nalcala
Computational Biologist at the International Agency for Research on Cancer-WHO
IARC-WHOLyon, France
Pinned Repositories
CancerGenomicsCloud_tutorial
Tutorial for the sevenbridges cancer genomics cloud
Courses
Slides from lectures and presentations
data_test
Small data files to test IARC nextflow pipelines
DESeq2
Differential gene expression analysis based on the negative binomial distribution
facets-nf
Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing
hatchet
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
LaTex
Repository with latex scripts
MIDASPOM
Bayesian Inference method for patch occupancy data
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
mutect-nf
Mutect pipeline with Nextflow
nalcala's Repositories
nalcala/CancerGenomicsCloud_tutorial
Tutorial for the sevenbridges cancer genomics cloud
nalcala/Courses
Slides from lectures and presentations
nalcala/data_test
Small data files to test IARC nextflow pipelines
nalcala/DESeq2
Differential gene expression analysis based on the negative binomial distribution
nalcala/facets-nf
Pipeline using facets for fraction and copy number estimate from tumor/normal sequencing
nalcala/hatchet
HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
nalcala/LaTex
Repository with latex scripts
nalcala/MIDASPOM
Bayesian Inference method for patch occupancy data
nalcala/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
nalcala/mutect-nf
Mutect pipeline with Nextflow
nalcala/mutect2_issue
files to reproduce mutect2 issue
nalcala/NGSCheckMate
Nextflow pipeline to detect matched BAMs with NGSCheckMate
nalcala/PopGenBounds
R scripts to explore diversity and differentiation statistics with respects to their mathematical bounds
nalcala/PostAlignment-nf
nalcala/ProjectLeadRship
R scripts to help project leadership
nalcala/Statistics
Repository with scripts for statistical analyses
nalcala/strelka2-nf