Pinned Repositories
amplicon-nf
btools
A set of R functions that help faciliate a lot of tedious processing
conda-menu
An (unofficial) menubar app for creating and launching conda virtual environments.
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
q2-summarizer
QIIME2 plugin for generating interactive summary data
RNAseq-workflow
A repository for setting up a RNAseq workflow
tumor-microbiome
A pan-cancer analysis of the microbiome in metastatic cancer (Battaglia et. al, Cell, 2024)
twbattaglia's Repositories
twbattaglia/RNAseq-workflow
A repository for setting up a RNAseq workflow
twbattaglia/MicrobeDS
A repository for large-scale microbiome datasets, formatted for phyloseq
twbattaglia/koeken
A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.
twbattaglia/btools
A set of R functions that help faciliate a lot of tedious processing
twbattaglia/tumor-microbiome
A pan-cancer analysis of the microbiome in metastatic cancer (Battaglia et. al, Cell, 2024)
twbattaglia/amplicon-nf
twbattaglia/geo-submitter
A webapp for preparing expression data for GEO
twbattaglia/conda-menu
An (unofficial) menubar app for creating and launching conda virtual environments.
twbattaglia/HANSolo-manuscript
Identification of patient-specific T cell neoantigens through HLA-agnostic genetic screens (Cattaneo et al, Nature Biotechnology, 2023)
twbattaglia/q2-summarizer
QIIME2 plugin for generating interactive summary data
twbattaglia/tumor-microbiome-nf
twbattaglia/btools-shiny
A shiny interactive dashboard for 16s microbial data analysis
twbattaglia/cookiecutter-rnaseq
A cookiecutter implementation of the RNAseq workflow described in https://github.com/twbattaglia/RNAseq-workflow
twbattaglia/snpcheck
Package for internal SNP-based sample swap detection
twbattaglia/assembly-nf
twbattaglia/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
twbattaglia/oncology-packages
Repo for storing links for interesting cancer bioinformatics packages
twbattaglia/sci2017_analysis
Data and analysis scripts for Matson et al. 2017 manuscript
twbattaglia/twbattaglia.github.io
repo for blogdown website