric vectors

#148 lipikakalson opened 6 months ago
1
How to interpret LogFC output? And how to find LogFC for single cells?

#147 thomasveith opened 6 months ago
1
Probabilities of each CNV state are missing in joint_post_2.tsv

#146 hxj5 opened 6 months ago
5
getting the order of cells in panel plots

#145 MigleMi opened 6 months ago
1
High ploidy cell lines

#144 thomasveith closed 3 months ago
5
About the phasing options

#143 SirKuikka opened 7 months ago
1
Performing comparative analysis of Numbat results across multiple patients

#142 scg-dgist opened 7 months ago
3
Troubleshoot Error - missing files in output directory

#141 RaghadShu closed 7 months ago
1
No SNPs left

#140 moOsmanMD opened 8 months ago
1