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Name: Youssef Abili
Type: User
Bio: 5000genomi@vda | Bioinformatics | Data Scientist | Entrepreneur Attitude
Location: Italy
Youssef Abili's Projects
adapters_trim
adapters_trim
annotatedvcfparser
Script to parse annotated vcf files (VEP,snpEff,ANNOVAR) to a csv table
awesome-cancer-variant-databases
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
bash-for-bioinformatics
Usefull bash script and tricks to play with sequences
cgi
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
civic
CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer.
conda2singularity
code to simply build a singularity image from a conda environment.
covid_rnaseq
Collection of GEO datasets of RNAseq. Main focused on analysis of GSE163426.
diva.wgs
DiVA.wgs (DNA Variant Analysis) is a pipeline for Next-Generation Sequencing Whole Genome data analysis
docker-4-bioinformatics
Short Course to get Bioinformaticians at CRUK-CI up-to-speed on Docker
docker-annotsv-cwl
Docker container for running AnnotSV
gatkgermline_hardfiltering
Perform GATK hard-filtering of germline SNVs and indels
gatkgermline_jointcalling_vqsr
Joint calling of gVCF, following GATK4 Best Practices
gatksomatic_pon
Nextflow implementation of Mutect2 Panel Of Normals subworkflow (GATK Best Practices)
mergevcf_mutectstrelka
Merge variants generated with Mutect2 and Strelka
r_for_bioinformatics
R tools for Bioinformatics
rnaseqfastq2counts
RNAseqFastq2Counts
sarek_vda
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow
vcf-to-tab
Converts Variant Effect Predictor (VEP) VCF output to tab-delimited file.
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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