Tiffany Delhomme's repositories
CancerGenomicsCloud_tutorial
Tutorial for the sevenbridges cancer genomics cloud
hyperstack
Nextflow pipeline to run the intercept method on needlestack calling with a step of FDR computation with ML
SimulateLowCovSeq-nf
Nextflow pipeline to simulate low coverage WES from existing BAM files and call/annotate variants with Strelka2
alignment4lanes-nf
Whole Exome/Whole Genome Sequencing alignment pipeline
Bash-tips-tricks
Tips and tricks (mainly for comp. gen.) in the Bash language
curriculum
Repository for my latex CV based on awesome-CV from @posquit0
Lesson-Notes
Repository containing notes from lessons in field of statistics, bioinformatics or even molecular biology
LiftOver-nf
Convert BED/VCF files between two genomes with nextflow
nf-scripts
folder of small nextflow scripts
NMF_VCF-nf
nextflow pipeline extracting mutational signatures from VCF files
pyclone_clonevol_analysis
Intra-tumor heterogeneity analysis with pyclone and clonevol
R-tips-tricks
Piece of R code
radiation_paper
Scripts associated with our radiation manuscript (https://doi.org/10.1101/2022.07.29.501997)
RegionalEnrichment-nf
Nextflow pipeline to conduct mutational regional enrichment analysis
S2_FPDB-nf
Run a strelka2 variant calling from public data bases, with a step of BAM downloading
samtools-merge-nf
Merge BAM files using samtools
SKATmutQTL-nf
Run the SKAT-O rare variant method for the mutQTL identification
SNV_clusters_sig-nf
Compute mutational signatures from clusters of SNVs
SV-simulation-nf
Nextflow pipeline to simulate structural variations in long reads sequencing data
variant-filtering-kidney2Hits
R scripts to filter variants from germline needlestack calling
variantfiltering-nf
nextflow pipeline to perform variant filtering on NGS data
VCF-tips-tricks
Piece of code to analyse VCF files
vcf_ancestry-nf
Nextflow pipeline that filters a VCF on a given ancestry from a PCA on 1000 genomes