twbattaglia Goto Github PK

amplicon-nf

assembly-nf

btools

A set of R functions that help faciliate a lot of tedious processing

btools-shiny

A shiny interactive dashboard for 16s microbial data analysis

conda-menu

An (unofficial) menubar app for creating and launching conda virtual environments.

cookiecutter-rnaseq

A cookiecutter implementation of the RNAseq workflow described in https://github.com/twbattaglia/RNAseq-workflow

geo-submitter

A webapp for preparing expression data for GEO

hansolo-manuscript

Identification of patient-specific T cell neoantigens through HLA-agnostic genetic screens (Cattaneo et al, Nature Biotechnology, 2023)

koeken

A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.

microbeds

A repository for large-scale microbiome datasets, formatted for phyloseq

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

oncology-packages

Repo for storing links for interesting cancer bioinformatics packages

q2-summarizer

QIIME2 plugin for generating interactive summary data

rnaseq-workflow

A repository for setting up a RNAseq workflow

sci2017_analysis

Data and analysis scripts for Matson et al. 2017 manuscript

snpcheck

Package for internal SNP-based sample swap detection

tumor-microbiome

A pan-cancer analysis of the microbiome in metastatic cancer (Battaglia et. al, Cell, 2024)

twbattaglia.github.io

repo for blogdown website