G

genomics

Clostridia characterization and typing pipeline

Code and thesis generation for my PhD Thesis titled "A Genomic Medicine Approach to Identifying Novel Drugs"

Crawl any filesystem for genome data, providing one-click opening in IGV

The analysis repository for the Schwannomatosis Open Research Collaborative (SWNTS).

Insight into the 3D organization of the genome, this question arises: Are the genes for the corresponding protein complexes, whose transcription needs to be orchestrated, located in the same 3D-chromatin domain? Using human protein complex database and high-resolution Hi-C data on normal and cancer human cells, I elaborated an R-based approach to normalize the data and statistically test the association to TAD (topologically associating domain) in my bioinformatics master's work.

A Machine Learning approaches to identify genetic variants associated with disease

Allele CAlling proCedure for Illumina Amplicon sequencing data.

Stability Sort: detect instability

the motif-variant probe: detect creation/destruction of sequence motifs as a result of mutations https://lpcdrp.gitlab.io/mvp

Migrated to https://github.com/fpozoc/trifid

Vibrio cholerae sequence type analysis. Identifies virulence-associated loci and assigns biotypes and serogroups.

batch data download from Genbank or RefSeq

My master thesis at NMBU

fasta toolkit for fasta file processing and modification

Use a suffix array structure in C++ to index genomic sequences.

Measure genomic intervals travelled by polymerase https://coregenomics.gitlab.io/polymerasewave/

New package repo & site: https://github.com/Pasquali-lab/UMI4Cats