kharchenkolab/numbat

Issues

• bulk_clones plot "CNV state" legend colors

  #182 opened 6 months ago by igordot
  6

• converting existing FACETS CNV calls from WGS to Numbat format for input to "segs_consensus_fix"

  #201 opened 22 days ago by ahwanpandey
  1

• The difference between cnv_state and cnv_state_map in joint_post result file

  #204 opened 22 days ago by Mashuaiii
  1

• Numbat running for two samples separately but crashes when I merge the two and perform the same analysis again

  #203 opened 22 days ago by quail768
  1

• Better error handling?!

  #202 opened a month ago by stela2502
  0

• (hom_rate > 0.4) {: missing value where TRUE/FALSE needed

  #200 opened 2 months ago by stela2502
  0

• other parameters to adjust when [1] "No CNV remains after filtering by LLR in pseudobulks. Consider reducing min_LLR."?

  #199 opened 2 months ago by whitneyt1
  1

• run_numbat() with multiple samples

  #196 opened 2 months ago by kobolock
  1

• Mouse genetic background - Both parental strains are reference C57

  #198 opened 2 months ago by radiasso
  1

• Error in vectbl_assign(x[[j]], i, recycled_value[[j]]): DLL requires the use of native symbols

  #197 opened 2 months ago by stela2502
  6

• CNV calling from 10X 5 prime GEX data

  #193 opened 3 months ago by cv55
  2

• memory usage error during run_numbat

  #171 opened 7 months ago by sxf-ux
  1

• plot_phylo_heatmap() does not work

  #195 opened 2 months ago by kobolock
  1

• ```run_numbat()``` error unclear

  #181 opened 6 months ago by cathalgking
  5

• Comparison to pseudobulk and sanity check of high major copy number

  #194 opened 3 months ago by Nikki-Burdett
  6

• n_states is 0 for CNV region with multiallelic CNVs are not called

  #178 opened 6 months ago by teng-gao
  0

• reorder cell order in heatmap output

  #192 opened 4 months ago by patelgrp
  2

• Error because of dplyr version

  #189 opened 4 months ago by KatharinaSchmid
  1

• Error: 'separate_longer_delim' is not an exported object from 'namespace:tidyr'

  #190 opened 4 months ago by fahmadimoughari
  2

• Numbat assigned clone coloring in Panel.png

  #191 opened 4 months ago by quail768
  0

• error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': 'seqnames' cannot contain NAs

  #165 opened 7 months ago by yulijia
  5

• segfault, caught bus error, non-existent physical address

  #188 opened 4 months ago by ahwanpandey
  6

• How to generate the plotEmbedding in a numbat object?

  #168 opened 5 months ago by christophechu
  1

• plot_phylo_heatmap

  #170 opened 7 months ago by Mashuaiii
  1

• gexp_roll_wide

  #169 opened 7 months ago by Mashuaiii
  1

• Excluding segs_loh causes multiple CNV states for the same segment

  #183 opened 5 months ago by teng-gao
  2

• Input only the gene expression matrix

  #187 opened 5 months ago by Mashuaiii
  2

• Fail during numbat : object 'seg' not found

  #186 opened 5 months ago by sxf-ux
  0

• saving numbat object after changing n_cut=k kvalue

  #185 opened 5 months ago by whitneyt1
  0

• Running numbat in multiple samples from same patient

  #176 opened 5 months ago by ccruizm
  1

• Duplicated segments in segs_consensus for NCI-N87

  #184 opened 5 months ago by teng-gao
  0

• Error in find_common_diploid(bulks, gamma = gamma, alpha = alpha, ncores = ncores) : Error in smooth_segs(., min_genes = min_genes) :

  #163 opened 6 months ago by whitneyt1
  6

• Error in mutate(., state = run_allele_hmm ... Not a matrix

  #177 opened 6 months ago by whitneyt1
  2

• Error in `mutate()`: ℹ In argument: `snp_index = 1:n()`. Caused by error: ! `snp_index` must be size 0 or 1, not 2.

  #167 opened 6 months ago by cathalgking
  8

• Better error handling when one of the pileup fails

  #179 opened 6 months ago by teng-gao
  0

• No SNPs left

  #180 opened 6 months ago by xiaoshanpai
  1

• How to use numbat in other species with a phased genome?

  #174 opened 7 months ago by xinghua1001
  3

• Chromosome Arms Summaries File Lacking

  #175 opened 7 months ago by DarioS
  0

• why genotype1 have tumor cells?

  #172 opened 7 months ago by BioAmelie
  1

• High Similarity of Clones' Profiles

  #173 opened 7 months ago by DarioS
  0

• Error: scheduled core X did not deliver a result

  #160 opened 8 months ago by ArthurDondi
  3

• Unclear Equivalence Between Different Patients

  #164 opened 7 months ago by DarioS
  2

• Numbat fails with 10X Visium Sample Data - Normal Human Prostate

  #166 opened 7 months ago by corecontingency
  1

• singularity - Error in value

  #161 opened 8 months ago by cathalgking
  4

• run_numbat error

  #162 opened 8 months ago by sneupane04
  2

• how to remove cnv like noise

  #159 opened 8 months ago by hanjun98
  2

• comprehension for 'Using prephased SNP profiles'

  #158 opened 8 months ago by hanjun98
  0

• Mouse data. "subscript out of bounds" error.

  #157 opened 8 months ago by zackb9
  1

• Cell Ranger Count Default Intronic Counting Impact

  #155 opened 8 months ago by DarioS
  1

• Overwrite identifiers

  #156 opened 8 months ago by SollyBunny
  1