parklab/ShatterSeek

Issues

• Interpreting the results

  #13 opened 4 years ago by beginner984
  3

• Definition of copy number oscillation

  #16 opened 3 years ago by yutito
  2

• Colored dots without connecting lines

  #41 opened 7 months ago by lichennan123
  1

• ShatterSeek on other references

  #40 opened a year ago by fabrimafe
  0

• Can I use this software on rstudio

  #38 opened 2 years ago by liuyunjiangdc
  0

• support mm10 genome

  #36 opened 2 years ago by noobugs
  1

• A question about strands

  #35 opened 2 years ago by mawh-SCU
  1

• Problems about the CN & SV input.

  #34 opened 2 years ago by mistClaud
  1

• Cannot allocate memory

  #33 opened 2 years ago by lilili123lj
  1

• Error in chisq.test(obs2, p = rep(1/4, 4)) : at least one entry of 'x' must be positive

  #9 opened 3 years ago by alvinwt
  14

• Only interchromosomal SVs used for chr_breakpoint_enrichment and pval_exp_chr ?

  #31 opened 3 years ago by e-sollier
  4

• Error in statistical_criteria

  #32 opened 2 years ago by chengwenxuan1997
  3

• How to use Manta output for ShatterSeek? No Strand info, and different SVtype

  #30 opened 3 years ago by arianlundberg
  3

• Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'nrow': wrong sign in 'by' argument

  #25 opened 3 years ago by sivamoke
  8

• Error in statistical_criteria(): error in evaluating the argument 'x' in selecting a method for function 'nrow': wrong sign in 'by' argument

  #29 opened 3 years ago by xlucpu
  2

• Error in h (simpleError (msg, call)): Error when evaluating the argument 'x' in the method selection for function 'nrow': 'to' must be a finite number

  #19 opened 3 years ago by masaver
  4

• Merge copy number segments to have different copy number values in adjacent segments

  #12 opened 3 years ago by tgong1
  4

• Warning when running sample data, error while plotting with chr no. and want to if shatter can be use with othrr organism data

  #27 opened 3 years ago by sonti-roy
  2

• plot_chromothripsis function is wrong

  #28 opened 3 years ago by Emma1997WTT
  1

• Multiple warnings when using tutorial data

  #24 opened 3 years ago by mdiaz09
  5

• run multiple samples

  #23 opened 3 years ago by mkinnaman
  1

• ShatterSeek PCAWG High Confidence and Low Confidence cutoffs

  #22 opened 3 years ago by ahwanpandey
  1

• can

  #20 opened 3 years ago by ahwanpandey
  1

• can't change color in plot_chromothripsis

  #21 opened 3 years ago by ahwanpandey
  1

• Link to visualizations is broken

  #18 opened 3 years ago by mchaisso
  3

• Got error when trying to execute ShatterSeek with other DOxxxx dataset

  #17 opened 3 years ago by wilsonwcyiu
  1

• Check-up prior to indexing possibly missing

  #4 opened 4 years ago by vladimirtomic
  4

• Having circos plot

  #14 opened 4 years ago by MaryGoAround
  1

• Is ShatterSeek compatible with hg19 and hg38 coordinates ?

  #15 opened 4 years ago by masaver
  1

• hg38 support

  #2 opened 5 years ago by tcashby
  5

• issue about layout with plots_chr[[4]]

  #11 opened 5 years ago by riddlexue
  1

• questions for SV cluster detection

  #10 opened 5 years ago by jiadong324
  5

• Define SVtype for ShatterSeek

  #6 opened 5 years ago by zhujack
  1

• take "INV" as input instead of "h2hINV" or "t2tINV"

  #1 opened 5 years ago by KeyTals
  1

• How to get more than one candidate region on each chromosome?

  #5 opened 5 years ago by weishwu
  1

• Code for assigning confidence to candidate regions

  #8 opened 6 years ago by nadiadavidson
  6

• Candidate chromothripsis regions always cover almost the entire chromosome

  #7 opened 6 years ago by weishwu
  6