PoisonAlien maftools issues

PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

http://bioconductor.org/packages/release/bioc/html/maftools.html

MIT License

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issues

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After sorted by one of sample annotations, is main plot sorted by mutation by that annotation

#1075 wangzunq opened 1 day ago
0
Multiple separate Gistic results from 3 cohorts

#1074 wangzunq opened 3 days ago
0
Error when using mafSurvival with TCGA samples

#1073 Mars-fi closed 4 days ago
2
somaticInteractions top not count cn samples when plotting

#1072 WandaC-S opened 1 week ago
0
An error occurred while generating oncoplots

#1071 haeseo00 opened 2 weeks ago
1
fix(DESCRIPTION): move curl to SystemRequirements

#1070 eliseomartelli closed 2 weeks ago
1
Add gridlines(boxes) in main area only

#1069 wangzunq opened 2 weeks ago
1
Reading subset Maf with whole copy number data.

#1068 HiraDatascience opened 3 weeks ago
1
Discrepency in Sample Numbers.

#1067 HiraDatascience opened 3 weeks ago
1
gistic : Error in file.info(file) : invalid filename argument

#1066 HiraDatascience opened 3 weeks ago
1
Label on right Bar is always the same independent of the data added

#1065 juferban opened 3 weeks ago
1
Applying inferHeterogeneity to ClonEvol

#1063 xiw588 closed 3 weeks ago
1
Allow 2 Variant_Classification shown on Oncoplot

#1062 wangzunq opened 3 weeks ago
17
coOncoplot keepGeneOrder do not work in maftools 2.21.2

#1061 WandaC-S closed 3 weeks ago
2
How to calculate the p-value between the mutation profiles for the 3 groups

#1059 sjb-a11y opened 1 month ago
1
No non-synonymous mutations found

#1058 aeozdemr closed 3 weeks ago
2
Copy number analysis using ASCAT

#1057 MaryGoAround closed 1 month ago
3
The variants are almost Silent

#1056 DayTimeMouse opened 1 month ago
1
Cannot find function Oncogenic Pathways

#1055 londonlondon20 opened 1 month ago
1
Questions of GISTIC and copy number alteration analysis

#1054 xiw588 opened 1 month ago
1
How to define colors for clinical features that use continuous values

#1053 PoisonAlien opened 2 months ago
1
Error applying colors to continuous clinicalFeatures

#1050 juferban opened 2 months ago
12
Error:long vectors not supported yet: memory.c:3940

#1049 Olsennnnn opened 2 months ago
1
The subsetMaf function is ineffective for screening samples and genes.

#1048 MECHANIC-LIJIAN closed 2 months ago
2
Issue with maftools::gtMarkers memory not mapped

#1047 grantn5 closed 1 week ago
2
Error :could not find function "OncogenicPathways"

#1046 HiraDatascience closed 2 months ago
3
Why are my lines in the GISTICChromPlot not straight?

#1045 HummelFa opened 2 months ago
4
sampleSwaps Error: Zero SNPs to analyze

#1044 tc86 opened 3 months ago
1
Border of gisticOncoPlot

#1043 maximus3219 closed 1 month ago
1
plotmafsummary mutated gene

#1042 bioinfomatio closed 1 month ago
1
selectedPathways argument in oncoplot not functioning properly with user-defined pathways

#1041 kbrar4013 opened 4 months ago
3
Discrepancy in MATH Scores

#1040 fatemedorri77 closed 2 months ago
1
Why is MNP excluded when reading.maf?

#1039 youngbee12 closed 2 months ago
1
gisticChromPlot for individual samples

#1038 MaryGoAround closed 1 month ago
2
filterMaf error

#1037 amootta closed 2 months ago
2
extractSignatures

#1036 ypmjx123 closed 2 months ago
2
unknown tumor_sample_barcode

#1035 ghost closed 3 months ago
1
Error in get_lp_data(maf = m1, geneID = gene, AACol = AACol1, refSeqID = refSeqID, : Structure for protein BAGE3 not found.

#1033 libiqing77 closed 2 months ago
3
Fixed Typo in read.maf.Rd

#1032 fabianjkrueger opened 5 months ago
0
Questions about MATH score

#1031 xiw588 closed 2 months ago
3
Length zero fix

#1030 eolaniru opened 5 months ago
0
Lollipopplot does not show complete protein length.

#1029 Arnob5105 closed 2 months ago
6
sampleSwaps.R: add an error message in case of missing index files

#1028 eolaniru closed 5 months ago
6
Error in if (dist <= mergeDist) { : missing value where TRUE/FALSE needed

#1027 Iononering closed 3 months ago
3
The get_col_df function seems to have a bug in the 6th line

#1026 canna1998 closed 2 months ago
3
lollipopPlot（）Report an error：Error in .getdomains(geneID = gene, refSeqID = refSeqID, proteinID = proteinID) : Structure for protein PPDPFL not found.

#1025 yaohuiovo closed 5 months ago
1
Different aa.lengths in lollipopPlot() and lollipopPlot2()

#1019 YarsnC closed 6 months ago
2
TMB plot (tcgaCompare): Burden changes depending on input order

#1018 FriederikeHanssen closed 4 months ago
3
Signature plot

#1017 Ind2022 closed 6 months ago
11
Getting error in lollipop plot

#1016 MaryGoAround closed 6 months ago
3