JEFworks-Lab/HoneyBADGER

Issues

• gene filtering different in HoneyBADGER object

  #39 opened 4 years ago by JocelynSP
  3

• Allele-mode for selecting normal cells

  #30 opened 5 years ago by hyristi
  2

• Error in calcCombCnvProb

  #48 opened 4 years ago by Rongtingting
  1

• example data starting from counts (not scaled or centered)

  #19 opened 6 years ago by brianjohnhaas
  3

• Error in summarizeResults for the allele-based approach

  #46 opened 4 years ago by myrthesmit
  0

• error in hb$summarizeResults

  #45 opened 4 years ago by UmairSeemab
  0

• Applying bayesian hierarchical model in integrating analyses tutorial

  #44 opened 4 years ago by viraj-rapolu
  0

• showing NULL in the step of calcGexpCnvBoundaries - getting started tutorial

  #43 opened 4 years ago by Rongtingting
  12

• no method for coercing this S4 class to a vector

  #42 opened 4 years ago by Joanne-PYL
  3

• Showing error when trying Getting_Started.Rmd

  #41 opened 4 years ago by Joanne-PYL
  0

• Error: Failed to install 'HoneyBADGER' from GitHub

  #40 opened 4 years ago by yaskermezli
  2

• What is the reason for only including snps in HoneyBADGER?

  #38 opened 4 years ago by Pentayouth
  2

• Error: subscript contains invalid names

  #34 opened 5 years ago by suyanxun
  9

• Filtering of identified CNVs

  #36 opened 5 years ago by Josephinedh
  2

• speed of running setAlleleMats step

  #37 opened 5 years ago by lixin4306ren
  0

• read bam files

  #35 opened 5 years ago by cq2019
  4

• Error in calcGexpCnvBoundaries when running with numeric chromosome names

  #33 opened 5 years ago by asabjorklund
  1

• error about "getCellAlleleCount" command line

  #17 opened 5 years ago by zhuxqdoctor
  13

• Error in summarizeResults

  #32 opened 5 years ago by rosaranli
  3

• vcf files for heterozygous SNPs

  #21 opened 5 years ago by photoonh
  6

• Add "next step" link to tutorial

  #22 opened 5 years ago by romagnolid
  1

• 10x data normalization problem

  #24 opened 5 years ago by mariamonberg
  3

• 10X + Honeybadger question

  #31 opened 5 years ago by NienkeMekkes
  2

• Warning in setGeneFactors and error in retestIdentifiedCnvs

  #29 opened 5 years ago by rosaranli
  0

• how to parallelize "calcGexpCnvBoundaries" and "retestIdentifiedCnvs" ?

  #27 opened 5 years ago by songw01
  1

• lt$setGexpDev

  #28 opened 5 years ago by BoXiaHB
  1

• error in retestIdentifiedCnvs

  #20 opened 6 years ago by akdess
  4

• Error in calcAlleleCnvBoundaries

  #26 opened 6 years ago by JLTrincado
  3

• error when connecting to BioMart

  #25 opened 6 years ago by HaotengYan
  2

• Errors in getSnpMats, getSnpMats10X, and getCellAlleleCount: unable to find an inherited method for function ‘seqnames’ for signature ‘"DataFrame"’

  #23 opened 6 years ago by koetjen
  6

• Usage of HoneyBADGER on 10x data?

  #14 opened 6 years ago by kokonech
  5

• Gene expression normalization

  #18 opened 6 years ago by lijiang825
  1

• error in summarizeResults

  #13 opened 6 years ago by csimona
  2

• Hi

  #15 opened 6 years ago by 1583767448
  5

• Error: dim(X) must have a positive length

  #12 opened 6 years ago by romanhaa
  2

• refCount and altCount matrixes are everywhere zero

  #11 opened 6 years ago by elimereu
  2

• reference for gene expression

  #10 opened 6 years ago by elimereu
  2

• How to prepare reference expression?

  #5 opened 7 years ago by saeedsaberi
  7

• Parameter tweaking for no CNV identified

  #1 opened 7 years ago by ahy1221
  16

• Package exports object named ref

  #7 opened 7 years ago by barkasn
  3

• unable to install HoneyBADGER packge

  #8 opened 7 years ago by hmassalha
  3

• Seurat and Honeybadger are not compatible

  #6 opened 7 years ago by saeedsaberi
  2

• When should I use HoneyBADGER

  #3 opened 7 years ago by saeedsaberi
  2

• Using conda

  #4 opened 7 years ago by saeedsaberi
  0