navinlabcode/copykit

Issues

• Automated detection of segments of interest

  #56 opened 3 years ago by aislyn
  1

• Error when smoothed_bincounts is not in the assay

  #97 opened a year ago by Puriney
  1

• mouse genome

  #96 opened a year ago by LeonLiu-ZL
  1

• RunSegmentation multipcf doesn't respect gamma parameter

  #94 opened a year ago by seedgeorge
  2

• application of CopyKit

  #95 opened a year ago by veramazzara
  1

• Normalise with 'normal' cells

  #93 opened a year ago by seedgeorge
  1

• Install Instructions

  #90 opened 2 years ago by akcasasent
  2

• Errors in the plotRatio() call

  #91 opened 2 years ago by srbehera
  5

• export IGV seg ratio file

  #89 opened 2 years ago by MinBio
  1

• runCountRead does not recognize .bam files

  #85 opened 2 years ago by Romeo1-1
  7

• germline gain not called in single cells

  #88 opened 2 years ago by proukakis
  4

• is there a way to get lists of CNVs

  #87 opened 2 years ago by proukakis
  4

• T2T-Chm13

  #86 opened 3 years ago by proukakis
  1

• scquantum

  #80 opened 3 years ago by teng-gao
  6

• fix colors on ratio heatmap

  #23 opened 4 years ago by aislyn
  2

• row-based subsetting for all plot functions

  #62 opened 3 years ago by aislyn
  1

• plotRatio() doesn't always let you plot a subset of bins

  #61 opened 3 years ago by aislyn
  4

• findVariableGenes returns NA's

  #79 opened 3 years ago by aislyn
  1

• name of findNormalCells is slightly misleading

  #78 opened 3 years ago by aislyn
  1

• The function name "filterCells()" is misleading because its function isn't actually filtering

  #58 opened 3 years ago by aislyn
  2

• calcInteger() does not catch failures in scquantum

  #54 opened 3 years ago by aislyn
  2

• plotPhylo should show a the distance bar in the xaxis

  #48 opened 3 years ago by darlanminussi
  1

• ggalluvial not loading with copykit

  #65 opened 3 years ago by aislyn
  1

• plotHeatmap() doesn't catch attempt to add multiple row labels in consensus mode

  #59 opened 3 years ago by aislyn
  1

• Progress bar for calcInteger()

  #55 opened 3 years ago by aislyn
  2

• remove point color (i.e. outline) on plotmetrics() plot

  #57 opened 3 years ago by aislyn
  1

• filterCells() is really slow

  #32 opened 3 years ago by aislyn
  5

• give functions the ability to name the slot it's being stored in

  #15 opened 3 years ago by aislyn
  4

• Have FindClusters() search for optimal k in the object by default

  #34 opened 4 years ago by aislyn
  1

• findClusters() factor order

  #33 opened 4 years ago by aislyn
  1

• make plotHeatmap() default label colors fixed, not stochastic (or at least not a surprise)

  #30 opened 4 years ago by aislyn
  1

• specify in documentation that findOptimalK() does not output a scCNA object

  #31 opened 4 years ago by aislyn
  1

• copykit missing import of metadata() from SummarizedExperiment()

  #29 opened 4 years ago by aislyn
  1

• runSegmentation throws dimension error

  #28 opened 4 years ago by aislyn
  2

• runMetrics producing threading-related error

  #27 opened 4 years ago by aislyn
  2

• Rsubread dependency

  #25 opened 4 years ago by darlanminussi
  0

• runVarbin

  #22 opened 4 years ago by darlanminussi
  1

• Make metadata more accessible in cell ratioplots

  #24 opened 4 years ago by aislyn
  1

• plotHeatmap fails to annotate when more than 9 superclones

  #21 opened 4 years ago by aislyn
  1

• readVarbinCNA "dir" argument is unclear

  #7 opened 4 years ago by aislyn
  4

• subclone consensus plots

  #16 opened 4 years ago by aislyn
  2

• load and store different segmentations

  #14 opened 4 years ago by aislyn
  2

• slice_min function in findClusters requires n value

  #20 opened 4 years ago by TapsiS
  1

• geneCopyPlot

  #18 opened 5 years ago by darlanminussi
  0

• phylo check

  #13 opened 5 years ago by darlanminussi
  1

• make plotting step from filterCells() separate from the filtering part

  #12 opened 5 years ago by aislyn
  3

• runMetrics

  #9 opened 5 years ago by darlanminussi
  1

• store correlation value from filterCells()

  #10 opened 5 years ago by aislyn
  1

• add option to plotMetrics() to color by a colData variable

  #11 opened 5 years ago by aislyn
  1

• copykit is not mandating tidyverse be in the library successfully

  #8 opened 5 years ago by aislyn
  7