GACGAMA

Hello! I've been trying to merge multiple gseaResult objects such as those from KEGG, Reactome and Wikipathways to generate one ridgeplot only, for an article I've done: ``` reactomegsea

Oncoplot gene bar sizes too small

1

**Describe the issue** Can't customize gene size bars, which make them too small! Even if I try sepwd_genes and sepwd_samples, nothing changes. Setting sepwd_genes to negative values increase the bar...

VCF2MAF failed to run

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Hello everyone! I'm trying to run VCF after sucessfully using VEP. When I use: ` vcf2maf --input-vcf /home/gabriel.gama/Mutect2_usingPoN/sample11_withPoN.vcf --output-maf /home/gabriel.gama/Mutect2_usingPoN/sample11_vcf2maf.vep.maf --ref-fasta /home/gabriel.gama/references/ENSEMBL/star/Homo_sapiens.GRCh38.dna.primary_assembly.fa ` I'm getting: ` STATUS: Running VEP and...

Hello! I've been trying to run STARSEQR with reads already aligned (with options for arriba, star-fusion and STARSEQR). When running with the following options: `starseqr.py -sb -sj -p -t 8...

Problem with pyaudio (Windows 10)

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Hello Everyone! I'm trying to install LedFx on my windows 10 machine. I installed the latest python, then the latest Anaconda (py 3.8), and all Visual Studio codes for pyaudio....

Hello everyone! I've been running BWA-MEM 2 to align some WGS samples with human reference grch38.p14 from NCBI, indexed with BWA-MEM2 I've been using: ``` script /home/scripts/alignment_ncbi.txt cat /home/bwa/samplespairstrimmed.csv |...

AI consensus calling error on WGS samples

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I'm trying to run somaticseq_parallel on some samples VCFs to call the AI consensus. The version for SomaticSeq is SomaticSeq v3.7.3. Version of XGBOOST is 2.0.2 I've run all mutation...

[Suggestion-Implementation] Add information to summary and annotations of results

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Hello Xihao! I would suggest two types of information that would be very informative in the summary and annotation of all steps. For quantitative phenotype, a simple mean/median of the...

This is related to #3709 Program rsem-generate-ngvector is still missing from RSEM package, version 1.3.1 (I think this is the most recent version). Not sure why it is missing again...

Hello This is related to #242 It seems like the newest version contains some old bugs for some reason When trying to generate .cnr files with fix command without antitarget...