hartleys/JunctionSeq

Issues

• DESeq2 version collision

  #36 opened 6 years ago by gfucile
  7

• Can JunctionSeq be used in long-read RNA-seq ONT data?

  #60 opened a year ago by kaanokay
  0

• Error : attempt to select less than one element in OneIndex

  #59 opened 3 years ago by ChoiJi-Hye
  0

• QoRTs/JunctionSeq with Rsubread alignment

  #58 opened 4 years ago by jmbono
  2

• Normalized gene counts of 0?

  #57 opened 4 years ago by alanbergland
  1

• Sig gene wtih the P-value as NA

  #56 opened 4 years ago by zhouqz
  2

• How can I write all results to JunctionSeq Object (jscs data) in R ?

  #41 opened 4 years ago by kaanokay
  1

• Annotation file appears to be missing information! Are you sure you are using the correct flattened annotation file, created by the QoRTs QC command?

  #35 opened 4 years ago by kaanokay
  2

• Junctionseq marked as deprecated in bioconductor.

  #55 opened 4 years ago by tbrittoborges
  0

• Missing genes in allGenes.results.txt

  #37 opened 6 years ago by sagarutturkar
  4

• splice junction usage between multiple tissues

  #26 opened 7 years ago by frankbioinfo
  3

• weird dispersion plot

  #54 opened 4 years ago by scseekers
  1

• writeCompleteResults : Error in data.frame(..., check.names = FALSE)

  #53 opened 4 years ago by YanliangDou
  0

• Unable to view splice junction tracks on ucsc browser

  #52 opened 4 years ago by varsha090597
  1

• estimateEffectSizes: Error in if (any(dispersion < 0)) stop("dispersion values must be non-negative")

  #49 opened 4 years ago by ashish674675
  2

• Error in estimateSizeFactorsForMatrix(counts.byGenes)

  #50 opened 4 years ago by HeenaBioinfo
  2

• independent filtering on the gene counts

  #48 opened 5 years ago by shivarice
  1

• Multiple conditions comparsion

  #40 opened 6 years ago by LOYON2019
  1

• Error: all samples have 0 counts for all genes. check the counting script

  #51 opened 4 years ago by HeenaBioinfo
  0

• error in reading decoder file

  #46 opened 5 years ago by CS791
  1

• Error: C stack usage 50949656 is too close to the limit"

  #47 opened 4 years ago by CS791
  5

• Zero counts for whole LY75

  #32 opened 7 years ago by cwtkiwi
  2

• labels of gene of interest in MA plot

  #45 opened 5 years ago by kaanokay
  0

• Error in cf[[pvn]] : subscript out of bounds

  #44 opened 5 years ago by nicholas-owen
  0

• How To Calculate PSI with JunctionSeq

  #38 opened 6 years ago by xysj1989
  1

• parallel run (nCores > 1) always fails

  #39 opened 6 years ago by slowsmile
  1

• can't install the packages 'backports','nlme'

  #42 opened 6 years ago by HL2007
  1

• plot interpretation

  #43 opened 6 years ago by natallah
  4

• Unable to locate counts file

  #34 opened 6 years ago by sanchari24
  0

• C stack usage is too close to the limit

  #33 opened 7 years ago by jxf413
  1

• Alterative junctionseq pipeline inquiry

  #27 opened 7 years ago by dejonggr
  6

• Estimated runtime and progress indicator

  #30 opened 7 years ago by mebbert
  3

• Error in names(res) <- nms

  #31 opened 7 years ago by mebbert
  10

• Dead links on JunctionSeq page

  #29 opened 7 years ago by mebbert
  1

• Two-pass alignment?

  #28 opened 7 years ago by mebbert
  0

• File interpretation problem

  #25 opened 7 years ago by Ambreen06
  4

• LogFC sign in sigGenes.results.txt

  #24 opened 7 years ago by ewilkie
  4

• Annotation file appears to be missing information!

  #18 opened 8 years ago by misik
  24

• Two libraries

  #23 opened 7 years ago by cwtkiwi
  2

• Comparing JunctionSeq to DEXSeq

  #19 opened 7 years ago by brgew
  1

• Summary Plots created by JunctionSeq

  #20 opened 8 years ago by Tomoya89
  2

• error about fitDisp

  #17 opened 8 years ago by aiminy
  2

• Required features in GTF file.

  #21 opened 8 years ago by brgew
  1

• Memory limit

  #10 opened 8 years ago by royfrancis
  5

• Gene-level expression estimates

  #16 opened 8 years ago by hooperj
  3

• Differential Usage Numbers only

  #14 opened 8 years ago by FallenAzazel
  6

• Can't successfully use numeric covariate with runJunctionSeqAnalyses()

  #15 opened 8 years ago by davemcg
  2

• dead link in help docs

  #12 opened 8 years ago by hobrien
  2

• buildAllPlotsForGene unable to create new directories

  #13 opened 8 years ago by hobrien
  4

• C stack usage 17723277 is too close to the limit

  #11 opened 8 years ago by KateK
  8