ChristofferFlensburg/superFreq

Issues

• river output CNV ploidy

  #77 opened 6 months ago by guillaume-rs
  7

• Explanation of fields in rivers files

  #81 opened 6 months ago by kmavrommatis
  1

• Error in base::basename(path, ...) : a character vector argument expected

  #85 opened 6 months ago by deb0612
  1

• CNA calls in the output

  #86 opened 6 months ago by zozcan89
  1

• CNV calls in Chr X and Y

  #87 opened 6 months ago by mike8115
  3

• Understanding columns in the CNA segment output file

  #88 opened 6 months ago by jsha129
  1

• Plotting only "LFC vs normals" or "SNP MAF" graph from the CNV figure

  #92 opened 6 months ago by ElsaMichelle
  1

• Error during running the recent version

  #94 opened 6 months ago by sohyoung27
  11

• Mv flag is too much (?)

  #96 opened 6 months ago by underbais
  5

• Tracking back the sequences of the clones

  #101 opened 6 months ago by maheshworpaudel5001
  1

• Issue connecting to GitLab server

  #110 opened 6 months ago by km-2021
  10

• Is it possible to track which subclones contain a specific genetic mutation in a superFreq riverplot?

  #111 opened 6 months ago by km-2021
  1

• Question about superFreq copy number call output

  #112 opened 6 months ago by km-2021
  1

• Some variants are missing in river.tsv

  #114 opened 6 months ago by pigyun906
  1

• Retrieve ploidy fit value / - How to compute Chromosome Instability (CIN) Index - Fraction Genome Altered (FGA) ?

  #118 opened 6 months ago by ZheFrench
  1

• Output graph optimization

  #119 opened 6 months ago by nerea-bilbao
  1

• SuperFreq cannot find varscan command

  #120 opened 6 months ago by avivneuronvision
  1

• Concermong about Normal reference

  #121 opened 6 months ago by km-2021
  1

• Columns of CNAbyGene.tsv file

  #125 opened 6 months ago by mlegarreta00
  1

• No reads in samples

  #127 opened 7 months ago by mlegarreta00
  1

• Plot interpretation

  #126 opened 7 months ago by Teezi
  2

• error: Flagging SNPs that are in noisy regions. New flags by sample:Killed

  #124 opened 7 months ago by Teezi
  8

• featureCounts setting: `Count read pairs : no`

  #123 opened 10 months ago by Teezi
  2

• Can reference normal files include the same bam file used for input?

  #122 opened 10 months ago by mlegarreta00
  1

• X11 display error

  #98 opened 2 years ago by maheshworpaudel5001
  5

• Ok, I had a closer look at the latest Rsubread version, and they have indeed changed syntax for how to tell it to to count raw reads (not fragments) in PE samples. And that is most likely they cause of the bug. I made a change to superFreq that reads out the Rsubread version and does the appropriate call. Running tests and will push online, but will (hopefully) be next week. You can either backdate Rsubread if you're in a hurry, or wait for me to finish the testing and push changes online.

  #117 opened a year ago by duanshumeng
  2

• VariantAnnotation step failing in v1.5.1

  #116 opened a year ago by samleenz
  2

• Recommendations to process large cohort of normal/tumoral RNASEQ pair

  #115 opened a year ago by ZheFrench
  7

• Input for ClonEvol

  #93 opened a year ago by pigyun906
  1

• Error during running the recent version with #94

  #103 opened a year ago by pigyun906
  2

• Failed annotation - "data set ‘entrez2symbol_hs’ not found"

  #113 opened a year ago by gbss2
  3

• WriteXLS error in large cohort analysis

  #109 opened 2 years ago by leap-ahead225
  8

• SuperFreq result interpretation for amplificaiton events from RNA-Seq

  #104 opened 2 years ago by akshaya1296
  4

• RNA mode

  #108 opened 2 years ago by km-2021
  1

• About reference

  #106 opened 2 years ago by km-2021
  1

• RNA mode

  #107 opened 2 years ago by km-2021
  1

• error in RNA mode

  #105 opened 2 years ago by km-2021
  1

• findCorrespondingNormal returns missing value

  #102 opened 2 years ago by hosseinvk
  5

• polyclonal or monoconal model from river plot

  #97 opened 2 years ago by ada6090
  9

• Could not parse the "#CHROM.." line

  #100 opened 2 years ago by maheshworpaudel5001
  6

• Successfully assigned alignments 0 error

  #99 opened 2 years ago by maheshworpaudel5001
  4

• Capture regions read

  #91 opened 3 years ago by arpanda
  4

• Error log is not clear !

  #90 opened 3 years ago by arpanda
  4

• wget download is not working

  #89 opened 3 years ago by arpanda
  5

• superFreq forces R and plots to be created on same path as control samples

  #84 opened 3 years ago by emauryg
  22

• New variants excel file

  #83 opened 4 years ago by UmairAhmadKhan97
  2

• Concatenating metadata for runSummaryPostAnalysis

  #82 opened 4 years ago by UmairAhmadKhan97
  2

• Memory Issues

  #79 opened 4 years ago by UmairAhmadKhan97
  11

• Hi Christoffer, I was wondering how to get B allele frequency from the characterized SNPs

  #80 opened 4 years ago by YuehuiZ
  2

• Error in featureCounts

  #78 opened 4 years ago by UmairAhmadKhan97
  3