PoisonAlien/maftools

Issues

• Issue with importing GISTIC data into maftools

  #993 opened 9 months ago
  3

• Too many multi_hit and missense mutation

  #992 opened a year ago
  2

• oncoplot Error.. out_of_bound

  #991 opened a year ago
  5

• resizing oncoplots

  #990 opened 9 months ago
  3

• clinicalEnrichment seems to ignore samples with no mutations

  #989 opened 9 months ago
  3

• pfamDomains throws uninformative error when failing to parse less common AAchanges

  #988 opened 10 months ago
  3

• Plot both arm-level(broad) versus focal amplifications (and deletions)

  #987 opened 9 months ago
  6

• Adding rows containing variants into maf file.

  #986 opened 10 months ago
  3

• Question about gisticChromPlot

  #983 opened 8 months ago
  6

• Oncoplot - Cell hight and width

  #982 opened a year ago
  2

• somaticInteractions not plotting certain pairwise interactions

  #981 opened 10 months ago
  7

• ICGC dataset error in plotmafSummary

  #980 opened a year ago
  1

• plotClusters() "genes=" argument doesn't accept a vector of gene names

  #979 opened a year ago
  2

• How to determine the value of captureSize?

  #977 opened a year ago
  1

• Feature request: Extend subsetMaf to drop samples by barcode

  #976 opened a year ago
  2

• lollipopPlot2 no plot, but lollipopPlot can plot for gene PALB2

  #975 opened a year ago
  3

• SomaticInteractions - pAjd method request

  #974 opened a year ago
  3

• Non standard Ti/Tv class: 1814TRUE

  #973 opened a year ago
  5

• A question about tmb()

  #972 opened a year ago
  2

• number beside SNV Class in plotmafsummary

  #971 opened a year ago
  1

• vc.nonSilent list

  #970 opened a year ago
  1

• dowload somaticinteractions table

  #969 opened a year ago
  2

• What is the difference between Start and i.Start

  #968 opened a year ago
  5

• Survival analysis can not be run

  #967 opened a year ago
  4

• Does Maftools support row annotations?

  #965 opened a year ago
  3

• font type used in oncoplot

  #964 opened a year ago
  2

• Missing required field error

  #963 opened a year ago
  3

• CNV differences between the two cohorts

  #962 opened a year ago
  1

• SBS1 counts of TCGA BRCA samples

  #960 opened a year ago
  7

• another tool than vcf2maf?

  #959 opened a year ago
  1

• Borderline

  #958 opened a year ago
  3

• A suggestion createOncoMatrix for pathways

  #956 opened a year ago
  5

• Save Silent Variants for downstream analysis

  #955 opened a year ago
  8

• I have written the co gisticChromPlot with vertical layout function I want to commit it into maftools

  #952 opened a year ago
  1

• bug:sortByGeneOrder() discard negative samples

  #951 opened a year ago
  5

• confused aa.length in lollipopPlot()

  #950 opened a year ago
  2

• trinucleotideMatrix function error in extracting 5' and 3' adjacent bases.

  #948 opened a year ago
  10

• Check `vc_nonSyn`` argumet in `read.maf` for details

  #947 opened a year ago
  2

• GISTIC file analysis

  #944 opened a year ago
  1

• How to combine multiple maf files without loss

  #943 opened a year ago
  5

• The question aboud the fisher.test in `trinucleotideMatrix`

  #942 opened a year ago
  2

• Set operations: intersectMAF and subsetMaf

  #941 opened a year ago
  3

• lollipopPlot can not show in_frame_del mutation

  #940 opened a year ago
  1

• extractSignatures

  #939 opened a year ago
  1

• legend not working when using samples argument in mafSurvival

  #937 opened a year ago
  2

• Customize column for showTumorSampleBarcode

  #936 opened a year ago
  3

• Do we need to filter the CNV data as well for each cohort while using the cohort analysis to compare cohorts?

  #934 opened 2 years ago
  1

• Lollipop Plot "structure for protein "DSEL" not found

  #933 opened a year ago
  1

• Manually add protein structure to solve the error: "structure for protein "-----" not found" by Lollipop Plot

  #932 opened a year ago
  2

• lollipopPlot text repel

  #931 opened a year ago
  2