beginner984

Sorry, I have four data like below ``` Patient_005=as.data.frame(read.table(text = " Driver SNV_Tumour_005 SNV_Organoid_005 INDEL_Tumour_005 INDEL_Organoid_005 Deletion_Organoid_005 ABCB1 * * * - - - ACVR1B * * - - -...

Having more than one sample

1

Hi immunarch team I have 10x TCR and BCR sequencing + 5' GEX I have several samples For one sample I know I should do like this ``` > setwd("/Users/angel/Downloads/p1_sample_feature_bc_matrix")...

Downloading Mutation data (hg19) for a cancer type

4

Hi I am trying to get `Mutation data (hg19)` for `ESCA` cancer in `maf `format; I have done so but I am getting error Can you help me please ```...

Sorry PlotFancyVJUsage supposed to show the frequency of various V-J junctions and PlotSpectratypeV to show CDR3 length distribution for clonotypes from top N Variable segment families anyway for the tops...

Sorry Whatever I look at the docs I can not get by which code I can plot this? Clonotype abundance plot  Please help me to fimd a function to...

Hi, Long time I am trying vcf2maf; It runs ok with test data but with my vcf I am getting error ``` -bash-4.1$ perl vcf2maf.pl --input-vcf /temp/hgig/fi1d18/strelka-2.9.2.centos6_x86_64/bin/demo_somatic_036_2post/results/variants/double_filtered_somatic_036_2post.snvs.vcf --output-maf tests/test.vep.maf --filter-vcf...

Hi I need `tumour variant allele count` from manta structural variant. I have annotated manta .vcf and now I have `Read.pairs...tumour` and `Split.reads...tumour`. Which one corresponds to `tumour variant allele...

Extracting some information from Strelka vcf

2

Hello I have a script extracting some fields like `TumorReadCount`, `tumorVariantAlleleCount`, `TumorReferenceAlleleCount`, `NormalReadCount`, `NormalAlleleCount`, `NormalReferenceCount `and `VAF `from .**_vcf Strelka_** This is my script ``` ## Iterate over all files...

Hello As I was not able to install velocyto.R on my window machine I then installed that on Rstudio cloud but I am all getting error just in the first...

Visualising the results of mutation origin

1

Hello I was able to run origin function but I don't know how to visualise that or any possible plot (if already produced by function) goes where This is the...