single-cell-genetics/cellSNP

Issues

• Adapting cellSNP for gene-of-interest / indels / multiple scRNA-seq samples

  #36 opened a year ago by ychenab
  0

• generating VCF for REGION_VCF from RNA-seq data

  #35 opened 2 years ago by gebdu
  1

• output sparse matrix

  #7 opened 5 years ago by bio-la
  11

• Chromosome naming in reference VCF files

  #23 opened 2 years ago by apredeus
  11

• KeyError: '.' in cellSNP/pileup_utils.py causing failure of temp file merging

  #22 opened 3 years ago by mpmargolis
  2

• Empty AD&DP mtx

  #20 opened 3 years ago by AnjaliC4
  23

• AD in cells

  #19 opened 4 years ago by penglbio
  1

• Some SNPs are not in gene

  #18 opened 4 years ago by penglbio
  1

• Does it work for mouse？

  #17 opened 4 years ago by mengchengyao
  1

• Wrong number of chromosomes in output file?

  #16 opened 4 years ago by VanessaOak
  3

• Run time estimation

  #9 opened 5 years ago by PeteHaitch
  3

• Change the flag filtering default to include PCR duplicates

  #13 opened 4 years ago by GWW
  4

• Running cellSNP on transcriptomic BAM from salmon alevin

  #14 opened 4 years ago by lmweber
  4

• Reference Genome

  #15 opened 4 years ago by OldManTae
  1

• Question about running cellSNP on merged BAM files from multiple samples

  #10 opened 5 years ago by lmweber
  4

• No SNPs called in more than 1 barcodes

  #8 opened 5 years ago by saisomesh2594
  3

• Is it expected to generate a "position x barcode" matrix?

  #6 opened 5 years ago by Griffan
  1

• Default nan-handling policy is a memory hog

  #5 opened 5 years ago by ivanov-v-v
  1

• RuntimeWarning: divide by zero encountered in log

  #4 opened 5 years ago by Griffan
  9

• Run time estimation

  #3 opened 5 years ago by coh-racng
  1

• Problem with New Version (0.1.3)

  #2 opened 5 years ago by elderni
  2

• Optimisation suggestions

  #1 opened 6 years ago by Shians
  1