VCCRI/Sierra

Issues

• Question on counting overlapping peaks

  #72 opened 3 months ago by HenriettaHolze
  1

• Can I force Sierra to include exons from gtf?

  #71 opened 3 months ago by HenriettaHolze
  2

• Changes in gene 3'UTR length

  #70 opened 8 months ago by TianYu-828
  1

• CountPeaks error when using Singleron Biotechnologies 3'-end BAM files

  #65 opened a year ago by hkarakurt8742
  4

• Interpretation of log2 fold changes in the result

  #69 opened 10 months ago by Kyung-TaeLee
  1

• PlotRelativeExpressionUMAP - can an additional function be added to bring out cells that are buried in the UMAP plot?

  #68 opened a year ago by ckong18
  0

• Coordinates of peaks across junctions after merging

  #67 opened a year ago by chvandijk
  5

• Error in PlotRelativeExpression functions

  #66 opened a year ago by hkarakurt8742
  1

• Error when running CountPeaks

  #48 opened 3 years ago by idupanloup
  8

• MergePeakCoordinates takes long time！

  #61 opened a year ago by cghchuwudai
  9

• Using Sierra with Singleron Biotechnologies Platform

  #64 opened a year ago by hkarakurt8742
  1

• Getting "Error in (function (x) : attempt to apply non-function"

  #63 opened a year ago by alanlamsiu
  3

• Paired-end & PlotRelativeExpression functions.

  #62 opened a year ago by OnegItzhak
  1

• issues with generating splice junction file

  #60 opened 2 years ago by ckong1806
  7

• [E::hts_open_format] Failed to open file

  #58 opened 2 years ago by ntsopoul
  1

• is it possible to generate a plot that shows global 3'UTR length change?

  #59 opened 2 years ago by ntsopoul
  0

• Sierra dataframe has 0 length

  #57 opened 2 years ago by top334
  1

• DUTest function Error

  #56 opened 2 years ago by hkarakurt8742
  1

• Generate GitHub Releases

  #53 opened 2 years ago by mfansler
  2

• FindPeaks Error--'x' values larger than vector length 'sum(width)'

  #55 opened 2 years ago by Jun2BCR
  2

• Cellranger mkref function parameters for Sierra

  #54 opened 2 years ago by hkarakurt8742
  1

• Chromosome name in FindPeaks // Help with Output

  #52 opened 2 years ago by Romeo1-1
  3

• Which alignment method and indexing options are suitable to use with Sierra?

  #50 opened 2 years ago by hkarakurt8742
  3

• CoveragePlot error with 'zoom_3UTR=TRUE '

  #49 opened 3 years ago by BettinaNa
  1

• Does the Sierra package have a detailed protocol, I would like to find.

  #51 opened 2 years ago by liuyu988
  1

• multithreading is not working for apply_DEXSeq_test_seurat module

  #42 opened 3 years ago by AidenSb
  2

• Error in peak calling

  #46 opened 3 years ago by idupanloup
  2

• peak discrepancy

  #47 opened 3 years ago by cag1343
  1

• 3'end database

  #44 opened 3 years ago by cag1343
  2

• Using data with batch effects in Sierra

  #45 opened 3 years ago by hkarakurt
  2

• umap coordinates for NewPeakSeurat

  #43 opened 3 years ago by leeanapeters
  3

• Error in x$.self$finalize()

  #34 opened 3 years ago by AidenSb
  6

• Error in CountPeaks step

  #41 opened 3 years ago by johnchamberlin
  2

• Problems reading genes with a quote (') in the name

  #37 opened 3 years ago by GeertvanGeest
  1

• DUTest() with genes containg ':' or space

  #39 opened 3 years ago by GeertvanGeest
  1

• PlotRelativeExpressionBox looks for tSNE

  #40 opened 3 years ago by GeertvanGeest
  2

• Error in CountPeaks()

  #35 opened 3 years ago by fciamponi
  5

• Using STARSolo SJ.out.tab?

  #36 opened 3 years ago by cnk113
  4

• PeakSeuratFromTransfer error

  #33 opened 3 years ago by Nbalb
  1

• GTF problem

  #32 opened 3 years ago by Lianqw
  2

• Clarification on UMI counting

  #31 opened 3 years ago by cnk113
  2

• Interpret results

  #29 opened 3 years ago by Vivianstats
  4

• User-defined pseudo-bulk samples?

  #30 opened 4 years ago by borshago
  1

• failed re-building ‘Sierra_vignette.rmd’

  #26 opened 4 years ago by Pchaskar
  1

• Error in SplitBam (extra argument to Rsamtools::ScanBamParam)

  #28 opened 4 years ago by borshago
  1

• Error in DUTest

  #27 opened 4 years ago by soobeomlee
  5

• Installation error on R.3.6.2

  #25 opened 4 years ago by hmgene
  2

• installation erro

  #24 opened 4 years ago by AidenSb
  7

• PeakSeuratFromTransfer or NewPeakSeurat Error

  #23 opened 4 years ago by aralbright
  7

• long reads

  #22 opened 4 years ago by ashokpatowary
  9