GoekeLab/proActiv

Issues

• Does getAlternativePromoters function work properly?

  #52 opened 3 months ago by Tianle-Li
  0

• Error in `[[<-`(`*tmp*`, name, value = new("SimpleIntegerList", elementType = "integer",

  #48 opened 6 months ago by mmpust
  4

• Couldn't find a BSgenome data package that matches genome assembly: oryCun2.0

  #51 opened 7 months ago by houruiyan
  2

• core dumped

  #50 opened 7 months ago by houruiyan
  1

• What is the mean of names(genomeStyles()) ?

  #49 opened 7 months ago by houruiyan
  2

• plotPromoters function not available in latest version

  #47 opened a year ago by notthathime
  1

• Error in EstimateSizeFactorsForMatrix: at least one zero

  #45 opened a year ago by notthathime
  1

• A little question about internal promoter^_^

  #46 opened a year ago by CuteGold0407
  0

• calculatePromoterReadCounts were not running

  #44 opened a year ago by GuangyaoL
  1

• could not find function "getAlternativePromoters"

  #42 opened a year ago by wenmm
  1

• preparePromoterAnnotation for different species

  #25 opened 3 years ago by gabee-chan
  5

• Identification of cancer-associated promoters

  #43 opened 2 years ago by alejandrogzi
  0

• used for 10x data

  #40 opened 2 years ago by houruiyan
  2

• cannot find extdata/testdata/bam

  #39 opened 2 years ago by houruiyan
  2

• Some question about getAlternativePromoters()

  #41 opened 2 years ago by ninjaxfy
  2

• Getting active/inactive and major/minor promoters when no condition is specified

  #38 opened 2 years ago by elenichri
  1

• some question about the paper

  #35 opened 2 years ago by ninjaxfy
  1

• DEXSeq hangs

  #34 opened 3 years ago by elenichri
  0

• estimating promoter activity from given bam files

  #33 opened 3 years ago by ninjaxfy
  4

• getAlternativePromoters (Bioconductor version dont have it)

  #26 opened 3 years ago by ashokpatowary
  1

• estimate promoter activity from bam file

  #3 opened 5 years ago by jonathangoeke
  2

• Docker image for proActiv

  #32 opened 3 years ago by NaotoKubota
  2

• Not summarized values across conditions

  #31 opened 3 years ago by elenichri
  3

• invalid class "DESeqDataSet" object error

  #30 opened 3 years ago by elenichri
  6

• update installation guide to Bioconductor

  #24 opened 3 years ago by jonathangoeke
  0

• getTranscriptRanges() function limits species this can be applied to

  #23 opened 3 years ago by G-Thomson
  2

• No major promoter when internal promoters are strong

  #22 opened 4 years ago by lukauskas
  2

• Example of how to generate junction file from fastq

  #21 opened 4 years ago by lukauskas
  1

• create a vignette with an example analysis script

  #11 opened 4 years ago by jleechung
  1

• proActiv throws error with xz-compressed Tophat2 junction file

  #17 opened 4 years ago by jleechung
  0

• optimize preparation of promoter annotation object

  #10 opened 4 years ago by jleechung
  1

• create proActiv wrapper to return summarizedExperiment with promoter ranges

  #6 opened 4 years ago by jonathangoeke
  1

• how to prepare promoterAnnotationData?

  #2 opened 5 years ago by xflicsu
  1